Synthetic Organic Chemistry - User contributions [en]

https://wiki.synorgchem.science.ru.nl/api.php?action=feedcontributions&feedformat=atom&user=Wtitulaer Synthetic Organic Chemistry - User contributions [en] 2026-04-08T10:42:52Z User contributions MediaWiki 1.43.5 https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=132 SOC workstation 2025-01-30T13:00:08Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> ==Available software==<br /> On the workstation we have the following software installed:<br /> {| class="wikitable" style="margin:auto"<br /> |+ Software installed on the SOC workstation (last updated 30.01.2025)<br /> ! Software !! Intended purpose !! License<br /> |-<br /> | 7-zip || Compressing and decompressing .zip files || n.a.<br /> |-<br /> | Avogardo || Small molecule modelling || n.a.<br /> |-<br /> | ChemOffice || Drawing molecules (chemdraw) or saving as .sdf || RU<br /> |-<br /> | GOLD|| Precise molecular docking with a genetic algorithm (GA) for pose sampling|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | Mogul|| Torsion angle checking against the CSD || Academic, RU-broad from solid state chemistry<br /> |-<br /> | Conquest|| Software to search the CSD|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | MOE|| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. || Rutjes group exclusive, 1 license<br /> |-<br /> | Wincoot || Inspecting electron density maps (EDMs) of biomolecules WARNING! Downloading precomputed EDM .mtz files from the PDB is no longer possible || Academic<br /> |- style="color: red"<br /> | YASARA Structure (currently no license) || Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program || Academic, wtitulaer personal<br /> |}<br /> <br /> <br /> If you require different software, please send a message to socmoe-access@science.ru.nl. For other software available to the SOC please check [[Molecular software]]<br /> <br /> =Maintenance (admin only)=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> ==Hardware checks==<br /> ===Disk checks (2/year)===<br /> Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.<br /> Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. <br /> Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should. <br /> <br /> ===CCleaner===<br /> Should run automatically but if changes needed, these need to be reconfigured per user.<br /> <br /> ===Windows updates (2/year)===<br /> Run windows 10 updates twice per year and book a slot for this. <br /> <br /> ==Software updating==<br /> The idea is to conservatively update the system. Should updates still be needed, here are recommendations.<br /> <br /> ===Teamviewer===<br /> Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).<br /> When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:<br /> * At advanced settings, Disable local input and Enable blackscreen<br /> * Ensure Full Access is selected<br /> * Deactivate random password<br /> * Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password. <br /> <br /> ==Transfer of access==<br /> Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.<br /> <br /> =Guidelines for adding new users=<br /> ==Terms of use==<br /> Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom. <br /> <br /> ==New user Teamviewer (remote access)==<br /> Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).<br /> Then do the following:<br /> * Admin makes a new user with the specified email address (preferably RU or science) with a password<br /> * Admin removes everything at the Advanced settings apart from the 'log sessions' setting<br /> * Admin sets permission to user<br /> * User receives email and makes the account<br /> * Now that the user is actually active, the share can be assigned to the user with a Read-only permission.<br /> <br /> Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely. <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> <br /> <br /> <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=131 SOC workstation 2025-01-30T12:56:41Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> ==Available software==<br /> On the workstation we have the following software installed:<br /> {| class="wikitable" style="margin:auto"<br /> |+ Software installed on the SOC workstation (last updated 30.01.2025)<br /> ! Software !! Intended purpose !! License<br /> |-<br /> | GOLD|| Precise molecular docking with a genetic algorithm (GA) for pose sampling|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | Mogul|| Torsion angle checking against the CSD || Academic, RU-broad from solid state chemistry<br /> |-<br /> | Conquest|| Software to search the CSD|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | MOE|| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. || Rutjes group exclusive, 1 license<br /> |- style="color: red"<br /> | YASARA Structure (currently no license) || Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program || Academic, wtitulaer personal<br /> |}<br /> <br /> <br /> If you require different software, please send a message to socmoe-access@science.ru.nl. For other software available to the SOC please check [[Molecular software]]<br /> <br /> =Maintenance (admin only)=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> ==Hardware checks==<br /> ===Disk checks (2/year)===<br /> Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.<br /> Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. <br /> Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should. <br /> <br /> ===CCleaner===<br /> Should run automatically but if changes needed, these need to be reconfigured per user.<br /> <br /> ===Windows updates (2/year)===<br /> Run windows 10 updates twice per year and book a slot for this. <br /> <br /> ==Software updating==<br /> The idea is to conservatively update the system. Should updates still be needed, here are recommendations.<br /> <br /> ===Teamviewer===<br /> Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).<br /> When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:<br /> * At advanced settings, Disable local input and Enable blackscreen<br /> * Ensure Full Access is selected<br /> * Deactivate random password<br /> * Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password. <br /> <br /> ==Transfer of access==<br /> Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.<br /> <br /> =Guidelines for adding new users=<br /> ==Terms of use==<br /> Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom. <br /> <br /> ==New user Teamviewer (remote access)==<br /> Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).<br /> Then do the following:<br /> * Admin makes a new user with the specified email address (preferably RU or science) with a password<br /> * Admin removes everything at the Advanced settings apart from the 'log sessions' setting<br /> * Admin sets permission to user<br /> * User receives email and makes the account<br /> * Now that the user is actually active, the share can be assigned to the user with a Read-only permission.<br /> <br /> Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely. <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> <br /> <br /> <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=130 SOC workstation 2025-01-30T12:53:32Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> ==Available software==<br /> On the workstation we have the following software installed:<br /> {| class="wikitable" style="margin:auto"<br /> |+ Software installed on the SOC workstation (last updated 30.01.2025)<br /> ! Software !! Intended purpose !! License<br /> |-<br /> | GOLD|| Precise molecular docking with a genetic algorithm (GA) for pose sampling|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | Mogul|| Torsion angle checking against the CSD || Academic, RU-broad from solid state chemistry<br /> |-<br /> | Conquest|| Software to search the CSD|| Academic, RU-broad from solid state chemistry<br /> |-<br /> | MOE|| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. || Rutjes group exclusive, 1 license<br /> |-<br /> | style="color:red" YASARA Structure (no <br /> |}<br /> <br /> <br /> If you require different software, please send a message to socmoe-access@science.ru.nl. For other software available to the SOC please check [[Molecular software]]<br /> <br /> =Maintenance (admin only)=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> ==Hardware checks==<br /> ===Disk checks (2/year)===<br /> Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.<br /> Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. <br /> Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should. <br /> <br /> ===CCleaner===<br /> Should run automatically but if changes needed, these need to be reconfigured per user.<br /> <br /> ===Windows updates (2/year)===<br /> Run windows 10 updates twice per year and book a slot for this. <br /> <br /> ==Software updating==<br /> The idea is to conservatively update the system. Should updates still be needed, here are recommendations.<br /> <br /> ===Teamviewer===<br /> Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).<br /> When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:<br /> * At advanced settings, Disable local input and Enable blackscreen<br /> * Ensure Full Access is selected<br /> * Deactivate random password<br /> * Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password. <br /> <br /> ==Transfer of access==<br /> Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.<br /> <br /> =Guidelines for adding new users=<br /> ==Terms of use==<br /> Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom. <br /> <br /> ==New user Teamviewer (remote access)==<br /> Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).<br /> Then do the following:<br /> * Admin makes a new user with the specified email address (preferably RU or science) with a password<br /> * Admin removes everything at the Advanced settings apart from the 'log sessions' setting<br /> * Admin sets permission to user<br /> * User receives email and makes the account<br /> * Now that the user is actually active, the share can be assigned to the user with a Read-only permission.<br /> <br /> Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely. <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> <br /> <br /> <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=129 SOC workstation 2025-01-30T12:48:09Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> ==Available software==<br /> On the workstation we have the following software installed:<br /> {| class="wikitable" style="margin:auto"<br /> |+ Software installed on the SOC workstation (last updated 30.01.2025)<br /> ! Software !! Intended purpose !! License<br /> |-<br /> | test || test || test<br /> |}<br /> <br /> <br /> If you require different software, please send a message to socmoe-access@science.ru.nl. For other software available to the SOC please check [[Molecular software]]<br /> <br /> =Maintenance (admin only)=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> ==Hardware checks==<br /> ===Disk checks (2/year)===<br /> Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.<br /> Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. <br /> Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should. <br /> <br /> ===CCleaner===<br /> Should run automatically but if changes needed, these need to be reconfigured per user.<br /> <br /> ===Windows updates (2/year)===<br /> Run windows 10 updates twice per year and book a slot for this. <br /> <br /> ==Software updating==<br /> The idea is to conservatively update the system. Should updates still be needed, here are recommendations.<br /> <br /> ===Teamviewer===<br /> Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).<br /> When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:<br /> * At advanced settings, Disable local input and Enable blackscreen<br /> * Ensure Full Access is selected<br /> * Deactivate random password<br /> * Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password. <br /> <br /> ==Transfer of access==<br /> Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.<br /> <br /> =Guidelines for adding new users=<br /> ==Terms of use==<br /> Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom. <br /> <br /> ==New user Teamviewer (remote access)==<br /> Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).<br /> Then do the following:<br /> * Admin makes a new user with the specified email address (preferably RU or science) with a password<br /> * Admin removes everything at the Advanced settings apart from the 'log sessions' setting<br /> * Admin sets permission to user<br /> * User receives email and makes the account<br /> * Now that the user is actually active, the share can be assigned to the user with a Read-only permission.<br /> <br /> Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely. <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> <br /> <br /> <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=127 Starting as a new student 2025-01-30T09:32:37Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz as a student or they are applied for by Marieke to C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. The minimal requirements according to the Boltje lab of ELN recording are found [[Chemotion#ELN minimal book keeping| here]].<br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br/><br /> See '''[[Booking Platform for Scientific Devices]]''' for more information.<br/><br /> <br /> '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br/><br /> <br /> ==== NMR in Huygens ====<br /> There are two NMRs in wing 4, floor 3 of the Huygens building: a 400 MHz and a 500 MHz. The 400 is always in automation mode, which means you add your sample to a queue, and it will measure your sample automatically. To minimize the waiting time during the day your experiments cannot be longer than 10 minutes. If they are, you will have to measure them during the night, either on the 400 or 500.<br/><br /> The 500 is not in automation mode during the day and will be available for students only for the night queue. <br/><br /> Please ask for training before using.<br/><br /> Training: Nuwanthika Kumarage.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br/><br /> The current mass tutors are Daan Hamstra and Robin Schenker for the ISQ in Huygens, and Enebie Ramos Caceres for the ISQ in Mercator 3.<br /> <br /> === Other equipment ===<br /> Below are some other devices which are available. Not all of these are necessary for working here, but you may find some of them useful.<br /> <br/><br /> <br /> ==== Purification equipment ====<br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ===== Preparative HPLC =====<br /> There are several preparative HPLCs available for purifying synthesized compounds:<br /><br /> Wing 1 in the Huygens building has two standard reverse phase prep HPLCs, and a larger one (for runs of 10-150 mg of sample) with a mass detector. All have autosamplers and automatic collectors.<br /><br /> '''[https://www.youtube.com/watch?v=QIFn-Pk-x9s Instructional video]'''<br /><br /> Please ask for training before using.<br /><br /> Training: Frank Veldhuizen, intern supervisor or other user.<br /> <br /> ===== Biotage Isolera =====<br /> We have several automatic flash chromatographs with column cartridges for quick purification after synthesis.<br /><br /> Most supervisors want their interns to learn by running several glass columns manually before being allowed to use the Biotage.<br /><br /> [[Media:Biotage_Isolera_quick_guide.pdf|Quick guide]]<br /><br /> Training: Intern supervisor or other user.<br /> <br /> </div><br /> <br /> ==== Analysis equipment ====<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ===== IR =====<br /> HG03.222<br/><br /> Infrared spectrums are usually not essential, but they are needed for full characterization of a compound. IR can also be useful for identifying functional groups that are otherwise difficult to characterize. For example, azide groups are hard to detect using NMR, but are easily found with IR spectroscopy. Samples can be pure solid, liquid, or dissolved in a volatile solvent. <br /><br /> Training: Frank Veldhuizen.<br /> <br /> ===== Analytical HPLC =====<br /> HG03.130<br/><br /> Used to determine the purity of a sample.<br/><br /> Training: Frank Veldhuizen, intern supervisor or other user.<br /> <br /> ===== Chiral HPLC =====<br /> HG03.130<br/><br /> Used to determine the racemization of a sample.<br/><br /> Training: Frank Veldhuizen, intern supervisor or other user.<br/><br /> <br /> ===== LC-MS =====<br /> HG03.411<br/><br /> The LC-MS (“The Fleet”) can be used to analyse samples and determine the mass of compounds.<br/><br /> Training: Robin Schenker, Helene Amatdjais-Groenen, Frank Veldhuizen.<br/><br /> <br /> ===== SFC =====<br /> HG03.120<br/><br /> SFC (supercritical fluid chromatography, also known as convergence chromatography or CC) is a chromatography method using supercritical CO2 as solvent. It is faster and more efficient than HPLC. Several columns (including chiral) are available. This instrument has a UV-Vis detector and a mass detector.<br/><br /> '''[https://www.youtube.com/watch?v=IQtY6gGv0yY Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> ===== TLC-MS =====<br /> HG03.115<br/><br /> This instrument can quickly make a mass spectrum of a spot on a TLC plate. Aluminium TLC plates are preferred for this device.<br/><br /> '''[https://www.youtube.com/watch?v=jhqlRvXpZSk Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> </div><br /> <br /> ==== Synthesis equipment ====<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ===== Synthesis microwave (currently out of order) =====<br /> Can be used to initiate reactions.<br/><br /> Training: ?<br/><br /> <br /> ===== Autoclave =====<br /> HG03.115 H9<br/><br /> For high pressure reactions up to 60 bar.<br/><br /> An extensive manual is available [[Media:Guide on how to use the Autoclave and external gas cylinders.pdf|here]].<br/><br /> Training: ?<br/><br /> <br /> ===== High pressure machine =====<br /> HG03.442<br/><br /> For high pressure reactions up to 15 kbar.<br/><br /> [[Media:Checklist High pressure.docx|Manual]]<br/><br /> Training: Frank Veldhuizen<br/><br /> <br /> </div><br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. See [[Waste disposal]].<br /> * Replace solid waste containers. See [[Waste disposal]].<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed [https://cncz.science.ru.nl/en/howto/chembiooffice/ here by CnCz]. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 1996'.<br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=126 SOC workstation 2025-01-29T17:14:45Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> =Maintenance=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> ==Hardware checks==<br /> ===Disk checks (2/year)===<br /> Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.<br /> Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command. <br /> Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should. <br /> <br /> ===CCleaner===<br /> Should run automatically but if changes needed, these need to be reconfigured per user.<br /> <br /> ===Windows updates (2/year)===<br /> Run windows 10 updates twice per year and book a slot for this. <br /> <br /> ==Software updating==<br /> The idea is to conservatively update the system. Should updates still be needed, here are recommendations.<br /> <br /> ===Teamviewer===<br /> Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).<br /> When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:<br /> * At advanced settings, Disable local input and Enable blackscreen<br /> * Ensure Full Access is selected<br /> * Deactivate random password<br /> * Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password. <br /> <br /> ==Transfer of access==<br /> Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.<br /> <br /> =Guidelines for adding new users=<br /> ==Terms of use==<br /> Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom. <br /> <br /> ==New user Teamviewer (remote access)==<br /> Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).<br /> Then do the following:<br /> * Admin makes a new user with the specified email address (preferably RU or science) with a password<br /> * Admin removes everything at the Advanced settings apart from the 'log sessions' setting<br /> * Admin sets permission to user<br /> * User receives email and makes the account<br /> * Now that the user is actually active, the share can be assigned to the user with a Read-only permission.<br /> <br /> Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely. <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> <br /> <br /> <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=125 SOC workstation 2025-01-29T16:57:29Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl<br /> <br /> {{{Access to the Station}}}<br /> {{{To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}}<br /> <br /> =Maintenance=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> <br /> ==Disk checks (2/year)==<br /> <br /> <br /> ==Teamviewer==<br /> Privacy black screen.<br /> Managed from admin account. <br /> At advanced settings you can fix Disable local input and Enable Blackscreen. Also have full access, deactivate random password. <br /> Personal password is the other password that allows to connect without the need to fill it in. <br /> Safe way, make screenshots before updating. <br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> Incoming LAN connections: accept (needed to have it run from ru-network as well).<br /> <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines mailing==<br /> Every new user gets the same email and document. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> ==CCleaner==<br /> Needs to be reconfigured per user.<br /> <br /> Intel rapid storage (icon). If everything is green, good. Drive of identical capacity needs to be installed as the mirror should it fail.<br /> Folder on the desktop with maintainance commands.<br /> Check SMART overall-health self-assessment test result: PASSED (if not, contact Hakim). Ran for both hard drives. Do this every six months. <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=124 SOC workstation 2025-01-29T16:56:28Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> {{Colored box|title=Access to the Station|content=To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}<br /> <br /> {{{Access to the Station}}}<br /> {{{To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}}<br /> <br /> =Maintenance=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> <br /> ==Disk checks (2/year)==<br /> <br /> <br /> ==Teamviewer==<br /> Privacy black screen.<br /> Managed from admin account. <br /> At advanced settings you can fix Disable local input and Enable Blackscreen. Also have full access, deactivate random password. <br /> Personal password is the other password that allows to connect without the need to fill it in. <br /> Safe way, make screenshots before updating. <br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> Incoming LAN connections: accept (needed to have it run from ru-network as well).<br /> <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines mailing==<br /> Every new user gets the same email and document. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> ==CCleaner==<br /> Needs to be reconfigured per user.<br /> <br /> Intel rapid storage (icon). If everything is green, good. Drive of identical capacity needs to be installed as the mirror should it fail.<br /> Folder on the desktop with maintainance commands.<br /> Check SMART overall-health self-assessment test result: PASSED (if not, contact Hakim). Ran for both hard drives. Do this every six months. <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=123 SOC workstation 2025-01-29T16:55:07Z

<p>Wtitulaer: </p> <hr /> <div>This is an admin maintenance guide for the SOC workstation.<br /> <br /> {{{Access to the Station}}}<br /> {{{To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}}<br /> <br /> =Maintenance=<br /> Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.<br /> <br /> The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.<br /> Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.<br /> <br /> ==Disk checks (2/year)==<br /> <br /> <br /> ==Teamviewer==<br /> Privacy black screen.<br /> Managed from admin account. <br /> At advanced settings you can fix Disable local input and Enable Blackscreen. Also have full access, deactivate random password. <br /> Personal password is the other password that allows to connect without the need to fill it in. <br /> Safe way, make screenshots before updating. <br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> Incoming LAN connections: accept (needed to have it run from ru-network as well).<br /> <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines mailing==<br /> Every new user gets the same email and document. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> ==CCleaner==<br /> Needs to be reconfigured per user.<br /> <br /> Intel rapid storage (icon). If everything is green, good. Drive of identical capacity needs to be installed as the mirror should it fail.<br /> Folder on the desktop with maintainance commands.<br /> Check SMART overall-health self-assessment test result: PASSED (if not, contact Hakim). Ran for both hard drives. Do this every six months. <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=122 SOC workstation 2025-01-29T14:38:02Z

<p>Wtitulaer: </p> <hr /> <div>=Maintenance=<br /> BIOS password lost, but should not be a problem. Physical jumper can circumvent this problem.<br /> <br /> ==Teamviewer==<br /> Privacy black screen.<br /> Managed from admin account. <br /> At advanced settings you can fix Disable local input and Enable Blackscreen. Also have full access, deactivate random password. <br /> Personal password is the other password that allows to connect without the need to fill it in. <br /> Safe way, make screenshots before updating. <br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> Incoming LAN connections: accept (needed to have it run from ru-network as well).<br /> <br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines mailing==<br /> Every new user gets the same email and document. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat<br /> <br /> The license.dat also goes into the moexxx/ folder.<br /> Since the current license goes up to MOE2025.01 we can just copy the previous license.dat file.<br /> <br /> ==Caveats on installed software==<br /> Office is unofficial.<br /> <br /> Knime (guidelines caveat mentioned there as well). Should always be ran as MSS user since the file system space would be registered to admin <br /> Wincoot only used from MSS.<br /> <br /> Always install software from the admin account<br /> <br /> <br /> Firefox & Chrome should update itself in the admin account. Extensions need to be updated in both accounts.<br /> Once a year check Notepad++. Knime instead of updating uninstall and reinstall.<br /> Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).<br /> <br /> ==CCleaner==<br /> Needs to be reconfigured per user.<br /> <br /> Intel rapid storage (icon). If everything is green, good. Drive of identical capacity needs to be installed as the mirror should it fail.<br /> Folder on the desktop with maintainance commands.<br /> Check SMART overall-health self-assessment test result: PASSED (if not, contact Hakim). Ran for both hard drives. Do this every six months. <br /> <br /> ==Suggestions from Hakim==<br /> - Purge non Rutjes / non-active users<br /> - Add the black screen not active remote access part / UPDATE<br /> - Maybe remove the Linux part from the guidelines<br /> - Consider removing the shutdown part through group policy changes from MSS just keep the restart<br /> - Consider overwriting the power button. <br /> - How to find the current Teamviewer users</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=121 SOC workstation 2025-01-29T13:19:44Z

<p>Wtitulaer: </p> <hr /> <div>=Maintenance=<br /> <br /> ==Teamviewer==<br /> Privacy black screen<br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines mailing==<br /> Every new user gets the same email and document. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.<br /> <br /> ==Mailing list==<br /> Mailman lists from CnCz, mailed by Hakim (some link to login with a password)<br /> For socmoe-announce you only need Membership Management.<br /> For adding, Mass Subscriptions<br /> Basically put people in, put people out.<br /> <br /> SOC-MOE-access list<br /> <br /> ==MOE downloads/licenses==<br /> At CCG, Download Request<br /> Request type => Existing customers<br /> Use the exact correct email address.<br /> Make sure the Daemon version / license manager version is good.<br /> 3 tokens/pc<br /> Increment part of the license file specifies the teaching licenses.<br /> Every year we should automatically get the new license after the payment is done. Then a new license.dat can be made and sent to CnCz. Check in April with Samuel if payment is done cause license is only issued once payment has been received.<br /> 31 May 2025 we need to buy another 3 years with annual payment and Samuel fixes the payment. Mauricio gets in touch and asks to renew.<br /> Emails come from MOE License Management<br /> Text goes into license.dat</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=120 SOC workstation 2025-01-29T12:48:28Z

<p>Wtitulaer: </p> <hr /> <div>==Maintenance==<br /> <br /> ==Teamviewer==<br /> Privacy black screen<br /> <br /> Licentiebeheer ILS Wietske (RU), Samuel handels the payment.<br /> ===New user===<br /> - Make a new user yourself with a password<br /> - Remove everything at Advanced apart from log sessions<br /> - Permission: user<br /> - User receives email and makes account<br /> - Now the user is active and the share can be assigned to the user with a Read-only permission<br /> <br /> ==Booking==<br /> Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.<br /> <br /> ==Guidelines==<br /> Every new user gets it. Currently it's a .pdf / .odt file.<br /> @Willem, include what software can be used by whom under which restrictions.</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=SOC_workstation&diff=119 SOC workstation 2025-01-29T12:24:48Z

<p>Wtitulaer: Created page with "TEst"</p> <hr /> <div>TEst</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=94 Starting as a new student 2024-10-10T12:50:54Z

<p>Wtitulaer: /* Going into the lab */</p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. The minimal requirements according to the Boltje lab of ELN recording are found [[Chemotion#ELN minimal book keeping| here]].<br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br/><br /> See [[Booking Platform for Scientific Devices]] for more information.<br/><br /> <br /> '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br/><br /> <br /> ==== NMR in Huygens ====<br /> There are two NMRs in wing 4, floor 3 of the Huygens building: a 400 MHz and a 500 MHz. The 400 is always in automation mode, which means you add your sample to a queue, and it will measure your sample automatically. To minimize the waiting time during the day your experiments cannot be longer than 10 minutes. If they are, you will have to measure them during the night, either on the 400 or 500.<br/><br /> The 500 is not in automation mode during the day and will be available for students only for the night queue. Please ask for training before using.<br/><br /> Training: Currently: stagebegeleider. Soon: Nuwanthika Kumarage.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br/><br /> The current mass tutors are Daan Hamstra and Robin Schenker for the ISQ in Huygens, and Enebie Ramos Caceres for the ISQ in Mercator 3.<br /> <br /> === Purification equipment ===<br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ==== Preparative HPLC ====<br /> There are several preparative HPLCs available for purifying synthesized compounds:<br /><br /> Wing 1 in the Huygens building has two standard reverse phase prep HPLCs, and a larger one (for runs of 10-150 mg of sample) with a mass detector. All have autosamplers and automatic collectors.<br /><br /> '''[https://www.youtube.com/watch?v=QIFn-Pk-x9s Instructional video]'''<br /><br /> Please ask for training before using.<br /><br /> Training: Intern supervisor or other user. <br /> <br /> ==== Biotage Isolera ====<br /> We have several automatic flash chromatographs with column cartridges for quick purification after synthesis.<br /><br /> Most supervisors want their interns to learn by running several glass columns manually before being allowed to use the Biotage.<br /><br /> (Manual)<br /><br /> Training: Intern supervisor or other user.<br /> <br /> </div><br /> <br /> <br /> === Analysis equipment ===<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ==== IR ====<br /> HG03.222<br/><br /> Infrared spectrums are usually not essential, but they are needed for full characterization of a compound. IR can also be useful for identifying functional groups that are otherwise difficult to characterize. For example, azide groups are hard to detect using NMR, but are easily found with IR spectroscopy. Samples can be pure solid, liquid, or dissolved in a volatile solvent. <br /><br /> Training: Frank Veldhuizen.<br /> <br /> ==== Analytical HPLC ====<br /> HG03.130<br/><br /> Used to determine the purity of a sample.<br/><br /> Training: Intern supervisor or other user.<br /> <br /> ==== Chiral HPLC ====<br /> HG03.130<br/><br /> Used to determine the racemization of a sample.<br/><br /> Training: Intern supervisor or other user.<br/><br /> <br /> ==== LC-MS ====<br /> HG03.411<br/><br /> The LC-MS (“The Fleet”) can be used to analyse samples and determine the mass of compounds.<br/><br /> Training: Robin Schenker, Helene Amatdjais-Groenen, Frank Veldhuizen.<br/><br /> <br /> ==== SFC (currently out of order) ====<br /> HG03.120<br/><br /> SFC (supercritical fluid chromatography, also known as convergence chromatography or CC) is a chromatography method using supercritical CO2 as solvent. It is faster and more efficient than HPLC. Several columns (including chiral) are available. This instrument has a UV-Vis detector and a mass detector.<br/><br /> '''[https://www.youtube.com/watch?v=IQtY6gGv0yY Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> ==== TLC-MS ====<br /> This instrument can quickly make a mass spectrum of a spot on a TLC plate. Aluminium TLC plates are preferred for this device.<br/><br /> '''[https://www.youtube.com/watch?v=jhqlRvXpZSk Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> </div><br /> <br /> === Synthesis equipment ===<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> ==== Synthesis microwave (currently out of order) ====<br /> Can be used to initiate reactions.<br/><br /> Training: ?<br/><br /> <br /> ==== Autoclave ====<br /> HG03.115 H9<br/><br /> For high pressure reactions up to 60 bar.<br/><br /> An extensive manual is available.<br/><br /> Training: ?<br/><br /> <br /> ==== High pressure machine ====<br /> HG03.442<br/><br /> For high pressure reactions up to 15 kbar.<br/><br /> Manual<br/><br /> Training: Frank Veldhuizen<br/><br /> <br /> </div><br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. See [[Waste disposal]].<br /> * Replace solid waste containers. See [[Waste disposal]].<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed [https://cncz.science.ru.nl/en/howto/chembiooffice/ here by CnCz]. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 1996'.<br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Chemotion&diff=93 Chemotion 2024-10-10T12:44:05Z

<p>Wtitulaer: </p> <hr /> <div>Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions with the experimentals, analyses performed and compound identifiers. A general use guide can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit?tab=t.0 here]. A key step is to always click the yellow save button after performing an action, since Chemotion does not automatically save any of your applied changes.<br /> <br /> ==ELN minimal book keeping==<br /> In order for the ELN to be an useful tool, the Boltje lab has agreed on standards which need to be present in order for an experiment to be signed off. These requirements/customs include:<br /> * '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.<br /> * '''Experiments are identified by the reaction in which they were synthesized.''' Chemotion automatically labels both starting materials (AAA-xx) and products with an unique code/identifier with your personal code, while the reaction/experiment is labelled with an R in the code (AAA-Rx), where the x is any number and AAA stands for your unique user identifier. These reaction and substance identifiers do not nicely correspond to each other and hence we have opted for the usage of the AAA-Rx reaction identifier for referencing a substance. Best practice is to give the compound also an additional identifier at the Name section.<br /> * '''The experimental is included at the description.''' A complete experimental stating amount and identity of reactants, reactions times and purification methods etc. is included with the experiment. This experimental should be unambiguous and state exactly what you did. This ensures that even if the reaction drawing does not allow you to specify chemicals or purification methods, your experiment will be reproducible.<br /> * '''Under the analyses tab of your reaction, you include all the recorded data'''. This means a picture of your TLC, the Rf-value, a low resolution mass, the recorded NMR-spectra and all other data. Keep in mind that for novel chemical entities (NCEs) that have not been synthesized before, more extensive characterization is obligatory!<br /> * '''NCEs are extensively characterized and reported under the analyses'''. A novel chemical entity needs to be characterized with a variety of techniques. For all NCEs synthesized at the SOC a high resolution mass spectrum (HRMS) needs to be recorded and a full characterization by NMR (<sup>1</sup>H-, <sup>13</sup>C-, <sup>1</sup>H-<sup>1</sup>H-COSY, <sup>1</sup>H-<sup>13</sup>C-HSQC and <sup>1</sup>H-<sup>13</sup>C-HMBC) are required. These spectra should be clean (no to almost none overlapping solvent peaks, high enough signal to noise ratio) so it can be unambiguously proven the compound was synthesized. If your NCE contains unique IR-active moieties such as azides, an IR-spectrum is also required. Similarly, if your molecule contains other NMR-active nuclei such as <sup>19</sup>F or <sup>31</sup>P, the respective NMR-spectrum should be recorded. If your molecule contains multiple stereocenters, the exact diastereoisomer/enantiomer should be determined by X-ray crystallography or selective NMR experiments such as TOCSY and NOESY. If your NCE will be tested in any biological assay, purity by HPLC needs to be provided (most journals reject data of samples with <95 % purity nowadays).</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Chemotion&diff=92 Chemotion 2024-10-10T12:35:56Z

<p>Wtitulaer: </p> <hr /> <div>Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions with the experimentals, analyses performed and compound identifiers. A general use guide can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit?tab=t.0 here]. A key step is to always click the yellow save button after performing an action, since Chemotion does not automatically save any of your applied changes.<br /> <br /> ==ELN minimal book keeping==<br /> In order for the ELN to be an useful tool, the Boltje lab has agreed on standards which need to be present in order for an experiment to be signed off. These requirements/customs include:<br /> * '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.<br /> * '''Experiments are identified by the reaction in which they were synthesized.''' Chemotion automatically labels both starting materials (AAA-xx) and products with an unique code/identifier with your personal code, while the reaction/experiment is labelled with an R in the code (AAA-Rx), where the x is any number and AAA stands for your unique user identifier. These reaction and substance identifiers do not nicely correspond to each other and hence we have opted for the usage of the AAA-Rx reaction identifier for referencing a substance. Best practice is to give the compound also an additional identifier at the Name section.<br /> * '''The experimental is included at the description.''' A complete experimental stating amount and identity of reactants, reactions times and purification methods etc. is included with the experiment. This experimental should be unambiguous and state exactly what you did. This ensures that even if the reaction drawing does not allow you to specify chemicals or purification methods, your experiment will be reproducible.<br /> * '''Under the analyses tab of your reaction, you include all the recorded data'''. This means a picture of your TLC, the Rf-value, a low resolution mass, the recorded NMR-spectra and all other data. Keep in mind that for novel chemical entities (NCEs) that have not been synthesized before, more extensive characterization is obligatory!<br /> * '''NCEs are extensively characterized and reported under the analyses'''. A novel chemical entity needs to be characterized with a variety of techniques. For all NCEs synthesized at the SOC a high resolution mass spectrum (HRMS) needs to be recorded and a full characterization by NMR (<sup>1</sup>H-, <sup>13</sup>C-, <sup>1</sup>H-<sup>1</sup>H-COSY, <sup>1</sup>H-<sup>13</sup>C-HSQC and <sup>1</sup>H-<sup>13</sup>C-HMBC) are required. If your NCE contains unique IR-active moieties such as azides, an IR-spectrum is also required. Similarly, if your molecule contains other NMR-active nuclei such as <sup>19</sup>F or <sup>31</sup>P, the respective NMR-spectrum should be recorded. If your molecule contains multiple stereocenters, the exact diastereoisomer/enantiomer should be determined by X-ray crystallography or selective NMR experiments such as TOCSY and NOESY.</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Chemotion&diff=91 Chemotion 2024-10-10T12:33:23Z

<p>Wtitulaer: </p> <hr /> <div>Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions with the experimentals, analyses performed and compound identifiers. A general use guide can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit?tab=t.0 here]. A key step is to always click the yellow save button after performing an action, since Chemotion does not automatically save any of your applied changes.<br /> <br /> ==ELN minimal book keeping==<br /> In order for the ELN to be an useful tool, the Boltje lab has agreed on standards which need to be present in order for an experiment to be signed off. These requirements/customs include:<br /> * '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.<br /> * '''Experiments are identified by the reaction in which they were synthesized.''' Chemotion automatically labels both starting materials with your personal code (AAA-xx) and the reaction/experiment (AAA-Rx), where the x is any number and AAA stands for your unique user identifier. These identifiers do not correspond to each other and hence we have opted for the usage of the AAA-Rx reaction identifier. Best practice is to give the compound also an additional identifier at the Name section.<br /> * '''The experimental is included at the description.''' A complete experimental stating amount and identity of reactants, reactions times and purification methods etc. is included with the experiment. This experimental should be unambiguous and state exactly what you did. This ensures that even if the reaction drawing does not allow you to specify chemicals or purification methods, your experiment will be reproducible.<br /> * '''Under the analyses tab of your reaction, you include all the recorded data'''. This means a picture of your TLC, the Rf-value, a low resolution mass, the recorded NMR-spectra and all other data. Keep in mind that for novel chemical entities (NCEs) that have not been synthesized before, more extensive characterization is obligatory!<br /> * '''NCEs are extensively characterized and reported under the analyses'''. A novel chemical entity needs to be characterized with a variety of techniques. For all NCEs synthesized at the SOC a high resolution mass spectrum (HRMS) needs to be recorded and a full characterization by NMR (<sup>1</sup>H-, <sup>13</sup>C-, <sup>1</sup>H-<sup>1</sup>H-COSY, <sup>1</sup>H-<sup>13</sup>C-HSQC and <sup>1</sup>H-<sup>13</sup>C-HMBC) are required. If your NCE contains unique IR-active moieties such as azides, an IR-spectrum is also required. Similarly, if your molecule contains other NMR-active nuclei such as <sup>19</sup>F or <sup>31</sup>P, the respective NMR-spectrum should be recorded. If your molecule contains multiple stereocenters, the exact diastereoisomer/enantiomer should be determined by X-ray crystallography or selective NMR experiments such as TOCSY and NOESY.</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Chemotion&diff=90 Chemotion 2024-10-10T12:24:41Z

<p>Wtitulaer: </p> <hr /> <div>Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions with the experimentals, analyses performed and compound identifiers. A general use guide can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit?tab=t.0 here]. A key step is to always click the yellow save button after performing an action, since Chemotion does not automatically save any of your applied changes.<br /> <br /> ==ELN minimal book keeping==<br /> In order for the ELN to be an useful tool, the Boltje lab has agreed on standards which need to be present in order for an experiment to be signed off. These requirements/customs include:<br /> * '''Experiments are identified by the reaction in which they were synthesized.''' Chemotion automatically labels both starting materials with your personal code (AAA-xx) and the reaction/experiment (AAA-Rx), where the x is any number and AAA stands for your unique user identifier. These identifiers do not correspond to each other and hence we have opted for the usage of the AAA-Rx reaction identifier. Best practice is to give the compound also an additional identifier at the Name section.<br /> * '''The experimental is included at the description.''' A complete experimental stating amount and identity of reactants, reactions times and purification methods etc. is included with the experiment. This experimental should be unambiguous and state exactly what you did. This ensures that even if the reaction drawing does not allow you to specify chemicals or purification methods, your experiment will be reproducible.<br /> * '''Under the analyses tab of your reaction, you include all the recorded data'''. This means a picture of your TLC, the Rf-value, a low resolution mass, the recorded NMR-spectra and all other data. Keep in mind that for novel chemical entities (NCEs) that have not been synthesized before, a HRMS and full characterization by NMR <sup>1</sup>H-NMR</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Chemotion&diff=89 Chemotion 2024-10-10T12:24:09Z

<p>Wtitulaer: Created page with "Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions w..."</p> <hr /> <div>Chemotion is an open-source electronic lab notebook (ELN) that is used at the synthetic organic chemistry department. It allows the user to keep track of performed reactions with the experimentals, analyses performed and compound identifiers. A general use guide can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit?tab=t.0 here]. A key step is to always click the yellow save button after performing an action, since Chemotion does not automatically save any of your applied changes.<br /> <br /> ==ELN minimal book keeping==<br /> In order for the ELN to be an useful tool, the Boltje lab has agreed on standards which need to be present in order for an experiment to be signed off. These requirements/customs include:<br /> * '''Experiments are identified by the reaction in which they were synthesized.''' Chemotion automatically labels both starting materials with your personal code (AAA-xx) and the reaction/experiment (AAA-Rx), where the x is any number and AAA stands for your unique user identifier. These identifiers do not correspond to each other and hence we have opted for the usage of the AAA-Rx reaction identifier. Best practice is to give the compound also an additional identifier at the Name section.<br /> * '''The experimental is included at the description.''' A complete experimental stating amount and identity of reactants, reactions times and purification methods etc. is included with the experiment. This experimental should be unambiguous and state exactly what you did. This ensures that even if the reaction drawing does not allow you to specify chemicals or purification methods, your experiment will be reproducible.<br /> * '''Under the analyses tab of your reaction, you include all the recorded data'''. This means a picture of your TLC, the Rf-value, a low resolution mass, the recorded NMR-spectra and all other data. Keep in mind that for novel chemical entities (NCEs) that have not been synthesized before, a HRMS and full characterization by NMR (1</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=88 Starting as a new student 2024-10-10T12:06:09Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. The minimal requirements according to the Boltje lab of ELN recording are found here.<br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br/><br /> See [[Booking Platform for Scientific Devices]] for more information.<br/><br /> <br /> '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br/><br /> <br /> ==== NMR in Huygens ====<br /> There are two NMRs in wing 4, floor 3 of the Huygens building: a 400 MHz and a 500 MHz. The 400 is always in automation mode, which means you add your sample to a queue, and it will measure your sample automatically. To minimize the waiting time during the day your experiments cannot be longer than 10 minutes. If they are, you will have to measure them during the night, either on the 400 or 500.<br/><br /> The 500 is not in automation mode during the day and will be available for students only for the night queue. Please ask for training before using.<br/><br /> Training: Currently: stagebegeleider. Soon: Nuwanthika Kumarage.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br/><br /> The current mass tutors are Daan Hamstra and Robin Schenker for the ISQ in Huygens, and Enebie Ramos Caceres for the ISQ in Mercator 3.<br /> <br /> === Purification equipment ===<br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ==== Preparative HPLC ====<br /> There are several preparative HPLCs available for purifying synthesized compounds:<br /><br /> Wing 1 in the Huygens building has two standard reverse phase prep HPLCs, and a larger one (for runs of 10-150 mg of sample) with a mass detector. All have autosamplers and automatic collectors.<br /><br /> '''[https://www.youtube.com/watch?v=QIFn-Pk-x9s Instructional video]'''<br /><br /> Please ask for training before using.<br /><br /> Training: Intern supervisor or other user. <br /> <br /> ==== Biotage Isolera ====<br /> We have several automatic flash chromatographs with column cartridges for quick purification after synthesis.<br /><br /> Most supervisors want their interns to learn by running several glass columns manually before being allowed to use the Biotage.<br /><br /> (Manual)<br /><br /> Training: Intern supervisor or other user.<br /> <br /> </div><br /> <br /> <br /> === Analysis equipment ===<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> <br /> ==== IR ====<br /> HG03.222<br/><br /> Infrared spectrums are usually not essential, but they are needed for full characterization of a compound. IR can also be useful for identifying functional groups that are otherwise difficult to characterize. For example, azide groups are hard to detect using NMR, but are easily found with IR spectroscopy. Samples can be pure solid, liquid, or dissolved in a volatile solvent. <br /><br /> Training: Frank Veldhuizen.<br /> <br /> ==== Analytical HPLC ====<br /> HG03.130<br/><br /> Used to determine the purity of a sample.<br/><br /> Training: Intern supervisor or other user.<br /> <br /> ==== Chiral HPLC ====<br /> HG03.130<br/><br /> Used to determine the racemization of a sample.<br/><br /> Training: Intern supervisor or other user.<br/><br /> <br /> ==== LC-MS ====<br /> HG03.411<br/><br /> The LC-MS (“The Fleet”) can be used to analyse samples and determine the mass of compounds.<br/><br /> Training: Robin Schenker, Helene Amatdjais-Groenen, Frank Veldhuizen.<br/><br /> <br /> ==== SFC (currently out of order) ====<br /> HG03.120<br/><br /> SFC (supercritical fluid chromatography, also known as convergence chromatography or CC) is a chromatography method using supercritical CO2 as solvent. It is faster and more efficient than HPLC. Several columns (including chiral) are available. This instrument has a UV-Vis detector and a mass detector.<br/><br /> '''[https://www.youtube.com/watch?v=IQtY6gGv0yY Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> ==== TLC-MS ====<br /> This instrument can quickly make a mass spectrum of a spot on a TLC plate. Aluminium TLC plates are preferred for this device.<br/><br /> '''[https://www.youtube.com/watch?v=jhqlRvXpZSk Instructional video]'''<br/><br /> Please ask for training before using.<br/><br /> Training: Frank Veldhuizen.<br/><br /> <br /> </div><br /> <br /> === Synthesis equipment ===<br /> <br /> <div class="toccolours mw-collapsible" style="width:600px; overflow:auto;"><br /> ==== Synthesis microwave (currently out of order) ====<br /> Can be used to initiate reactions.<br/><br /> Training: ?<br/><br /> <br /> ==== Autoclave ====<br /> HG03.115 H9<br/><br /> For high pressure reactions up to 60 bar.<br/><br /> An extensive manual is available.<br/><br /> Training: ?<br/><br /> <br /> ==== High pressure machine ====<br /> HG03.442<br/><br /> For high pressure reactions up to 15 kbar.<br/><br /> Manual<br/><br /> Training: Frank Veldhuizen<br/><br /> <br /> </div><br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. See [[Waste disposal]].<br /> * Replace solid waste containers. See [[Waste disposal]].<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed [https://cncz.science.ru.nl/en/howto/chembiooffice/ here by CnCz]. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 1996'.<br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=69 Starting as a new student 2024-10-03T07:58:37Z

<p>Wtitulaer: /* Chemdraw */</p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed [https://cncz.science.ru.nl/en/howto/chembiooffice/ here by CnCz]. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 1996'.<br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=68 Starting as a new student 2024-10-03T07:58:08Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> Chemdraw is a molecular drawing software which allows us to draw compounds and reactions. The Chemdraw installation guide is detailed [https://cncz.science.ru.nl/en/howto/chembiooffice/ here by CnCz]. Within SOC we adhere to the 'ACS Document 1996' drawing style which is activated with 'File | Apply Document Settings From | ACS Document 19996'. <br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=67 Starting as a new student 2024-10-03T07:37:59Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> MestreNova is a licensed software with which we can analyze recorded NMR-spectra. MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=66 Starting as a new student 2024-10-03T07:35:49Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> MestreNova can be obtained from the [https://cncz.science.ru.nl/en/howto/install-share/ install network drive of CnCz], where also an install guide is found.<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Team_029&diff=65 Team 029 2024-09-12T10:06:49Z

<p>Wtitulaer: Created page with "This page was created to summarize useful links for members of lab M3.03.029/1 . * [https://surfdrive.surf.nl/files/index.php/s/3cbheTLgYw6kEzb Surfdrive] * [https://chemotio..."</p> <hr /> <div>This page was created to summarize useful links for members of lab M3.03.029/1 .<br /> <br /> * [https://surfdrive.surf.nl/files/index.php/s/3cbheTLgYw6kEzb Surfdrive]<br /> * [https://chemotion.science.ru.nl/home Chemotion]<br /> * [https://bookings.science.ru.nl/ Booking system]</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=64 Starting as a new student 2024-09-05T09:09:36Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=63 Starting as a new student 2024-09-05T09:08:53Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [[Molecular Software]].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=62 Starting as a new student 2024-09-05T09:08:10Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) which can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [Molecular Software].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=61 Starting as a new student 2024-09-04T15:18:42Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to pencils and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> === Other measuring equipment ===<br /> @Frank Veldhuizen<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true when working from home, leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [[Regular lab events]].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers.<br /> * Most labs have a weekly cleaning moment. Please be present for these moments.<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [Molecular Software].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Main_Page&diff=60 Main Page 2024-09-04T13:37:29Z

<p>Wtitulaer: </p> <hr /> <div>Welcome to the wiki of Synthetic Organic Chemistry. This wiki serves to help find relevant information for employees and students. Furthermore, the wiki is dedicated for a large part to molecular modelling software tutorials etc. <br /> Editing of pages is highly encouraged but keep in mind that everyone who has a science account can access the information on this wiki. <br /> <br /> == Useful pages ==<br /> * [[Regular lab events]]<br /> * [[Starting as a new student]]<br /> * Starting as a new employee<br /> * The booking system for measuring equipment<br /> * [[Molecular software]]<br /> <br /> == Developer ==<br /> <br /> <strong>MediaWiki has been installed.</strong><br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.<br /> <br /> == Getting started ==<br /> * [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]<br /> * [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]<br /> * [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]<br /> * [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]<br /> * [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=59 Starting as a new student 2024-09-04T13:37:06Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [Molecular Software].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=58 Starting as a new student 2024-09-04T13:35:03Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account. Afterwards you can take the test with a Safety Officer. Upon successful completion, you will be showed around the lab in particular regarding the safety equipment such as emergency showers and CO2 fire extinguishers.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below. '''Ensure you make a backup''' of all the data you record since the measured data is deleted at least biannually from the machine due to storage space.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis.<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [Molecular Software].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive is similar to google-drive but the data is stored inside the Radboud rather than on a server from a big company. If your supervisor uses surf-drive he/she can invite you to a drive where you can share your material.<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'. Should you like some refreshers, you can use the links below:<br /> *[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]<br /> *[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]<br /> <br /> ===Column chromatography===<br /> You can find a nice guide to column chromatography here:<br /> <br /> ===Reaxys===<br /> <br /> ===Some useful lab tips===</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=57 Starting as a new student 2024-09-04T13:22:16Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers<br /> <br /> == General (analysis) software ==<br /> Please ensure you have access to all standard office softwares such as word, excel, powerpoint and a pdf-reader (or any equivalent thereof). Outside of those, there are a few additional softwares we regularly use at the SOC<br /> <br /> ===Chemdraw===<br /> (to be filled)<br /> <br /> ===MestreNova===<br /> (to be filled)<br /> ===<br /> <br /> =Other useful but non-mandatory things=<br /> == Molecular modelling software ==<br /> At the SOC we have a workstation that has multiple molecular modelling software packages installed, as well as a cluster for running larger calculations. More info can be found at [Molecular Software].<br /> <br /> == Shared drives & back-ups: Surf-drive ==<br /> Surf-drive (to be filled)<br /> <br /> ==Knowledge transfer ==<br /> === NMR ===<br /> As a student of the SOC, you will record and analyze a lot of NMR spectra. Most of the relevant topics regarding NMR and MS are explained in the master course 'Instrumental Analysis in (Bio) Molecular Chemistry (NWI-MOL404)'.</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=56 Starting as a new student 2024-09-04T13:12:23Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Synthesizing a new compound ==<br /> Whenever you synthesize a compound, you should measure NMR- MS-spectra, and record the Rf-value of the compound to confirm it is actually the correct compound. Compounds should be stored in clearly labelled (pill) jar, reporting the experiment code, name of the compound and the structure. If the compound has known hazard statements, these should also be included here. When you synthesize a '''novel compound''' (a new chemical entity (NCE), ensure you always do a full characterization (see below). It is good practice to '''keep an aliquot''' (~10 mg) of all compounds you synthesize in case you later need to repeat an analysis<br /> <br /> ===Full characterization of a NCE===<br /> <br /> (to be filled)...<br /> <br /> == How to behave in the lab ==<br /> In order to have a productive and healthy working environment, please adhere at least to these rules:<br /> * If you finish a general reagent/solvent, you should write this on the relevant whiteboard. An employee will then order it in Labservant. This also holds for the cleaning acetone.<br /> * If you finish the home-made solutions such as brine or 1 M NaOH in H2O, please prepare a new bottle of the solution. If you're uncertain how-to, please ask an employee.<br /> * Keep the general working area and benches clean and tidy.<br /> * Replace liquid waste containers '''before''' they are full but rather at 80% capacity. <br /> * Replace solid waste containers<br /> <br /> == Molecular modelling software ==<br /> <br /> =Other useful but non-mandatory things=</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=55 Starting as a new student 2024-09-04T12:59:13Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> =The mandatory stuff=<br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Molecular modelling software ==<br /> <br /> =Other useful but non-mandatory things=</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=54 Starting as a new student 2024-09-04T12:58:42Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> <br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account.<br /> <br /> == Working from home, vacation or being sick ==<br /> When you are absent from work, please ensure your lab members know you are absent. This holds true working from home (wfh), leaving early on the day, taking vacation or being sick.<br /> <br /> == Regular lab events ==<br /> Regular lab events are generally lab specific and are found at [Regular lab events].<br /> <br /> == Molecular modelling software ==<br /> <br /> =Other useful but non-mandatory things=</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=53 Starting as a new student 2024-09-04T12:51:11Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> <br /> == Registration & Access to the wings ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{Technician huygens}} for working in Huygens.<br /> * Obtain a '''physical lab journal''' (in addition to penciles and other office supplies) can be acquired from the secretary office in Hg and from {{Technician mercator}} in M3. <br /> * Gain access to the '''electronic lab notebook (ELN)''' for which we currently use [https://chemotion.science.ru.nl/home chemotion]. Daniel Blanco-Ania is the responsible person for this and can give you access. Hence, send an email to him or pass by his office. '''Important:''' as a student you need to share your ELN with your supervisor and you should close experiments after 3 weeks of completing them. A more extensive guide on using Chemotion can be found [https://docs.google.com/document/d/1wdaeXOB5fZVcQ8pyIDBOKXN5hEscbM5El8OwFzIN1Jw/edit here]. <br /> <br /> == Lab equipment access ==<br /> Laboratory equipment such as mass spectrometers and NMRs are expensive and in high-demand with a lot of people in the university. Hence, you need training from the respective responsible person for the device and need to book a timeslot. The booking can be done at [https://bookings.science.ru.nl/portal the booking portal], where you can login at the top right with your S/U/E number. All the relevant personnel per device can be found on that website, but as a student of the SOC you will at least need access for the equipment below.<br /> <br /> === NMR access ===<br /> NMRs for general use are found in the Huygens (a 400 MHz and 500 MHz) and in M3. Generally the NMRs operate in automation mode, meaning you only need to add your sample to the que and your specified measurements will be performed automatically. Please ensure you submit your samples to the night-queue and not the day-queue when your measurement will take longer ~10 minutes. If you are the first to put in a sample to the night-queue '''you''' are responsible for starting the queue (please ask your supervisor how to this). You can access measured spectra at \\nmrspectra-srv.science.ru.nl\nmrspectra which you can add as an external drive to your pc and access via your science account.<br /> <br /> === MS access ===<br /> There are various mass spectrometers available to SOC but most students will only manually operate the ISQs. A guide on how to operate the ISQs can be found [https://gitlab.science.ru.nl/jzelenka/isq/-/blob/master/README.md here], which you will need to read prior to getting training for the ISQs. After measuring your MS samples, you can retrieve the results either directly from the computers or via \\msspectra-srv.science.ru.nl\msspectra by adding this external drive to your pc and access via your science account</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Template:Technician_huygens&diff=52 Template:Technician huygens 2024-09-04T12:26:09Z

<p>Wtitulaer: Created page with "Samuel Bosma (samuel.bosma@ru.nl)"</p> <hr /> <div>Samuel Bosma (samuel.bosma@ru.nl)</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=51 Starting as a new student 2024-09-04T12:25:08Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from {{Technician mercator}} for working in Mercator and {{}} for working in Huygens.</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Template:Technician_mercator&diff=50 Template:Technician mercator 2024-09-04T12:24:11Z

<p>Wtitulaer: Created page with "Hernando Tuñon (hernando.tunon@ru.nl)"</p> <hr /> <div>Hernando Tuñon (hernando.tunon@ru.nl)</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=49 Starting as a new student 2024-09-04T12:22:28Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant '''safety equipment''' such as a lab coat and safety goggles. These can be obtained from</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=48 Starting as a new student 2024-09-04T12:21:49Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/ here]. If you are reading this page from the Wiki than the Science account corresponds to the SAML login you used to access this wiki.<br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}}. She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''<br /> * The '''checklist for new members of the Molecular Chemistry Cluster'''. This document declares that you have been introduced to everyone and have all the necessary rights etc. This should be signed of course after all these events have taken place.<br /> <br /> After signing the forms, {{Secretary}} will ensure you have access to the relevant wings (generally for our group wings 1,2,4,8 on the third floor of the Huygens building and the rooms on the third floor in Mercator 3). Keep in mind that as a student you can only access these wings during working hours and hence not in the evening or weekends. You should also be added to the relevant mailing lists (orgchem-group@science.ru.nl & rutjes-group@science.ru.nl). Please verify yourself that you have been added to these since important information will be communicated through those email lists.<br /> <br /> == Going into the lab ==<br /> In order to go into the lab you need to take care of the following things:<br /> * Complete the '''safety test'''. Prior to taking the test you need to acquaint yourself with the safety manual (found [https://orgchem.pages.science.ru.nl/safetymanual/ here]) which requires a Science account.<br /> * Obtain the relevant safety equipment such as a lab coat and safety goggles. These can be obtained from</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Template:Secretary&diff=47 Template:Secretary 2024-09-04T12:08:00Z

<p>Wtitulaer: </p> <hr /> <div>Marieke Egbertzen (marieke.egbertzen@ru.nl)</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=46 Starting as a new student 2024-09-04T12:07:36Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/] <br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary {{Secretary}} . She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=45 Starting as a new student 2024-09-04T12:07:04Z

<p>Wtitulaer: </p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/] <br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary test:{{Secretary}} Marieke Egbertzen (marieke.egbertzen@ru.nl). She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Template:Secretary&diff=44 Template:Secretary 2024-09-04T12:06:26Z

<p>Wtitulaer: Created page with "Marieke Egbertzen"</p> <hr /> <div>Marieke Egbertzen</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Starting_as_a_new_student&diff=43 Starting as a new student 2024-09-04T12:04:22Z

<p>Wtitulaer: Created page with "When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of th..."</p> <hr /> <div>When you start as a new student, there will be a lot of information to process, forms to sign and trainings to follow. This page was created to help you gain an overview of the things that need to be done.<br /> There are a few things you will have to take care of yourself, preferably before starting the internship:<br /> * Obtaining a '''Radboud campus card''' with an S/U/E number. If you do not have such a card yet and are not a student from the Radboud, you can contact sa@dpo.ru.nl with your request. They will want a picture from you for on the campus card. They will contact you when you can pick it up (used to be at the Erasmus building (E 19.02).<br /> * A '''science account''', which you can get from C&Cz. You will need this account in order to access the VPN and get your mass/NMR spectra. A guide for obtaining a science account is found at [https://cncz.science.ru.nl/en/howto/login/] <br /> <br /> == Registration & Access ==<br /> In order to work in the department of synthetic organic chemistry, you will have to register as an intern with our secretary Marieke Egbertzen (marieke.egbertzen@ru.nl). She will ask you to read & sign the following documents:<br /> * The ''' registration new employees''', which you can fill in yourself and send to Marieke.<br /> * The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.<br /> * A non-disclosure agreement (NDA), which you can fill in yourself and send to Marieke. the form's name currently is '''Declaration Guest researchers 2023.docx'''</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Dock_3.8&diff=42 Dock 3.8 2024-08-28T15:57:04Z

<p>Wtitulaer: </p> <hr /> <div>DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://doi.org/10.1038/s41596-021-00597-z here]. The software can be used by academics upon requesting a license and currently runs on cn142. <br /> <br /> ==Pros & Cons of DOCK as docking software==<br /> * '''Pro''' DOCK is generally a lot faster than other docking software available.<br /> * '''Pro''' DOCK generally produces accurate poses if sampling is increased<br /> * '''Pro''' Tuning of parameters can be done through manipulating the spheres and scoring functions, allowing for better optimization.<br /> * '''Con''' DOCK doesn't generates conformers of ligands on-the-fly and requires additional software to do this.<br /> * '''Con''' DOCK doesn't have very clear documentation, requiring more hands-on programming knowledge/experience to use.<br /> <br /> Basically, DOCK is the go-to virtual screening software on our cluster.<br /> =How to use=<br /> ==Protein-ligand complex files to generate==<br /> DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to<br /> <br /> ==Initializing DOCK on cn142==<br /> In order to run DOCK 3.8 programs, the correct environment first needs to be loaded. '''EDIT: A more sophisticated login script will appear soon (hopefully). For now do the actions below'''.<br /> Ssh into cn142 then:<br /> <pre><br /> source /opt/molmech/login_molmech.sh<br /> module load poetry<br /> cd /opt/molmech/modules$ cd /opt/molmech/DOCK38/DOCK_Release_Apr_21_2023/pydock3/<br /> poetry shell<br /> </pre><br /> ==Using BLASTERMASTER==<br /> <br /> ==Using DOCKOPT==<br /> <br /> ==Docking with SLURM==</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Dock_3.8&diff=41 Dock 3.8 2024-08-28T15:55:23Z

<p>Wtitulaer: </p> <hr /> <div>DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://doi.org/10.1038/s41596-021-00597-z here]. The software can be used by academics upon requesting a license and currently runs on cn142. <br /> <br /> ==Pros & Cons of DOCK as docking software==<br /> * '''Pro''' DOCK is generally a lot faster than other docking software available.<br /> * '''Pro''' DOCK generally produces accurate poses if sampling is increased<br /> * '''Pro''' Tuning of parameters can be done through manipulating the spheres and scoring functions, allowing for better optimization.<br /> * '''Con''' DOCK doesn't generates conformers of ligands on-the-fly and requires additional software to do this.<br /> * '''Con''' DOCK doesn't have very clear documentation, requiring more hands-on programming knowledge/experience to use.<br /> <br /> Basically, DOCK is the go-to virtual screening software on our cluster.<br /> =How to use=<br /> ==Protein-ligand complex files to generate==<br /> DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to<br /> <br /> ==Initializing DOCK on cn142==<br /> In order to run DOCK 3.8 programs, the correct environment first needs to be loaded. '''EDIT: A more sophisticated login script will appear soon (hopefully). For now do the actions below'''.<br /> Execute the<br /> <br /> <pre><br /> #!/bin/bash<br /> echo "This is a script"<br /> cd /path/to/directory<br /> ls -l<br /> </pre><br /> ==Using BLASTERMASTER==<br /> <br /> ==Using DOCKOPT==<br /> <br /> ==Docking with SLURM==</div>

Wtitulaer https://wiki.synorgchem.science.ru.nl/index.php?title=Dock_3.8&diff=40 Dock 3.8 2024-08-28T15:43:13Z

<p>Wtitulaer: Created page with "DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://..."</p> <hr /> <div>DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://doi.org/10.1038/s41596-021-00597-z here]. The software can be used by academics upon requesting a license and currently runs on cn142. <br /> <br /> ==Pros & Cons of DOCK as docking software==<br /> * '''Pro''' DOCK is generally a lot faster than other docking software available.<br /> * '''Pro''' DOCK generally produces accurate poses if sampling is increased<br /> * '''Pro''' Tuning of parameters can be done through manipulating the spheres and scoring functions, allowing for better optimization.<br /> * '''Con''' DOCK doesn't generates conformers of ligands on-the-fly and requires additional software to do this.<br /> * '''Con''' DOCK doesn't have very clear documentation, requiring more hands-on programming knowledge/experience to use.<br /> <br /> Basically, DOCK is the go-to virtual screening software on our cluster.<br /> =How to use=<br /> ==Protein-ligand complex files to generate==<br /> DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to<br /> <br /> ==Using BLASTERMASTER==<br /> <br /> ==Using DOCKOPT==<br /> <br /> ==Docking with SLURM==</div>

Wtitulaer