See section 3.5 of the [https://orgchem.pages.science.ru.nl/safetymanual/ safety manual] for the official rules. Below is described how waste is commonly handled in the labs.

== Waste disposal in Huygens wing 1 ==

=== Liquid waste ===
Full liquid waste containers are to be moved to the waste cabinet in the transfer room (by the labs near the entrance to the wing) with appropriate stickers. On the waste container should be a sticker detailing the type of waste, filled in with the department (SOC), the lab location where the waste container came from, and the date on which the container is moved into the transfer room. If this sticker contains any hazard symbols, a sticker of a larger version of this symbol should also be applied. These stickers can be found in the transfer room and on the windowsills in the labs. New stickers can be ordered through Lab Servant. 
Do not fill liquid waste containers more than 80%. 
 
Note that only waste containers made of plastic (jerry cans of 5 or 10 liters) are allowed to be moved to the transfer room. Waste containers made of glass (such as often used in personal fume hoods) are to be emptied into plastic ones. 
 
Empty liquid waste containers can be found in the hallway by the transfer room, or in several locations around the lab. Order new ones through Lab Servant if they run out. 
 
If you are unsure which type of waste container (sticker) is needed, consult the [[:File:Liquid waste flow chart.jpeg|Liquid waste flow chart]].

=== Solid waste ===
This includes silica from the chromatography columns, soiled paper and glass contaminated with chemicals, but with the exception of heavy metals, needles and special waste products (see above) such as ink cartridges, batteries and adhesives. Each lab has one or multiple solid waste containers. These are either round brown containers with a beige lid, or black containers. When full, these must have stickers placed on them (label 5.12 and ADR label toxic) and must be moved to the transfer room.
Empty solid waste containers can be found in the transfer room or just outside it. Order new ones if they run out. 
Many people have a small solid waste container in their fume hood, which they empty into their lab’s solid waste container. Be sure not to let this one become too full for safety reasons. 

Solid heavy metals, to prevent ignition, are collected in liquid waste containers according to the [[:File:Liquid waste flow chart.jpeg|Liquid waste flow chart]].

=== Glass ===
Glass, when contaminated with chemicals, can be collected separately in a similar brown container with beige lid or in a solid waste container (See above). The appropriate labels should be attached to the container (label 5.12 and ADR label toxic). 
Clean glass is collected in a glass waste container in the laboratory. Rinse glass first if it has been contaminated with chemicals, or let solvents evaporate in the fume cupboard. IMPORTANT: remove the original labels or render them illegible.

=== Empty bottles ===
Empty bottles are rinsed with acetone. Depending on how hazardous the previous contents of the bottle were, it may be necessary to rinse thoroughly with other solvents. The bottle is then placed in a fume hood without its cap for several days, until all liquid inside is evaporated. The small sticker with the matrix bar code and SC number is removed from the bottle and placed by a computer, where it can be checked out of the Lab Servant system by an employee. All hazard symbols and text about the chemical are crossed out with a black marker, and the bottle is disposed of in a glass waste container. The cap is disposed of in the plastic waste or kept for future use. 
When the glass waste container is full, it can be emptied in wing 2.

=== Needles ===
Needles (and other sharp implements such as scalpels) must be disposed of in a Sharpsafe, a yellow container intended for sharp waste. Preferably, this container is only used for needles without the covers, as putting the cover back on the needle is an additional risk and the covers take up extra space. To detach a needle from a syringe in a safe manner, the incisions in the SharpSafe lid can be used. A SharpSafe should NOT be used for glass; neither for syringes, tubing or any other non-sharp thing you might attach to a needle. When full, close the lid of the Sharpsafe (which is irreversible) and move it to the transfer room. 

=== Normal trash bin ===
Most labs have a standard bin by the sinks. These are emptied by the cleaners when full. These are mostly used for used paper towels. If paper towels have come into contact with any chemicals other than water, put them in the solid waste containers instead. 
Other waste that can typically be considered clean, such as packaging materials may also go in here. Note that gloves, even unused ones, do '''NOT''' go in the normal trash bins, but in the solid waste containers.

=== Plastic and paper waste ===
Most labs have bins for (clean) plastic and paper waste. These bins can be emptied in the container storage room next to the elevator opposite Wing 1.

=== Page notes ===
Not sure about: 
Packaging materials and clean gloves in normal trash? 
Empty bottles that held solids? Same as liquid? 
How to empty glass bin in wing 2.

File:Chemical Resistance Gloves Chart.pdf

2025-07-22T07:50:02Z

Fveldhuizen:

Waste disposal

2025-07-22T07:47:47Z

Fveldhuizen: /* Liquid waste */

2025-04-02T11:05:54Z

Fveldhuizen:

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.
There are a few things you will have to take care of yourself, preferably before starting the internship:
* 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).
* 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].
=The mandatory stuff=
== Registration & Access to the wings ==
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:
* The ''' registration new employees''', which you can fill in yourself and send to Marieke.
* The '''registration in wings Cluster Orgchem.docx''' for which you will need a signature from your supervisor.
* 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'''
* 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.

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.

== Going into the lab ==
In order to go into the lab you need to take care of the following things:
* 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.
* 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.
* 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.
* 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]].

== Lab equipment access ==
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. 
See '''[[Booking Platform for Scientific Devices]]''' for more information. 

'''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.

=== NMR access ===
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. 

==== NMR in Huygens ====
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. 
The 500 is not in automation mode during the day and typically not available for students. 
Please ask for training before using. 
Training: Nuwanthika Kumarage.

=== MS access ===
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. 
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.

=== Other equipment ===
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.
 

==== Purification equipment ====
<div class="toccolours mw-collapsible" style="width:600px; overflow:auto;">

===== Preparative HPLC =====
There are several preparative HPLCs available for purifying synthesized compounds: 
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. 
'''[https://www.youtube.com/watch?v=QIFn-Pk-x9s Instructional video]''' 
Please ask for training before using. 
Training: Frank Veldhuizen, intern supervisor or other user.

===== Biotage Isolera =====
We have several automatic flash chromatographs with column cartridges for quick purification after synthesis. 
Most supervisors want their interns to learn by running several glass columns manually before being allowed to use the Biotage. 
[[Media:Biotage_Isolera_quick_guide.pdf|Quick guide]] 
Training: Intern supervisor or other user.

</div>

==== Analysis equipment ====

<div class="toccolours mw-collapsible" style="width:600px; overflow:auto;">

===== IR =====
HG03.222 
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. 
Training: Frank Veldhuizen.

===== Analytical HPLC =====
HG03.130 
Used to determine the purity of a sample. 
Training: Frank Veldhuizen, intern supervisor or other user.

===== Chiral HPLC =====
HG03.130 
Used to determine the racemization of a sample. 
Training: Frank Veldhuizen, intern supervisor or other user. 

===== LC-MS =====
HG03.411 
The LC-MS (“The Fleet”) can be used to analyse samples and determine the mass of compounds. 
Training: Robin Schenker, Helene Amatdjais-Groenen, Frank Veldhuizen. 

===== SFC =====
HG03.120 
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. 
'''[https://www.youtube.com/watch?v=IQtY6gGv0yY Instructional video]''' 
Please ask for training before using. 
Training: Frank Veldhuizen. 

===== TLC-MS =====
HG03.115 
This instrument can quickly make a mass spectrum of a spot on a TLC plate. Aluminium TLC plates are preferred for this device. 
'''[https://www.youtube.com/watch?v=jhqlRvXpZSk Instructional video]''' 
Please ask for training before using. 
Training: Frank Veldhuizen. 

</div>

==== Synthesis equipment ====

<div class="toccolours mw-collapsible" style="width:600px; overflow:auto;">

===== Synthesis microwave =====
Can be used to initiate reactions at high temperature. 
Training: Frank Veldhuizen? 

===== Autoclave =====
HG03.115 H9 
For high pressure reactions up to 60 bar. 
An extensive manual is available [[Media:Guide on how to use the Autoclave and external gas cylinders.pdf|here]]. 
Training: ? 

===== High pressure machine =====
HG03.442 
For high pressure reactions up to 15 kbar. 
[[Media:Checklist High pressure.docx|Manual]] 
Training: Frank Veldhuizen 

</div>

== Working from home, vacation or being sick ==
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.

== Regular lab events ==
Regular lab events are generally lab specific and are found at [[Regular lab events]].

== Synthesizing a new compound ==
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.

===Full characterization of a NCE===

(to be filled)...

== How to behave in the lab ==
In order to have a productive and healthy working environment, please adhere at least to these rules:
* 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.
* 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.
* Keep the general working area and benches clean and tidy.
* Replace liquid waste containers '''before''' they are full but rather at 80% capacity. See [[Waste disposal]].
* Replace solid waste containers. See [[Waste disposal]].
* Most labs have a weekly cleaning moment. Please be present for these moments.

== General (analysis) software ==
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

===Chemdraw===
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'.

===MestreNova===
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.

== When leaving the lab ==
When finished with your internship, it is important to leave the lab in a good state, and the data of your experiments should be stored properly. Use the checklist below to make sure you do not miss anything. 
[[Media:Leaving the lab - To do list interns.pdf | Leaving the lab Checklist]]

=Other useful but non-mandatory things=
== Molecular modelling software ==
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]].

== Shared drives & back-ups: Surf-drive ==
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.

==Knowledge transfer ==
=== NMR ===
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:
*[https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/Spectrpy/nmr/nmr1.htm#nmr1 The basics]
*[https://organicchemistrydata.org/hansreich/resources/nmr/?page=nmr-content%2F The more advanced]

===Reaxys===

===Some useful lab tips===

2024-11-27T11:28:54Z

Fveldhuizen: Manual for the high pressure synthesis instrument

== Summary ==
Manual for the high pressure synthesis instrument

2024-10-15T09:07:51Z

Fveldhuizen: