Chemotion - Revision history

Fveldhuizen at 09:51, 7 April 2025

2025-04-07T09:51:01Z

← Older revision		Revision as of 09:51, 7 April 2025
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	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.		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. Chemotion can be accessed [https://chemotion.science.ru.nl/home here]. 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.

	==ELN minimal book keeping==		==ELN minimal book keeping==

Wtitulaer at 12:44, 10 October 2024

2024-10-10T12:44:05Z

← Older revision		Revision as of 12:44, 10 October 2024
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	* '''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.		* '''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.
	* '''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!		* '''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!
	* '''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.		* '''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).

Wtitulaer at 12:35, 10 October 2024

2024-10-10T12:35:56Z

← Older revision		Revision as of 12:35, 10 October 2024
Line 4:		Line 4:
	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:		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:
	* '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.		* '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.
	* '''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.		* '''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.
	* '''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.		* '''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.
	* '''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!		* '''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!
	* '''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.		* '''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.

Wtitulaer at 12:33, 10 October 2024

2024-10-10T12:33:23Z

← Older revision		Revision as of 12:33, 10 October 2024
Line 3:		Line 3:
	==ELN minimal book keeping==		==ELN minimal book keeping==
	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:		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:
			* '''The reaction includes all starting materials and products with known stereochemistry if applicable'''.
	* '''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.		* '''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.
	* '''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.		* '''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.
	* '''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		* '''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!
			* '''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.

Wtitulaer at 12:24, 10 October 2024

2024-10-10T12:24:41Z

← Older revision		Revision as of 12:24, 10 October 2024
Line 5:		Line 5:
	* '''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.		* '''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.
	* '''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.		* '''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.
	* '''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		* '''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

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..."

2024-10-10T12:24:09Z

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..."

New page

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.

==ELN minimal book keeping==
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:
* '''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.
* '''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.
* '''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