Add and modify an ELN entry
Introduction
This view allows creating and edit an electronic laboratory notebook entry (reactions).
User preferences
To define user preferences and snippets you should click on the Prefs button.
Predefined sentences
To define a snippet first associate to it a key that is composed of lowercase letters and then define the corresponding sentence. The sentence may contain not only reagents like r1, r2 but also meta information that can be inserted using _ followed by the meta field name like _temperature. If a snippet contains those fields you will be able to update their values automatically.
Each snippet should be associated with a key composed of lowercase letters.
You can then insert snippets by typing their key that will be automatically replaced and updated with the current values.
PubChem lookup and autoupdate
You can also define if you would like to have automatic safety lookup in PubChem as well as automatic updates of the reagents and meta information that has been inserted in the procedure.
Don't forget to Save preferences!
Organic reaction
When preparing a new organic reaction the idea is first to add the different reagents and then to fill the schema with simple clicks. The concept behind it is that either the product is commercially or it was synthesized before. Therefore, all the chemical structures of the reagents are already known.
Lookup for a product
You should use the column code in order to lookup for a product.
In this column you may either enter:
- CAS number
- product name
- molecular formula
- product code (practical to retrieve a product you synthesized before)
A molecular formula may be entered the way a chemist think about it. Meaning you are allowed to use groups and parenthesis like Me2CHCOCl.
Once the string entered press tab in order to trigger the lookup. The system will search in a reference database of 400000 molecules and also for all the internal products you have access to.
Click on the right product to copy the name, structure and density.
Defining the quantities
The reagent calculator is connected to databases and can retrieve information about a chemical. For instance in the "code" you may enter a molecular formula, name or CAS number and the system will look for commercially available chemicals. You can then select the molecule you want to add in the table.
- If you enter a new sample and change the molecular formula, molecular weight will be automatically calculated. In the molecular formula you may enter groups like Et, Ph, Ts, ... as well as parentheses.
- The purity may be entered in
%,M(molar),mM(millimolar) orL(loading). Molar is expressed in mmoles / mL and loading is expressed by mmoles / g and is practical for solid phase synthesis. - The first reagent for which you add a quantity will be defined as 1 equivalent. You may still change this anytime. After defining the first quantity you will probably want to define the other reagents from the equivalent columns rather than the quantity (except probably for the solvent).
- One the equivalents are specified those samples are “connected”. This means that if you change the quantity of one of the reagents all the quantity will change.
- It is possible to remove the link between the reagents by unselecting the “Link” checkbox.
Drawing the schema
JSME is a simple-to-use and powerful tool developed by Peter Ertl and Bruno Bienfait. In order to draw the reaction we will start by adding the chemical structures from the reagent table.
It is possible to select a molecule by going hover it. Once selected you can move this molecule (just click around and drag the mouse).
Even if the molecule does not appear as being selected you can still act on it. In instance, you can:
- copy to the molecule to the other side of the reaction by clicking on the arrow.
- click on the white rectangle to delete this selected molecule.
If you would like to draw efficiently the molecules directly in the editor click on the little question mark and try to learn all the shortcuts.
JSME
JSME Help and Basic Instructions
JSME Menu
shows molecule SMILES
clears the editing area (or the current molecule, if structure contains several parts)
starts new molecule component (when multipart option or reaction input are enabled)
delete mode (click on atom or bond to delete it)
deletes functional group - choose this option and then click bond connecting the group with the main skeleton
starts atom numbering or reaction mapping (when this option is enabled)
query atom / SMARTS (when this option is enabled)
switches between allowed charged states on clicked atom
reaction input (when reactions are enabled)
undo
redo
next ring will be added as a spiro ring
version information and link to the help page
input stereo bond, click existing stereo bond to cycle through possible types (up, dowm, orientation)
powerful chain tool, allows creation of various chains and rings; click single bond to change it to double
allows input of inorganic atoms or atoms in nonstandard valence state (in this case enter the atom symbol enclosed in [], for example the carbene carbon will be [C])
opens functional group popup menu
move selected atom useful when drawing crowded structures (visible when enabled in options)
Basic Editing
Rings are added connected by a single bond (when not added to a terminal atom); if you want to add a spiro ring press SHIFT ⇧ when adding it. An alternative way to add a spiro ring (that may be used also on touch devices) is to press the icon; the next ring will be then added as spiro.
With single bond selected, a click on existing single bond changes it to double.
With the powerful chain tool you can draw chains, saturated rings and by clicking on single bond change it to a double bond.
Molecule may be moved by "dragging" free space and rotated by pressing also the SHIFT ⇧ key.
JSME Keyboard Shortcuts
If you are using JSME often, learn the following shortcuts. They will speed-up your editing considerably.
ESC returns to the standard editing state (carbon, single bond)
d or Del starts delete mode
atoms C, N, O, P, S, F, L (for Cl), B (for Br), I, H, R
bonds - for single bond, = for double bond
rings 3..8 for 3 to 8 membered rings, 1 for phenyl and 0 for furyl
groups a - COOH, y - NO2, z - SO3H, t - tert. butyl, ft - CF3
Stereochemistry
Stereochemistry at C4 centers, double bonds and allenes is supported. Use the up / down wedge bonds to indicate stereochemistry at the C4 centers. Remember, that only bonds with a "sharp point" towards the atom are considered. When creating SMILES the editor tries to guess missing stereo features, in unresolvable cases an error message is issued and the SMILES without stereo information is created.
When the "autoez" option is set, SMILES with E,Z stereochemistry on all non-ring double bonds will be generated automatically. Without this keyword (or for ring double bonds) you have to mark a double bond as stereo by clicking on it with the stereo bond button selected. The bond color will change to magenta.
Stereochemistry may be completely disabled by the "nostereo" option.
Atom Numbering
Atom numbering (marking) is enabled by the option "number" (for reaction input this is default). Button appears in the menu. To mark an atom the "numbering mode" must be on, selected by clicking the 123 button. The atom number is chosen by pressing respective keys on your keyboard (i.e. 2 or 12); then atom(s) must be clicked. To delete the number pres 0 at your keyboard and then click the atom.
Input of Multipart Structures
By default only non-disconnected structures may be entered. This may be changed by a "multipart" option. A button appears in the menu. A new molecule may be started only after clicking this button, then selecting a proper template (atom, ring or bond) and clicking free space in the drawing area. Without clicking the NEW button first clicking the free space has the same effect as in the standard mode (i.e moving or rotation of the last touched molecule). In the multipart mode the button deletes the last touched molecule.
Reaction Input
Reaction input is enabled with the option "reaction". Buttons , and appear in the menu and arrow appears also in the drawing area. Now simply draw reactant(s), product(s) and modulator(s) (modulators have to be above the arrow) as explained in the description of input of multipart structures. The arrow button enables simplified input of reactions. After clicking it, the reactant will be copied to the product (including atom numbering, if any).
Query Features
Query button (when enabled in the options) launches a query window that allows creation of SMARTS atom or bond queries by combining various atom attributes. Select the SMARTS options in this panel and then click the respective atom or bond in the molecule.
Copy and Paste
Right mouse click opens the Copy and Paste pop-up menu that allows to copy the molecule as SMILES or MOL file or paste MOL , SDF, or RXN files into the editor.
On supported touch devices, the menu can be opened by �touch and hold� on the surface of the editor.
Keyboard shortcuts Ctrl C (for copy) and Ctrl V (for paste) are supported on most browsers.
Drag and Drop of Files in the Editor
Some HTML 5 compatible browsers support the drag and drop of files. Starting with version 2013-03-24, JSME accepts dropping of text files in the format MOL, SDF and RXN.
To drag molecule from the editor into the appropriate destination (for example Word or text document, or desktop) drag the icon in the lower right corner of the editor.
Check analysis
A reaction contains various sample. Sample can be either isolated and purified products or just any analysis related to the reaction.
A sample contains all the analysis related to it (NMR, GC, IR, Mass, etc) and each of the analysis have a specific view to process them.
It is now possible to jump directly to the corresponding analysis view by clicking on the corresponding color bullet from the sample list.
To create a new sample, you simply need to click on the button Add empty sample and choose a batch name, this will create a new batch where you can include any type of spectra and additional information. Once you refresh the page in the global reaction, you will see the new batch in the list. If you click on the batch, there will be a preview of the information you have entered.
Some tips for organic reactions
You can specify the purity of a reagent.
Specifying the purity of a reagent
The purity of a reagent may be specified using 3 possibles units:
%: purity as mass ratio- like 40% HNMe2 in water
M(ormM): moles/liter (or mmoles/liter)- like 1.6M BuLi
L: loading: mole/kg- useful for solid phase synthesis
?: unknown purity- when working with natural products like wood or in material science the sample does not have a molecular formula and therefore it is not possible de define the number of mmoles. Using
?as units allows to freely define weight, density and volume.
- when working with natural products like wood or in material science the sample does not have a molecular formula and therefore it is not possible de define the number of mmoles. Using
The system will calculate continuously the molecular formula of all the reagents and products.
Products theoretical information
When you draw products of reaction the application will calculate continuously the expected quantities for 100% and one equivalent.
This value is also updated when you change the quantities in the reagent table.
There is an easy to deal with mixture of solvents.
Calculate mixture of solvents volume to reach specific concentration
For some reactions it is important to calculate the solvent to reach a specific concentration and in some cases it can be a mixture of solvents.
The reagent table allows dealing with mixture of solvent. In this case we would like to work in DMSO/H2O in a ratio (70/30):
- For the solvents enter the number of equivalent so that the sum is
1 - Enter the concentration you want to achieve in the 'Purity' column of all the solvents.
In some cases it is required to add many times the same reagent.
Same reagent multiple times
In some reactions such as in the example below, the product is formed via the combination of multiple reagent molecules.
In this example the mixture of ethylene glycol with triethyl orthoformate yields a cyclic orthoester. In order to enter the quantities for this kind of reaction you need to specify correctly the number of equivalents of the reagent that limits the yield. In this case the triethyl orthoformate limits the yield, so we enter two equivalents for this reagent.
This will allow calculating correctly the expected quantity of the product as well
In some cases it is required to copy manually the structure of a reaction product.
Copy product as molfile
If a sample was created using method other than from the reaction the chemical structure, molecular formula and molecular weight will not be copied automatically. This is the case for example when a sample is analyzed by NMR and the sample is created automatically during importation.
There is a simple way to copy / paste the chemical structure of the product.
The product is copied as a molfile and can be paste in a sample entry.
It could be pasted for example in ChemDraw using Edit -> Paste Special -> Mol text
Insert snippets, reagents and meta information
It is possible to define an unlimited number of snippets and to recall them directly in the procedure by typing its abbreviation (followed by Tab, Space, or Enter).
All the reagents can also be inserted by entering r followed by the reagent number. i.e. r2.
The ELN also allows to add an unlimited number of meta information key-value pairs. Those meta information can not only be inserted in the procedure but also in snippets. In order to include the meta information you should type _ followed by the name of the property. For example _temperature. The use of meta information allows to centralize all the parameters that change from one reaction to another. This is especially useful in the case of parallel synthesis.
It is also possible to define default meta information, that can be reused in any new or old reaction. To retrieve the default meta information, just click on the 
button.
You can add at any time labels to the list of default meta information in the following panel.
Insertion of predefined sentences
In order to insert predefined sentences you can click on the clipboard icon.
A dialog containing the list of predefined sentences will appear, and you should
click on the one you want.
Miscellaneous
Drag drop images
You may just copy / paste an image of the “Drop or paste” zone, and it will be inserted in the procedure.
Calculate solvent volume to reach specific concentration
For some reaction it is important to calculate the solvent to reach a specific concentration.
The reagent table allows to do this:
- For the solvent enter as number of equivalent '1'
- Enter the concentration you want to achieve in the 'Purity' column.
Safety information
When looking for commercial products you may decide to also lookup for safety information in PubChem.
To activate this feature, click on prefs and check Activate safety lookup. Don't forget to save your new preferences!
It is also possible to directly edit the safety information by clicking in the Hazard pictogram column and entering the various GHS pictogram code separated by a comma.
More information from PubChem about the chemical can also be found by clicking on the 'i' icon.
The safety information can be updated by clicking on the 
icon. This will automatically update the safety information from PubChem.