Molecular Structure

Mnova allows the user to import Molecular Structures, and to interact with them.

Currently, molecular structures can be imported as a .mol, .cdx, cdxml, .mrv or .sdf files by simply using the Open command (or by dragging & dropping the file to the Mnova icon or interface) exactly in the same way as this would be applied to a spectrum. Support to 'drag & drop' operations are currently limited to ACD ChemSketch, Marvin and ChemDraw.

You can also import reactions in cdxml format:

If you have OpenBabel installed, you will also be able to load (or copy&paste) molecular structures in INCHI and SMILE formats. For example you can copy to clipboard each line above (molecules in SMILE and INCHI formats) and then run Mnova and paste them as molecular structures:

COc1cc(ccc1)C#N

InChI=1S/C9H7F3O2/c10-6-2-1-5(7(11)8(6)12)9-13-3-4-14-9/h1-2,9H,3-4H2

You can also copy structures as MDL SK format (with abbreviated groups), to do that just copy the molecular structure to the clipboard (from ChemDraw for example) and follow the menu 'Edit/Paste Special':

You can keep the numbering from ChemDraw or the abbreviated structures by using the 'ChemDraw Exchage file' from the dialog box above.

If you are using IsisDraw, please keep in mind that you will need to select the capability to copy your molecules as mol files in the 'Options/General Settings' menu.

The molecular structure can be handled (resized, moved, aligned, copied, pasted, etc) exactly in the same way as all other Mnova objects. Molecular structures can be imported in a separate page or into a page already occupied by another object, such as for example its applicable spectrum.

The first thing you will notice when interacting with molecular structures, is the fact that atoms will become highlighted in a red transparent box when the mouse hovers over them. Clicking on an specific atom will make it the active atom and highlight in a red box with pink background, as can be seen in the figure below. This atom selection will become essential when interacting with the molecule, as will be explained in the following chapters.

Mnova will allow you to customize the appearance of the molecule, by using the object 'Properties' dialog box. This box can be accessed by double clicking on the molecule, or by right clicking and then scrolling down to 'Properties'.

The 'Properties' dialog box will allow you to customize the size of the molecule, its angle with respect to the paper (geometry properties) and all representation properties, such as whether or not to show explicit carbon and hydrogen atoms, whether to show atom numbers, the length and spacing of bonds, etc. It is therefore possible to achieve many different representations of the same molecule, as the figure below shows.

To customize the appearance of all the atom labels of the molecule, just double click on this button . From the 'Macro Editor' dialog box, you can add information about 'annotations', 'atom number', 'assignments', 'predicted chemical shift', etc.

In the example below, it is shown an atom label which contains information about the 'atom number' and the 'predicted chemical shift':

Double clicking on the applicable atom to edit its label:

You can add a macro for the atom label (as it is shown a few lines above) in order to include information such as 'annotations', 'atom number', 'assignments' (chemical shift list, range or average), 'predicted chemical shifts' etc...

When you have more than one assignments to the same atom, you can use the 'Multiple Display' parameter to show the assignments as a list (when no value is added), as a range (when settings rng) or as an average value (when setting avg).

Typing the $ prefix to add greek letters to the number; for example $a, 4$b, 22$g$d21 will be converted into α, 4β, 22γδ21:

To define an isotope, you only need to enter the value of the mass number in the "Isotope" field. For example, in case of a C atom you can type 12, 13 and 14. The isotope number (and the charge) of an atom can be deleted by typing 0 or by deleting the number of the field.

You can type any annotation, such a comment or a different numbering (just by changing the value of the 'Number' cell). You can change the color of the atom or of the highlight or even to add any property just by clicking on the this button .

In that case we have changed the number to the atom 25 (the new number is 99) and added a macro to show the 'Atom Number', the 'Annotation' (Test) and the 'Custom Property' (Vinyl), changing the color to green with a yellow highlight:

Highlight an atom and type the desired number to renumber it. If the new number already exists, the symbols # will appear on the duplicated numbers.

The new numbering can be exported in a mol file and you can 'import molecule styles' (for the 'Edit/Paste Special' feature) by selecting the applicable option in the File/Preferences/Molecules menu.

The "keyboard editing always available" preference, will allow you to type any letter when hovering the mouse over an atom.

Right clicking on any atom number of the molecular structure will display a context menu which will allow you to show the assignments, prediction, number, annotations or stereodescriptors as atom labels: