COSY prediction
Introduction
This tool allows you to predict the COSY spectrum of your sample or any other molecule. COSY (homonuclear correlation spectroscopy) is a two-dimentional nuclear magnetic resonance spectroscopic technique. It gives data plotted in a space defined by two frequency axes rather than one. It is used to identify spins which are coupled to each other. 2-bond and 3-bond H-H coupling are visible by COSY, as well as long range coupling with long acquisition time. The cross-peaks (not on the diagonal) show scalar J-coupling correlations. This method is very useful when the multiplets overlap or when the second order coupling complicates the 1D spectrum. You can see below an example of COSY spectrum of ethylbenzene.
The structure of the currently selected sample will be already drawn so that you may go ahead and click Calculate to calculate and simulate its COSY spectrum right away. If you wish to simulate the spectrum of another molecule, you can draw it or you can paste the structure in the form of a molfile or a SMILES string. Structure drawing is powered by JSME. You may also drop or paste a JCAMP-DX file to superimpose an experimental spectrum over prediction.
How is a JCAMP-DX file structured.
JCAMP-DX file format
JCAMP-DX (Joint Committee on Atomic and Molecular Physical Data Exchange) is a standard file format for the exchange of spectra and related physical and chemical information between different spectrometers, databases or other systems.
The information is stored using ASCII characters and the file can be viewed, corrected and annotated with a text editor. The spectra are stored as a table containing (x,y) coordinate pairs. Besides the data points, it is possible to store metainformation and make comments. The file extension is .jdx.
A JCAMP-DX document is composed of an unlimited number of Labelled Data Records (LDRs). Each LDR starts with a “##” and ends with “=”. Any space, comma, slash or hyphen is removed and the text is written with capital letters.
Some examples of Data Labels:
- TITLE : title of the experiment
- END : the last line of the file
- XUNITS : the units reported on the x-axis
- NPOINTS : number of points
Two important LDRs are “XYDATA” and “PEAKTABLE”, which contain the spectral information. The former gives information in the form of a table where the first value in a line stands for an x coordinate and any subsequent values are y-coordinates with an equidistant increment on the x-axis. The latter provides information as a collection of (X,Y) pairs.
It is commonplace to compress the data tables. For instance, the table of numbers can be replaced by a line of characters (pseudo-digits). Among these pseudo-digits, there are PAC, SQZ, DIF, DIFDUP.
An example of compressed data using DIFDUP
An in depth description is given in the original paper by McDonald and Wilks. Insofar as JCAMP-DX is a well-described and accessible format, it partially aligns with the FAIR (Findable, Accessible, Interoperable, Reusable) principles . It is interoperable and reusable. Provided that the user makes it findable and accessible, JCAMP-DX will fully comply with the aforementioned principles.
The simulated COSY spectrum, the 1H projection and the chemical structure with explicit hydrogens are linked, hovering over a peak in the spectrum will highlight the corresponding atoms in the structure and hovering over an atom will highlight the corresponding peaks in the spectrum.
1H chemical shifts and coupling constants are predicted using Spinus. Simulation from predicted parameters uses the method described in DOI:10.1016/j.jmr.2010.12.008. COSY correlations are calculated based on atom-to-atom paths in the molecule: a correlation is shown in the COSY whenever two hydrogens are joined by a path traversing no less than Minimal number of bonds and no more than Maximal number of bonds. You may adjust these Simulation parameters in the module right next to the Calculate button.