Presentation of this work
The goal of this work is the implementation of an interactive online tool, in the field of chemistry, allowing the visualization of chemical molecules commonly studied in analytical chemistry class at ISPB Lyon 1. The tool allows anyone to visualize for the selected molecules, the interactivity between a 3D molecular model from theoretical data and an infrared spectrum obtained experimentally.
Moreover, this work makes possible, through a guide integrated to it, to reproduce the whole process with new molecules. All the steps are detailed, from the choice of the molecule to its integration on the website.
With this documentation page, we aim to present the pedagogical project behind this exercise thesis, as well as the tools used during this project.
Presentation of the main tool, JSmol
This tool allows anyone who wishes to do so, to simultaneously visualize a 3D representation of the available molecules, obtained theoretically by calculation, as well as the experimental IR spectrum of these molecules.
Interactivity proposed by the tool allows, when an absorption band is requested on the IR spectrum of a molecule, to obtain the animation of the part of the 3D molecule linked to this band. Moreover, type of vibration (stretching or bending) is indicated for the absorption bands, as well as the corresponding wave number.
Pedagogical project
The pedagogical objective is the realization of an interactive online tool, for pharmacy students in Lyon, applied to mid-infrared spectrometry.
We have selected ten chemical molecules with a pedagogical interest. Five of these molecules are studied in the second year of pharmacy at ISPB Lyon 1.
This thesis work was made in three points:
- The experimental measurement of infrared spectrum of chemical molecules, using the Spectrum Two spectrometer in the laboratory.
- The construction of “hybrid” files, in extended JCAMP-MOL format, composed of both theoretical data obtained by calculation with physical chemistry software, and experimental infrared data.
- Creation of this website, in order to insert the interactive tool and the data on the molecules of interest.
The experimental measurement is performed in laboratory for all ten molecules. We use a Fourier transform spectrometer Spectrum Two from Perkin-Elmer. It allows us to obtain the infrared spectrum experimentally in JCAMP-DX format.
Note that for three of the chemical molecules in this thesis (propanoic acid, 4-ethyltoluene, 2-Methyl-2-propen-1-ol), it was not possible to obtain the raw materials to measure the infrared spectra in the laboratory. Therefore, we retrieved experimental infrared spectra in digital format directly from the NIST database.
For the construction of the hybrid files, we went through several steps:
- We obtain on ChemSpider belonging to the Royal Society of Chemistry, the 3D coordinates, as a file in MOL format, of the ten molecules of interest.
- Using Avogadro ORCA software, we geometrically optimize the 3D coordinates, then we save in XYZ file containing the optimized coordinates of each atom composing each molecule.
- Thereafter, using ORCA software, we use the XYZ file, in an input file, allowing the calculation of the vibrational modes of the molecule.
- We obtain an output file, which contains all the data on the chemical molecules with predicted vibrational modes.
- We choose the vibrational modes to animate for the different molecules using the Gabedit software, by visualizing the theoretical data previously obtained.
- Theoretical and experimental data for each molecule are compiled in a file in the extended JCAMP-MOL format with .dx extension.
The website was created in HTML format for creation of the pages. The use of the javascript language was necessary for the implementation of the interactive tool. This tool allows to visualize the interactivity between the theoretical data and the experimental data
We are now going to present the tools used, as well as the links towards the sites of the designers of these various tools.
Presentation of the differents tools
The realization of this pedagogical project requires the use of several software, which we will now present.
The Orca software is a free software of physical chemistry developed by Frank Neese et al. This software allows to carry out calculations concerning the chemistry of molecules. In our case, it was used to calculate the vibrational modes of molecules in a theoretical way. It is available for several platforms, including Windows, macOS and Linux.
Neese, F. “The ORCA program system” Wiley interdisciplinary Reviews - Computational Molecular Science, 2012, Vol 2., Issue 1, Pages 73–78
Avogadro ORCA is a free software for building and visualizing molecules. It allows to visualize molecular models in 3D from different data sources. It comes from the Avogadro project, which aims to propose an editor and visualization of chemical molecules. In our case, it was used to optimize the geometry of the studied chemical molecules. It was also used to choose which vibrational modes to animate for the molecules. It is available for several platforms, including Windows, macOS and Linux.
Avogadro: an open-source molecular builder and visualization tool. Version 1.XX.
Gabedit is a free software for visualization and modeling of molecules. It is developed by Allouche, A.-R., senior lecturer in chemistry at the University of Lyon 1, France. In our case, the software helped us to choose the vibrational modes to animate for the molecules. It is available for several platforms, including Windows, macOS and Linux.
Gabedit—A graphical user interface for computational chemistry softwares. Allouche, A.-R., Journal of Computational Chemistry, 32 (2011) 174–182.
The JSmol software, a JavaScript-only (HTML5) version of Jmol, is a software for visualization and modeling of molecules. In our case, the JSmol software allows us to display the molecules under 3D forms. The use of this software in its Javascript version allows our website to display at the same time the 3D molecular structure, and the corresponding IR spectrum. It is also available as a stand-alone application under the name JSpecView, for several platforms, including Windows, macOS and Linux.
Jmol: an open-source Java viewer for chemical structures in 3D.
JCAMP-MOL File format
To visualize jointly the model and the IR spectrum, we had to use a hybrid file. It is in this perspective that the “hybrid” file format JCAMP-MOL was developed by R. Hanson and R. Lancashire, a file format allowing interactivity between theoretical 3D molecular data and experimental IR spectroscopy data of a molecule. The JCAMP-MOL file is an extension of the standard JCAMP-DX format. JCAMP-DX is the commonly used file format for spectroscopy data. It was created by the Jcamp (Joint Committee on Atomic and Molecular Physical Data), and allows the storage of spectroscopy data, both NMR and IR for example. This type of file has been reworked by the two authors R. Hanson and R. Lancashire, in order to allowinteractivity between experimental data of an IR spectrum with the theoretical data of the 3D molecule model.
Article about JCAMP-DX formatJCAMP-DX: A Standard Form for the Exchange of Infrared Spectra in Computer Readable Form ROBERT S. McDONALD and PAUL A. WILKS, JR
Article about JCAMP-MOL formatJCAMP-MOL: A JCAMP-DX extension to allow interactive model/spectrum exploration using Jmol and JSpecView Robert M. Hanson Robert J. Lancashire