Skip to content

Latest commit

 

History

History
74 lines (65 loc) · 3.64 KB

paper.md

File metadata and controls

74 lines (65 loc) · 3.64 KB
Raw
title tags authors affiliations date bibliography
tesliper: a theoretical spectroscopist's little helper
Python
chemistry
spectroscopy
Gaussian
chemical computing
optical spectroscopy
spectral simulations
workflow automation
batch processing
name orcid affiliation
Michał M. Więcław^[corresponding author]
0000-0001-7884-8982
1
name index
Institute of Organic Chemistry, Polish Academy of Sciences
1
26 January 2022
paper.bib

Summary

tesliper is a software package for the bulk processing of Gaussian (quantum chemistry calculations software) output files regarding conformational searches and spectra simulations. Simulation of a molecule's optical spectra usually requires structure optimization and calculation of the electronic properties of multiple conformers of the studied molecule. Gaussian [@gaussian] is one of the most commonly used software packages to perform such calculations and tesliper was created to aid the handling and analysis of these calculations' outputs.

It allows for easy exclusion of conformers that are not suitable for further analysis: erroneous, not optimized, of higher energy or lower contribution than a desired threshold. It also implements a geometry comparison feature: an RMSD sieve, enabling the filtering out of similar structures. A theoretical IR, VCD, UV, ECD, Raman, and ROA spectra may be calculated for individual conformers or as a population-weighted average. Offering a graphical user interface and Python API, it is easily accessible by the users' preferred method of interaction with the computer: visual or textual.

Statement of Need

Simulation of optical spectra of organic compounds has become a routine task for chemical analysts. For example, it is a necessary step in one of the increasingly popular methods of establishing a compound's absolute configuration through comparison of recorded and simulated circular dichroism spectra. However, the process of obtaining a simulated spectrum may be cumbersome, as it usually involves analyzing a large number of potentially stable conformers of the studied molecule.

Several software packages capable of simulating a spectrum from Gaussian calculations are already available, e.g. SpecDis [@specdis], CDspecTech [@cdspectech], ComputeVOA [@computevoa], ChemCraft [@chemcraft], or GaussView [@gaussview]. However, each of these programs has some severe limitations, for example they are not freely available (ComputeVOA, ChemCraft, GaussView) or cannot simulate certain types of spectra (SpecDis, ComputeVOA, ChemCraft). Other packages lack important features, like comparison of conformers' geometry (SpecDis, CDspecTech, GaussView) or population-based spectra averaging (ComputeVOA, ChemCraft, GaussView).

Even with adoption of one or more of the software packages mentioned above, the process is often suboptimal, incomplete, or unable to be done in an automated fashion. Many research groups tackle this problem with home-brewed scripting solutions that are usually not easily adjusted or extended, or with manual work, which may be extremely time-consuming. There is a clear need for a simple interface to automate tedious parts of the typical spectra simulation workflow. tesliper aims to satisfy this need.

Acknowledgements

Many thanks to the scientists, who advised me on the domain-specific details and helped to test the software:

References