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tesliper: a theoretical spectroscopist's little helper |
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26 January 2022 |
paper.bib |
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.
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.
Many thanks to the scientists, who advised me on the domain-specific details and helped to test the software:
- Joanna Rode ORCID iD 0000-0003-0592-4053
- Magdalena Jawiczuk ORCID iD 0000-0003-2576-4042
- Marcin Górecki ORCID iD 0000-0001-7472-3875