Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input

Susanta Das, Laleh Dinpazhoh, Kiyoto Aramis Tanemura, Kenneth M. Merz

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


We implemented an ab initio CCS prediction workflow which incrementally refines generated structures using molecular mechanics, a deep learning potential, conformational clustering, and quantum mechanics (QM). Automating intermediate steps for a high performance computing (HPC) environment allows users to input the SMILES structure of small organic molecules and obtain a Boltzmann averaged collisional cross section (CCS) value as output. The CCS of a molecular species is a metric measured by ion mobility spectrometry (IMS) which can improve annotation of untargeted metabolomics experiments. We report only a minor drop in accuracy when we expedite the CCS calculation by replacing the QM geometry refinement step with a single-point energy calculation. Even though the workflow involves stochastic steps (i.e., conformation generation and clustering), the final CCS value was highly reproducible for multiple iterations on L-carnosine. Finally, we illustrate that the gas phase ensembles modeled for the workflow are intermediate files which can be used for the prediction of other properties such as aqueous phase nuclear magnetic resonance chemical shift prediction. The software is available at the following link: https://github.com/DasSusanta/snakemake_ccs.

Original languageEnglish
Pages (from-to)4995-5000
Number of pages6
JournalJournal of Chemical Information and Modeling
Issue number16
StatePublished - 28 Aug 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2023 American Chemical Society.


The authors disclosed receipt of the following financial support for the research, authorship, and publication of this article: NIH (grant 1U2CES030167–01).

FundersFunder number
National Institutes of Health1U2CES030167–01


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