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Visualization of Electron Density Changes Along Chemical Reaction Pathways

Lander, Chance and Satalkar, Vardhan and Yang, Junjie and Pan, Xiaoliang and Pei, Zheng and Chatterji, Aayushi and Liu, Chungen and Nicholas, Kenneth M. and Cichewicz, Robert H. and Yang, Zhibo and Shao, Yihan (2022) Visualization of Electron Density Changes Along Chemical Reaction Pathways. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20220513-557778000

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Abstract

We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity S_N2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed N₂O fragmentation, where the N–O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.26434/chemrxiv-2022-tfqnnDOIDiscussion Paper
https://resolver.caltech.edu/CaltechAUTHORS:20220908-194009803Related ItemJournal article
ORCID:
AuthorORCID
Satalkar, Vardhan0000-0001-5134-0062
Yang, Junjie0000-0002-6726-6538
Pan, Xiaoliang0000-0002-6399-4853
Liu, Chungen0000-0001-7839-0799
Nicholas, Kenneth M.0000-0002-5180-1671
Cichewicz, Robert H.0000-0003-0744-4117
Yang, Zhibo0000-0003-0370-7450
Shao, Yihan0000-0001-9337-341X
Additional Information:The content is available under CC BY 4.0 License. Chance Lander and Vardhan Satalkar contributed equally to this work. Financial support from the National Science Foundation (CHE-2102071 to ZY and YS; CHE-1566213 to KMN), the National Institutes of Health (R01GM135392 to YS), and the Cope Scholar Award (to KMN) are acknowledged. YS thanks Dr. Tom Cundari for suggesting [3+2] cycloaddition as a test case. YS also thanks Ginny Kim for helpful discussions. Computational resources and services used in this work were provided by the OU Supercomputing Center for Education and Research (OSCER).
Funders:
Funding AgencyGrant Number
NSFCHE-2102071
NSFCHE-1566213
NIHR01GM135392
COPE Health ScholarsUNSPECIFIED
Subject Keywords:chemical reactions; electron density; reaction pathway; density functional theory; spin-crossing reactions
DOI:10.26434/chemrxiv-2022-tfqnn
Record Number:CaltechAUTHORS:20220513-557778000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220513-557778000
Official Citation:Lander C, Satalkar V, Yang J, et al. Visualization of Electron Density Changes Along Chemical Reaction Pathways. ChemRxiv. 2022. doi:10.26434/chemrxiv-2022-tfqnn
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114723
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:18 May 2022 14:43
Last Modified:08 Sep 2022 19:41

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