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research article

Machine Learning-Guided Approach for Studying Solvation Environments

Basdogan, Yasemin
•
Groenenboom, Mitchell C.
•
Henderson, Ethan
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January 1, 2020
Journal of Chemical Theory and Computation

Molecular-level understanding and characterization of solvation environments are often needed across chemistry, biology, and engineering. Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics-based cluster-continuum approach for calculating single-ion solvation free energies. This approach uses a global optimization procedure to identify low-energy molecular clusters with different numbers of explicit solvent molecules and then employs the smooth overlap for atomic positions learning kernel to quantify the similarity between different low-energy solute environments. From these data, we use sketch maps, a nonlinear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. After testing this approach on different ions having charges 2+, 1+, 1-, and 2-, we find that the solvation environment around each ion can be seen to usually become more similar in hand with its calculated single-ion solvation free energy. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies within 5% of experimental measurements for most cases, and it should be transferable for the study of other systems where dynamics simulations are not easily carried out.

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Type
research article
DOI
10.1021/acs.jctc.9b00605
Web of Science ID

WOS:000508474800049

Author(s)
Basdogan, Yasemin
Groenenboom, Mitchell C.
Henderson, Ethan
De, Sandip  
Rempe, Susan B.
Keith, John A.
Date Issued

2020-01-01

Publisher

AMER CHEMICAL SOC

Published in
Journal of Chemical Theory and Computation
Volume

16

Issue

1

Start page

633

End page

642

Subjects

Chemistry, Physical

•

Physics, Atomic, Molecular & Chemical

•

Chemistry

•

Physics

•

quasi-chemical theory

•

hydration free-energy

•

density-functional theory

•

gibbs free-energy

•

molecular-dynamics

•

ab-initio

•

continuum calculations

•

ion solvation

•

gas phase

•

water

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
COSMO  
Available on Infoscience
March 3, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/166801
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