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Issue 13, 2020
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Low-dimensional projection approach for efficient sampling of molecular recognition and polymer aggregation

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Abstract

The one-dimensional projection (ODP) approach is extended to two-dimensional umbrella sampling (TDUS) and is applied to three different complex systems in combination with a reactive force field (ReaxFF). TDUS is capable of showing detailed features of the free-energy surface (FES) of the double-proton transfer of the acetic acid dimer. It also revealed the direct relationship between the types of hydrogen bonding and binding strengths in the case of adrenaline molecular recognition by SIVSF (Serine, Isoleucine, Valine, Cysteine, and Phenylalanine). The study of polymer aggregation using TDUS shows that aggregation is preferred with a less-polar solvent, which is also consistent with the experimental observation of a tape-casting process. Therefore, TDUS can be generally useful in FES explorations from simple chemical reactions to complex processes of molecular recognition and polymer aggregation.

Graphical abstract: Low-dimensional projection approach for efficient sampling of molecular recognition and polymer aggregation

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Article information


Submitted
25 Dec 2019
Accepted
28 Feb 2020
First published
02 Mar 2020

Phys. Chem. Chem. Phys., 2020,22, 6953-6963
Article type
Paper

Low-dimensional projection approach for efficient sampling of molecular recognition and polymer aggregation

H. Nakata and C. H. Choi, Phys. Chem. Chem. Phys., 2020, 22, 6953
DOI: 10.1039/C9CP06964J

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