Atomistic description of molecular binding processes based on returning probability theory

Kasahara, Kento; Masayama, Ren; Okita, Kazuya; Matubayasi, Nobuyuki

doi:https://doi.org/10.1063/5.0070308

Atomistic description of molecular binding processes based on returning probability theory

Kasahara, Kento; Masayama, Ren; Okita, Kazuya et al.

Journal of Chemical Physics, 2021, 155(20), 204503

Number of Access:448（2025-08-29 00:54 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/97733

Link to primary information

File	Format	Terms of use	Size	Views	Date.Available	Description	information
JChemPhys_155_20_204503	pdf	None	6.60 MB	99	2024.08.19

Item Information

Output File Export EndNote Basic Export Mendeley

Title	Atomistic description of molecular binding processes based on returning probability theory
Creator	NRID 1000010824469 1000010824469 ORCID 0000-0001-7138-250X 0000-0001-7138-250X researchmap permalink kasakento kasakento Scopus Author ID 56245700800 56245700800 CreatorName Kasahara, Kento
	CreatorName Masayama, Ren
	CreatorName Okita, Kazuya
	NRID 1000020281107 1000020281107 ORCID 0000-0001-7176-441X 0000-0001-7176-441X researchmap permalink nbyk_MTBYS nbyk_MTBYS Scopus Author ID 7003410578 7003410578 CreatorName Matubayasi, Nobuyuki
Description	Kasahara K., Masayama R., Okita K., et al. Journal of Chemical Physics 155, 204503 (2021) https://doi.org/10.1063/5.0070308.
Abstract	The efficiency of molecular binding such as host-guest binding is commonly evaluated in terms of kinetics, such as rate coefficients. In general, to compute the coefficient of the overall binding process, we need to consider both the diffusion of reactants and barrier crossing to reach the bound state. Here, we develop a methodology of quantifying the rate coefficient of binding based on molecular dynamics simulation and returning probability (RP) theory proposed by Kim and Lee [J. Chem. Phys. 131, 014503 (2009)]. RP theory provides a tractable formula of the rate coefficient in terms of the thermodynamic stability and kinetics of the intermediate state on a predefined reaction coordinate. In this study, the interaction energy between reactants is utilized as the reaction coordinate, enabling us to effectively describe the reactants' relative position and orientation on one-dimensional space. Application of this method to the host-guest binding systems, which consist of β-cyclodextrin and small guest molecules, yields the rate coefficients consistent with the experimental results.
Publisher	American Institute of Physics Inc.
Source Title	Journal of Chemical Physics
Volume (Issue)	155(20)
Page	204503
Date of Issued	2021-11-28
Language	English
Handle URL	https://hdl.handle.net/11094/97733
PISSN	00219606
eISSN	10897690
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1063/5.0070308
Access Rights	open access
CopyRight	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Kasahara K., Masayama R., Okita K., et al. Atomistic description of molecular binding processes based on returning probability theory. Journal of Chemical Physics 155, 204503 (2021) and may be found at https://doi.org/10.1063/5.0070308.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Journal of Chemical Physics. 2021, 155(20), p. 204503
DC.title	Atomistic description of molecular binding processes based on returning probability theory
DC.creator	Kasahara, Kento
	Masayama, Ren
	Okita, Kazuya
	Matubayasi, Nobuyuki
DC.publisher	American Institute of Physics Inc.
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2021-11-28
DC.identifier	https://doi.org/10.1063/5.0070308
DC.description	Kasahara K., Masayama R., Okita K., et al. Journal of Chemical Physics 155, 204503 (2021) https://doi.org/10.1063/5.0070308.
DCTERMS.abstract	The efficiency of molecular binding such as host-guest binding is commonly evaluated in terms of kinetics, such as rate coefficients. In general, to compute the coefficient of the overall binding process, we need to consider both the diffusion of reactants and barrier crossing to reach the bound state. Here, we develop a methodology of quantifying the rate coefficient of binding based on molecular dynamics simulation and returning probability (RP) theory proposed by Kim and Lee [J. Chem. Phys. 131, 014503 (2009)]. RP theory provides a tractable formula of the rate coefficient in terms of the thermodynamic stability and kinetics of the intermediate state on a predefined reaction coordinate. In this study, the interaction energy between reactants is utilized as the reaction coordinate, enabling us to effectively describe the reactants' relative position and orientation on one-dimensional space. Application of this method to the host-guest binding systems, which consist of β-cyclodextrin and small guest molecules, yields the rate coefficients consistent with the experimental results.
DC.rights	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Kasahara K., Masayama R., Okita K., et al. Atomistic description of molecular binding processes based on returning probability theory. Journal of Chemical Physics 155, 204503 (2021) and may be found at https://doi.org/10.1063/5.0070308.
DC.format	97733
citation_title	Atomistic description of molecular binding processes based on returning probability theory
citation_author	Kasahara, Kento
	Masayama, Ren
	Okita, Kazuya
	Matubayasi, Nobuyuki
citation_publisher	American Institute of Physics Inc.
citation_language	English
citation_date	2021-11-28
citation_journal_title	Journal of Chemical Physics
citation_volume	155
citation_issue	20
citation_firstpage	204503
citation_doi	https://doi.org/10.1063/5.0070308
citation_public_url	https://hdl.handle.net/11094/97733

Atomistic description of molecular binding processes based on returning probability theory

Link to primary information

Item Information

Show details