Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes

Returning probability theory enables us to systematically analyze host-guest binding kinetics in terms of the thermodynamic and kinetic properties of the intermediate state existing in the binding processes with the molecular dynamics (MD) simulation. In order to employ this theory, we need to compu...

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Veröffentlicht in:	Chemistry letters 2022-08, Vol.51 (8), p.823-827
Hauptverfasser:	Kasahara, Kento, Masayama, Ren, Matsubara, Yuya, Matubayasi, Nobuyuki
Format:	Artikel
Sprache:	eng
Schlagworte:	Binding Kinetics Molecular dynamics Probability theory Time correlation functions
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creator	Kasahara, Kento Masayama, Ren Matsubara, Yuya Matubayasi, Nobuyuki
description	Returning probability theory enables us to systematically analyze host-guest binding kinetics in terms of the thermodynamic and kinetic properties of the intermediate state existing in the binding processes with the molecular dynamics (MD) simulation. In order to employ this theory, we need to compute the returning probability, a time-correlation function for describing the kinetics of the intermediate state. Here, we present a methodology to realize the efficient calculation of the probability with the memory kernel construction.
doi_str_mv	10.1246/cl.220236
format	Article
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source	Oxford University Press Journals All Titles (1996-Current)
subjects	Binding Kinetics Molecular dynamics Probability theory Time correlation functions
title	Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes
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