'Dynamic Distance' Reaction Coordinate for Competing Bonds: Applications in Classical and Ab Initio Simulations

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• 作者：Christian Burisch ; Phineus R. L. Markwick ; Nikos L. Doltsinis ; J&uuml ; rgen Schlitter
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2008
• 出版时间：January 2008
• 年：2008
• 卷：4
• 期：1
• 页码：164 - 172
• 全文大小：1520K
• 年卷期：v.4,no.1(January 2008)
• ISSN：1549-9626

文摘

A versatile reaction coordinate, the "dynamic distance", is introduced for the studyof reactions involving the rupture and formation of a series of chemical bonds or contacts. Thedynamic distance is a mass-weighted mean of selected distances. When implemented as ageneralized constraint, the dynamic distance is particularly suited for driving activated processesby controlled increase during a simulation. As a single constraint acting upon multiple degreesof freedom, the sequence of events along the resulting reaction pathway is determinedunambiguously by the underlying energy landscape. Free energy profiles can be readily obtainedfrom the mean constraint force. In this paper both theoretical aspects and numerical implementation are discussed, and the unique and diverse properties of this reaction coordinate aredemonstrated using three examples: In the framework of Car-Parrinello molecular dynamics,we present results for the prototypical double proton-transfer reaction in formic acid dimer andthe photocycle of the guanine-cytosine DNA base pair. As a classical mechanical example,the opening of the binding pocket of the enzyme rubisco is analyzed.