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Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects

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Abstract

We present two methods that address the computational complexities arising in hydrogen transfer reactions in enzyme active sites. To address the challenge of reactive rare events, we begin with an ab initio molecular dynamics adaptation of the Caldeira–Leggett system-bath Hamiltonian and apply this approach to the study of the hydrogen transfer rate-determining step in soybean lipoxygenase-1. Through direct application of this method to compute an ensemble of classical trajectories, we discuss the critical role of isoleucine-839 in modulating the primary hydrogen transfer event in SLO-1. Notably, the formation of the hydrogen bond between isoleucine-839 and the acceptor-OH group regulates the electronegativity of the donor and acceptor groups to affect the hydrogen transfer process. Curtailing the formation of this hydrogen bond adversely affects the probability of hydrogen transfer. The second part of this paper deals with complementing the rare event sampled reaction pathways obtained from the aforementioned development through quantum nuclear wavepacket dynamics. Essentially the idea is to construct quantum nuclear dynamics on the potential surfaces obtained along the biased trajectories created as noted above. Here, while we are able to obtain critical insights on the quantum nuclear effects from wavepacket dynamics, we primarily engage in providing an improved computational approach for efficient representation of quantum dynamics data such as potential surfaces and transmission probabilities using tensor networks. We find that utilizing tensor networks yields an accurate and efficient description of time-dependent wavepackets, reduced dimensional nuclear eigenstates and associated potential energy surfaces at much reduced cost.

Graphical abstract: Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects

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Publication details

The article was received on 22 May 2019, accepted on 22 Jul 2019 and first published on 22 Jul 2019


Article type: Paper
DOI: 10.1039/C9FD00071B
Faraday Discuss., 2019, Advance Article

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    Challenges in constructing accurate methods for hydrogen transfer reactions in large biological assemblies: rare events sampling for mechanistic discovery and tensor networks for quantum nuclear effects

    N. DeGregorio and S. S. Iyengar, Faraday Discuss., 2019, Advance Article , DOI: 10.1039/C9FD00071B

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