Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.

Meiyi Liu,Katelyn N Youmans,Jiali Gao

doi:10.3390/molecules23102644

Meiyi Liu, Katelyn N Youmans + Show 1 more

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https://doi.org/10.3390/molecules23102644

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Abstract

A dual QM and MM approach for computing equilibrium isotope effects has been described. In the first partition, the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) method, in which a solute molecule is treated quantum mechanically, and the remaining solvent molecules are approximated classically by molecular mechanics. In the second QM/MM partition, differential nuclear quantum effects responsible for the isotope effect are determined by a statistical mechanical double-averaging formalism, in which the nuclear centroid distribution is sampled classically by Newtonian molecular dynamics and the quantum mechanical spread of quantized particles about the centroid positions is treated using the path integral (PI) method. These partitions allow the potential energy surface to be properly represented such that the solute part is free of nuclear quantum effects for nuclear quantum mechanical simulations, and the double-averaging approach has the advantage of sampling efficiency for solvent configuration and for path integral convergence. Importantly, computational precision is achieved through free energy perturbation (FEP) theory to alchemically mutate one isotope into another. The PI-FEP approach is applied to model systems for the 18O enrichment found in cellulose of trees to determine the isotope enrichment factor of carbonyl compounds in water. The present method may be useful as a general tool for studying isotope fractionation in biological and geochemical systems.

Highlights

Stable isotope compositions in plants and organisms are sensitive to the environment in which biosynthesis takes place
The potential energy function used in the present study follows a combined quantum mechanical and molecular mechanical (QM/MM) approach, in which the electronic structure of the solute molecule is described by a quantum chemical model and the rest of the solvent molecules are approximated by molecular mechanical force fields [14,29,30,31,32]
First we consider the convergence of path integral simulations for computing the ratio of the quantum mechanical partition function (Equation (18)) with respect to the number of beads to represent the discretized paths or ring polymers

Summary

Introduction

Stable isotope compositions in plants and organisms are sensitive to the environment in which biosynthesis takes place. Where R = [18 O]/[16 O] is an isotope ratio, and VSMOW (Vienna standard mean ocean water) is the international standard for oxygen and hydrogen. Another commonly used term is the equilibrium isotope fractionation factor of different compounds A and B, or the same compounds in two different media ( indicated by A and B), denoted by α A/B = R A /R B. For example, the enrichment of 18 O of acetone in water can be described by the isotope fractionation factor between the carbonyl compound and water in aqueous solution [6]. There is a global average δ18 O of 27‰ enrichment in cellulose of trees relative to the source water during its biosynthesis [7]

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