Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments

Abstract

Proton transfer in water‐based environments occurs because of hydrogen‐bond interaction. There are many interesting physicochemical phenomena in this field, causing fast structural diffusion of hydronium and hydroxide ions. During the last few decades, to support experimental observations and measurements, quantum‐mechanical molecular dynamics (QMMD) simulations with reasonable accuracy and efficiency have significantly unraveled structural, energetic, and dynamical properties of excess proton in aqueous environments. This review summarizes the state‐of‐the‐art QMMD studies of proton transfer processes in aqueous solutions and complex systems including bulk liquid water, ice phases, and confined water in nanochannel/nanoporous materials as well as reports on CO2 scrubbing by amine‐based chemical absorption. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Electronic Structure Theory > Semiempirical Electronic Structure Methods Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

“…For a review of the first experimental observations and quantum-mechanical analysis of the “flip-flop” hydrogen bonds see ( Saenger et al, 1985 ; Jeffrey and Saenger, 1991 ). Below are some representative publications analyzing the mechanisms of delocalized hydrogen bonds and “water wires” ( Cui and Karplus, 2003 ; Cukierman, 2003; Marx, 2006 ; Yan et al, 2007 ; Sakti et al, 2019 ; Setny, 2020 ). The analysis of structural conformational changes coupled with proton transfer processes shows that the covalent docking reactions described in this study are highly cooperative processes, and future studies should probably also take into account the quantum-dynamical effects associated with cooperative proton transfer mechanisms.…”

Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer

“…The QM level used in this study was the DFTB3 method, which indicates the self-consistent-charge DFTB (SCC-DFTB) method derived from a third order expansion of the density functional theory (DFT). The adopted DFTB parameter set was 3OB, − which has been well calibrated, especially, for the proton transfer reactions as described in Section . ,,, Grimme’s DFT-D3 dispersion correction with the Becke–Johnson damping scheme was adopted. , The DC method with 4 × 4 × 4 Å 3 cubic grids, resulting in ca. 660 subsystems, and a buffer radius of 5 Å was employed to reduce the computational costs.…”

“…The adopted DFTB parameter set was 3OB, 87−89 which has been well calibrated, especially, for the proton transfer reactions as described in Section 3.1. 59,66,67,90 Grimme's DFT-D3 dispersion correction with the Becke−Johnson damping scheme was adopted. 91,92 The DC method with 4 × 4 × 4 Å 3 cubic grids, resulting in ca.…”

“…One of the advantages of the DC-DFTB method is that the computational cost of the total QM system is in principle comparable with that of the small QM region when using a massively parallel machine. The DC-DFTB-MD simulations were successful in describing various chemical/physical phenomena in complex systems. − The program system, D cdftbmd , has been distributed to the academic community through a special web site…”

Accurate diffusion coefficients of the excess proton and hydroxide in water via extensive ab initio simulations with different schemes

“…[4][5][6][7][8][9][10][11][12] As seen in those studies, interpreting the experimental results is not straightforward, and it is necessary to employ computer simulations to obtain a complete picture of the diffusion process of these species. However, despite the vast computational work already done, 3,[13][14][15] an accurate and affordable method capable of reproducing the experimental diffusion coefficients of the H + (aq) and OH − (aq) was yet to be found. Indeed, water is one of the most difficult substances to accurately model in silico, and even finding a reliable approach for simulating a) Electronic mail: daniel.munozsan@upm.es pure water is being a challenge in itself.…”