Non-conventional force fields for applications in spectroscopy and chemical
          reaction dynamics

Koner, Debasish; Salehi, Seyedeh Maryam; Mondal, Padmabati; Meuwly, Markus

doi:10.1063/5.0009628

Cited by 38 publications

(41 citation statements)

References 169 publications

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“…A comprehensive discussion of these reactive force fields can be found in refs. 13,14 . Among these force fields, the empirical ReaxFF was widely used in MD simulation of combustion systems due to its computational efficiency 15 , but its accuracy and reliability are of significant concern [16][17][18] .…”

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confidence: 99%

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

et al. 2020

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Combustion is a complex chemical system which involves thousands of chemical reactions and generates hundreds of molecular species and radicals during the process. In this work, a neural network-based molecular dynamics (MD) simulation is carried out to simulate the benchmark combustion of methane. During MD simulation, detailed reaction processes leading to the creation of specific molecular species including various intermediate radicals and the products are intimately revealed and characterized. Overall, a total of 798 different chemical reactions were recorded and some new chemical reaction pathways were discovered. We believe that the present work heralds the dawn of a new era in which neural network-based reactive MD simulation can be practically applied to simulating important complex reaction systems at ab initio level, which provides atomic-level understanding of chemical reaction processes as well as discovery of new reaction pathways at an unprecedented level of detail beyond what laboratory experiments could accomplish.

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confidence: 99%

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

et al. 2020

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“…An alternative to instantaneous normal modes is to obtain instantaneous frequencies from solving the 1-or 3-dimensional nuclear Schrödinger equation. For this, the corresponding 1or 3-d PES is scanned for a given snapshot with frozen environment 41,50,53 and represented as a RKHS. This is a computationally much more demanding approach, in particular in 3 spatial dimensions.…”

Section: Vibrational Spectra and Frequency Correlation Functionsmentioning

confidence: 99%

Site-Selective Dynamics of Azidolysozyme

Salehi¹,

Meuwly²

2021

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The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN 3 ) in Lysozyme is characterized. It is found that AlaN 3 is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼ 15 cm −1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2 which reported a frequency span of ∼ 10 cm −1 for replacements of Val, Ala, or Glu by azidohomoalanine (AHA). For the frequency fluctuation correlation functions (FFCFs) the long-time decay constants τ 2 range from ∼ 1 to ∼ 10 ps which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e. static component ∆ 0 ∼ 0 ps −1 ) or to a remaining, static contribution of ∼ 0.5 ps −1 (corresponding to 2.5 cm −1 ), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.

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“…The coupling between inter-and intramolecular degrees of freedom -such as the hydrogen bonding network in solution, or the conformational dynamics of biological macromolecules -can be investigated by monitoring the fluctuation of a fundamental vibrational frequency, which is the amide-I mode in the present work. Computationally, this information is accessible from either instantaneous normal modes (NM), 5,25,30 the solution of a reduced-dimensional nuclear Schrödinger equation, 31,32 or from spectroscopic maps. 33 This frequency trajectory (ω(t) or ν(t) for harmonic or anharmonic vibrations, respectively) is then used to determine the frequency fluctuation correlation function which can be directly compared with experimental measurements.…”

Section: Introductionmentioning

confidence: 99%

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine-Trimer

Mondal¹,

Cazade²,

Das³

et al. 2021

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The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution is characterized from molecular dynamics (MD) simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1-d infrared spectra, the frequency splitting between the two amide-I groups is 10 cm −1 from the PC, 13 cm −1 from the MTP, and 47 cm −1 from SCC-DFTB simulations, compared with 25 cm −1 from experiment. The frequency trajectory required for determining the frequency fluctuation correlation function (FFCF) is determined from individual (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component ∆ 2 0 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala) 3 . Contrary to that, for the analysis excluding mode-mode coupling (INM) the FFCF decays to zero too rapidly and for simulations with a PC-based force field the ∆ 2 0 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including P II , β, α R , and α L ), whereas that covered by the MTP-based simulations is dominated by P II with some contributions from β, α R . This agrees with and confirms recently reported, Bayesian-refined populations based on 1-dimensional infrared experiments. Full normal mode analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

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Non-conventional force fields for applications in spectroscopy and chemical reaction dynamics

Cited by 38 publications

References 169 publications

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Site-Selective Dynamics of Azidolysozyme

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine-Trimer

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