Temporal quantum mechanics/molecular mechanics: Extending the time scales accessible in molecular dynamics simulations of reactions

Dayal, P.; Weyand, Sabine; McNeish, Joanne; Mosey, Nicholas J.

doi:10.1016/j.cplett.2011.09.079

Cited by 9 publications

(5 citation statements)

References 34 publications

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“…Alternatively, a chemical reaction can be followed along time as the progression coordinate, which is the situation encountered in experiments. 21,22 This is the purpose of adiabatic reactive molecular dynamics (ARMD) that was originally developed for reactions in the condensed phase. 14,15,21,23 More recently, ARMD has also been applied to gas-phase systems such as the vibrationally induced photodissociation of sulfuric acid (H 2 SO 4 ).…”

Section: Introductionmentioning

confidence: 99%

“…This introduces a dependence on the choice of the coordinates that is not always desirable, e.g., if multiple bond rearrangements can occur. Alternatively, a chemical reaction can be followed along time as the progression coordinate, which is the situation encountered in experiments. , This is the purpose of adiabatic reactive molecular dynamics (ARMD) that was originally developed for reactions in the condensed phase. ,,, More recently, ARMD has also been applied to gas-phase systems such as the vibrationally induced photodissociation of sulfuric acid (H 2 SO 4 ). Here, the excitation of a higher overtone (ν 9 ≥ 4) of a local OH-stretching vibration can lead to photodissociation into water and sulfur-trioxide (H 2 O + SO 3 ) on the picosecond to nanosecond time scale. , However, the ARMD trajectories were not suitable for final state analysis of the reaction products because they were based on an explicitly time-dependent Hamiltonian that does not conserve total energy during crossing.…”

Section: Introductionmentioning

confidence: 99%

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Multisurface Adiabatic Reactive Molecular Dynamics

Nagy

Yosa

Meuwly

2014

J. Chem. Theory Comput.

136

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Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multisurface Adiabatic Reactive Molecular Dynamics

Nagy

Yosa

Meuwly

2014

J. Chem. Theory Comput.

136

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“…The fitted, three-dimensional PES is reactive and allows to describe both, the Fe-CO and Cu-CO states. However, alternative procedures to follow chemical reactions in condensedphase simulations are available, including reactive molecular dynamics, 59,[62][63][64][65] reformulations of it, 66 or the empirical valence bond (EVB) formalism. 67…”

Section: Photodissociation and Ligand Transfermentioning

confidence: 99%

CO-dynamics in the active site of cytochrome c oxidase

Soloviov

Meuwly

2014

The Journal of Chemical Physics

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The transfer of CO from heme a3 to the Cu(B) site in Cytochrome c oxidase (CcO) after photolysis is studied using molecular dynamics simulations using an explicitly reactive, parametrized potential energy surface based on density functional theory calculations. After photodissociation from the heme-Fe, the CO ligand rebinds to the Cu(B) site on the sub-picosecond time scale. Depending on the simulation protocol the characteristic time ranges from 260 fs to 380 fs which compares with an estimated 450 fs from experiment based on the analysis of the spectral changes as a function of time delay after the photodissociating pulse. Following photoexcitation ≈90% of the ligands are found to rebind to either the Cu(B) (major component, 85%) or the heme-Fe (minor component, 2%) whereas about 10% remain in an unbound state. The infrared spectra of unbound CO in the active site is broad and featureless and no appreciable shift relative to gas-phase CO is found, which is in contrast to the situation in myoglobin. These observations explain why experimentally, unbound CO in the binuclear site of CcO has not been found as yet.

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“…Many attempts have been made to modify a nonreactive force field reactive for various reaction systems. [34][35][36][37][38][39][40][41] Since numerous efforts have been devoted to make the force fields applicable to a variety of reactions, the literature list given here is far from complete. There are also some specialized models that render the N=N bond torsion to be reactive.…”

Section: Introductionmentioning

confidence: 99%

Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface

Tian

Wen

2013

The Journal of Chemical Physics

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It is a challenge to simulate the switching process of functional self-assembled monolayers (SAMs) on metal surfaces, since the systems consist of thousands of atoms and the switching is triggered by quantum-mechanical events. Herein a molecular dynamics simulation with a reactive rotation potential of N=N bond is implemented to investigate the dynamic conformational changes and packing effects on the stimuli-responsive isomerization of the terminally thiol functionalized azobiphenyls (AZOs), which are bound on the Au(111) surface. To, respectively, distinguish the time evolutions that start from cis and trans initial configurations, two different functions are established to model the potential energy curves for cis-to-trans and trans-to-cis transitions, instead of the only one cosine function used in the conventional non-reactive force fields. In order to simulate the conformation transitions of the AZO film on surface, a random switching function, depending on the N=N twisting angle, is constructed to consider both forward and backward cis∕trans isomerization events and to trigger the reaction by changing the N atom types automatically. The factors that will influence the isomerization process, including the choice of ensembles and thermostat algorithms, the time intervals separating each switching, and the forms of the switching function, are systematically tested. Most AZO molecules switch from the cis to trans configuration with a coverage of 5.76 × 10(-6) mol∕m(2) on a picosecond time scale, and a low coverage might make the switching irreversible, which is in agreement with the experiments.

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Temporal quantum mechanics/molecular mechanics: Extending the time scales accessible in molecular dynamics simulations of reactions

Cited by 9 publications

References 34 publications

Multisurface Adiabatic Reactive Molecular Dynamics

Multisurface Adiabatic Reactive Molecular Dynamics

CO-dynamics in the active site of cytochrome c oxidase

Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface

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