Conformation-dependent dynamics of macromolecular ions in the gas phase under an electrostatic field: A molecular dynamics simulation

Tamadate, Tomoya; Orii, Takaaki; Higashi, Hidenori; Ōtani, Yoshio; Kumita, Mikio; Seto, Takafumi

doi:10.1080/02786826.2018.1557319

Cited by 4 publications

(1 citation statement)

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“…They additionally enable detailed accounting of the effect of ionneutral gas collisions, obviating the need to assume either specular or diffuse gas atom scattering upon collision, i.e. all degrees of freedom in ions and gas atoms are modeled 48,49 . This is an important feature in ion-ion recombination calculations, as the model required to accurately depict gas atom or molecule scattering from an ion without modeling ion internal degrees of freedom (frozen ion models) has been found strongly dependent on ion chemical composition and size.…”

Section: Molecular Dynamics Based Probability Calculationmentioning

confidence: 99%

Calculation of the ion–ion recombination rate coefficient via a hybrid continuum-molecular dynamics approach

Tamadate

Higashi

Seto

et al. 2020

The Journal of Chemical Physics

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Accurate calculation of the ion-ion recombination rate coefficient has been of longstanding interest, as it controls the ion concentration in gas phase systems and in aerosols. We describe the development of a hybrid continuum-molecular dynamics approach to determine the ion-ion recombination rate coefficient. The approach is based on the limiting sphere method classically used for transition regime collision phenomena in aerosols. When ions are sufficiently far from one another, ion-ion relative motion is described by diffusion equations while within a critical distance, molecular dynamics (MD) simulations are used to model ion-ion motion. MD simulations are parameterized using the AMBER force-field as well as by considering partial charges on atoms. Ion-neutral gas collisions are modeled in two mutually exclusive cubic domains composed of 10 3 gas atoms each, which remain centered on the recombining ions throughout calculations. Example calculations are reported for NH 4 + recombination with NO 2 in He, across a pressure range from 10 kPa to 10,000 kPa. Excellent agreement is found in comparison of calculations to literature values for the 100 kPa recombination rate coefficient (1.0 x 10 -12 m 3 s -1 ) in He. We also recover the experimentally observed increase in recombination rate coefficient with pressure at sub-atmospheric pressures, and the observed decrease in recombination rate coefficient in the high pressure continuum limit. We additionally find that non-dimensionalized forms of rate coefficients are consistent with recently developed equations for the dimensionless charged particle-ion collision rate coefficient based on Langevin dynamics simulations.

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Section: Molecular Dynamics Based Probability Calculationmentioning

confidence: 99%