Estimation of Solvent Diffusion Coefficients Using Molecular Dynamics Simulations

Bareman, James P.; Reid, Robert I.; Hrymak, Andrew N.; Kavassalis, Tom A.

doi:10.1080/08927029308022511

Cited by 6 publications

(7 citation statements)

References 4 publications

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“…This was also the conclusion reached from studies of n-alkanes31 and solvents such as toluene and tetrahydrofuran. 32 The force field for the lipids is the same as that employed in the work of Slouch et al33 except that the hydrocarbon chain 1,4 interactions were scaled by 0.6. The water potential employed was a flexible version of the SPClike potential34 which has been shown to be in good agreement with both experiment and the computed properties of other water models.…”

Section: Methodsmentioning

confidence: 99%

Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations

Alper¹,

Stouch²

1995

J. Phys. Chem.

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Section: Methodsmentioning

confidence: 99%

Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations

Alper¹,

Stouch²

1995

J. Phys. Chem.

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“…In addition to the RDF, Drabowicz calculated the THF center-of-mass and angular velocity autocorrelation functions. A second MD study took advantage of Jorgenson's model but reported only the diffusion constant . The authors in this study had removed the partial charges (and therefore the dipole moment) from the THF molecules in their calculation, so it is unclear whether their reported diffusion constant is relevant to either the simulated or experimental fluid .…”

Section: Introductionmentioning

confidence: 99%

Understanding Nonequilibrium Solute and Solvent Motions through Molecular Projections: Computer Simulations of Solvation Dynamics in Liquid Tetrahydrofuran (THF)

2003

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In this paper, we investigate the solvation dynamics of the weakly polar organic solvent tetrahydrofuran (THF) via classical molecular dynamics simulation. We find that the relaxation dynamics of all of the rotational and translational degrees of freedom of neat THF occur on similar time scales and have similar power spectra, making it impossible to use spectral density analysis to discern which specific molecular motions are involved in solvation. Instead, we probe the molecular origins of solvation dynamics using a nonequilibrium projection formalism that we originally outlined in M. J. Bedard-Hearn et al., J. Phys. Chem. A 2003, 107 (24), 4773. Here, we expand this formalism and use it to study the nonequilibrium solvation dynamics for a model reaction in THF in which a charge is removed from an anionic Lennard-Jones (LJ) solute, leaving behind a smaller neutral atom. The solute parameters are chosen to model the photodetachment of an electron from a sodium anion, Na- → Na0, to compare to the results of ultrafast spectroscopic experiments of this reaction being performed in our lab. We are able to explain the hidden breakdown of linear response for this system that we uncovered in our previous work in terms of the dynamical properties of the neat liquid and the structural properties of the solutions. In particular, our nonequilibrium projection analysis shows that four distinct solvation mechanisms are operative: (1) a rapid relaxation (t ≤ 700 fs) caused by longitudinal translational motions that dramatically change the local solvation structure; (2) a slower relaxation (t > 700 fs) caused by diffusive longitudinal translational motions that completes the transformation of the long-range solute−solvent packing; (3) an early-time relaxation (t < 500 fs) caused by solvent rotational motions that destabilizes the (unoccupied) anion ground state via Coulomb interactions; (4) a longer time process (t ≥ 500 fs) caused by solvent rotational motions that increases the solvation energy gap. This last process results from the LJ interaction component of the solvent rotational motions, as the nonequilibrium dynamics bring smaller THF−oxygen sites closer to the excited solute in place of larger THF−methylene sites. Overall, the simulations indicate that nonequilibrium solvation dynamics involves cooperative motions of both the solute and solvent and consists of multiple competing relaxation processes that can affect the solvation energy gap in opposite directions.

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“…Furthermore, many studies have employed approximations such as "united atoms" and short-range (8-10 A) truncation of electrostatic forces, which, although so widespread as to be a standard, have recently been shown to have significant effects on calculated dynamical properties (Mul- ler-Plathe et al, 1992; Bareman et al, 1993;Pant and Boyd, 1993;Yoon et al, 1993;Alper et al, 1993a;Auffinger et al, 1996;Loncharich and Brooks, 1989;Smith and Pettitt, 1991;Kitson et al, 1993;Cheatham et al, 1995;Schreiber and Steinhauser, 1992). Primarily as a result of increased computer power, simulation of biomembranes has become more detailed and longer, and has dealt with increasingly complex phenomena (Stouch and Bassolino, 1996; Basso- lino-Klimas et al, 1995;Alper et al, 1993b;Bassolino et al, 1993;Stouch, 1993;Pastor et al, 1991;Damodaran et al, 1992;Egberts and Berendsen, 1988;Xing and Scott, 1989; Shinoda et al, 1995;Heller et al, 1993;Venable et al, 1993;Huang et al, 1994;Essex et al, 1994;Wilson and Pohorille, 1994;Raghaven et al, 1992; Chiu et al, 1995; Woolf and Roux, 1996).…”

Section: Introductionmentioning

confidence: 99%

Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations

Shen¹,

Bassolino²,

Stouch³

1997

Biophysical Journal

117

112

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To probe the fundamentals of membrane/protein interactions, all-atom multi-nanosecond molecular dynamics simulations were conducted on a single transmembrane poly(32)alanine helix in a fully solvated dimyristoyphosphatidylcholine (DMPC) bilayer. The central 12 residues, which interact only with the lipid hydrocarbon chains, maintained a very stable helical structure. Helical regions extended beyond these central 12 residues, but interactions with the lipid fatty-acyl ester linkages, the lipid headgroups, and water molecules made the helix less stable in this region. The C and N termini, exposed largely to water, existed as random coils. As a whole, the helix tilted substantially, from perpendicular to the bilayer plane (0 degree) to a 30 degrees tilt. The helix experienced a bend at its middle, and the two halves of the helix at times assumed substantially different tilts. Frequent hydrogen bonding, of up to 0.7 ns in duration, occurred between peptide and lipid molecules. This resulted in correlated translational diffusion between the helix and a few lipid molecules. Because of the large variation in lipid conformation, the lipid environment of the peptide was not well defined in terms of "annular" lipids and on average consisted of 18 lipid molecules. When compared with a "neat" bilayer without peptide, no significant difference was seen in the bilayer thickness, lipid conformations or diffusion, or headgroup orientation. However, the lipid hydrocarbon chain order parameters showed a significant decrease in order, especially in those methylene groups closest to the headgroup.

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Estimation of Solvent Diffusion Coefficients Using Molecular Dynamics Simulations

Cited by 6 publications

References 4 publications

Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations

Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations

Understanding Nonequilibrium Solute and Solvent Motions through Molecular Projections: Computer Simulations of Solvation Dynamics in Liquid Tetrahydrofuran (THF)

Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations

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