ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiabatic surfaces and the pathway for primary electron transfer in a photosynthetic reaction centerMassimo Marchi, John N. Gehlen, David Chandler, Marshall NewtonCite this: J. Am. Chem. Soc. 1993, 115, 10, 4178–4190Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 1993https://pubs.acs.org/doi/10.1021/ja00063a041https://doi.org/10.1021/ja00063a041research-articleACS PublicationsRequest reuse...

This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties surface were computed by extensive molecular simulations lysozyme in which lasted total 28 ns. Our results indicate that rotational vicinity 3-7 times slower than bulk depending on how hydration shell defined calculation. We have also verified translational retardations similar to relaxation. common assumption nuclear magnetic dispersion (NMRD)...

Water around biomolecules slows down with respect to pure water, and both rotation translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations water several designed protein models establish connection between appearance water−protein interactions. For first we quantify separate effect topological energetic disorder on dynamics. When a static structure is simulated, show that types contribute slow...

This paper reports results from four nanosecond constant pressure and temperature simulations of sodium di-2-ethylhexylsulfoccinate (AOT) water reverse micelles (RMs) in an apolar solvent, isooctane. The concentration our simulated was chosen to fall a range which nature corresponds the L2 phase ternary system. To knowledge, this is first study develop full molecular model for AOT solvent. We address here problems shape RM its hydrophilic inner core. For AOT−water system, we obtain...

In this study, we present a new molecular dynamics program for simulation of complex systems. The program, named ORAC, combines state-of-the-art (MD) algorithms with flexibility in handling different types and sizes molecules. ORAC is intended simulations systems specifically designed to treat biomolecules efficiently effectively solution or crystalline environment. Among its unique features are: (i) implementation reversible symplectic multiple time step (or r-RESPA, reference system...

This study deals with a novel molecular simulation technique, named adiabatic bias dynamics (MD), which provides simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way biasing potential is updated during runs, technique allows some additional effort computation free energy change experienced trajectory. The method has been applied nontrivial problem: unfolding an atomistic model...

Analysis of a 60-picosecond molecular dynamics trajectory the reaction center Rhodopseudomonas viridis provides an understanding observations concerning vibrational coherence and nonexponential kinetics primary charge transfer in photosynthesis. Complex arises from energy gap correlations that persist beyond 1 picosecond.

Long range electrostatic forces are involved at a fundamental level in many biological phenomena. Their prohibitive computational costs often prevents their correct calculation molecular dynamics (MD) simulations of molecules. In this paper we present method to handle efficiently and exactly interactions MD with periodic boundary conditions. Our scheme employs multiple time step r-RESPA integration algorithm combination the Ewald summation technique, is specifically targeted simulation large...

Constant pressure and temperature algorithms have been derived based on a reversible multiple time step (r-RESPA) approach new modification of the particle mesh Ewald method. As such they provide very fast accurate tools for simulation complex molecular systems in ensembles other than microcanonical. We also developed novel scaling scheme named atomic group which is similar to scaling, but has important computational advantages when used conjunction with bond constraints. The investigation...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal expansion of structure I ethylene oxide hydrateJohn S. Tse, W. Ross. McKinnon, and Massimo. MarchiCite this: J. Phys. Chem. 1987, 91, 15, 4188–4193Publication Date (Print):July 1, 1987Publication History Published online1 May 2002Published inissue 1 July 1987https://pubs.acs.org/doi/10.1021/j100299a047https://doi.org/10.1021/j100299a047research-articleACS PublicationsRequest reuse permissionsArticle Views413Altmetric-Citations89LEARN ABOUT...

We present the new release of ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at atomistic level. The previous code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and temperature simulations. has been supplemented with most advanced techniques for enhanced sampling in systems including replica exchange solute tempering, metadynamics steered molecular dynamics. All these computational...

This paper deals with the development and validation of new potential parameter sets, based on CHARMM36 GLYCAM06 force fields, to simulate micelles two anomeric forms (α β) N-dodecyl-β-maltoside (C12G2), a surfactant widely used in extraction purification membrane proteins. In this context, properties such as size, shape, internal structure, hydration C12G2 anomer were thoroughly investigated by molecular dynamics simulations results compared experiments. Additional also performed older...

We present the first comparative molecular dynamics investigation for a dodecylphosphocholine (DPC) micelle performed in condensed phase using CHARMM36, GROMOS53A6, GROMOS54A7, and GROMOS53A6/Berger force fields set of parameters developed anew. Our potential consists newly derived RESP atomic charges, which are associated with Amber99SB field proteins. This new is expressly designed simulations peptides transmembrane proteins micellar environment. To validate this ensemble, DPC composed 54...

In this paper we describe the implementation of a very fast molecular dynamic method to realistically handle electrostatic interactions in simulations solvated proteins. Our scheme is based on recently proposed reversible multiple time step (r-RESPA) algorithm and new modification particle mesh Ewald method. While latter technique provides accurate representation Coulombic for infinite systems, r-RESPA exploits separation force into components with increasingly longer scales corresponding...

In this paper, we deal with the handling of electrostatic forces in complex molecular systems. particular, focus on instabilities experienced by reversible multiple time step algorithms when used conjunction Ewald summation techniques for periodic We show that energy conservation is negatively affected intra-molecular term due to excluded contacts required most frequently modern force fields biomolecular These effects are a non-complete cancellation and at intermediate or long steps.

Abstract This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable molecular dynamics simulations photosynthetic proteins by being compatible with AMBER field. To our knowledge, this is first based on reliable set density functional reference data methyl bacteriochlorophyll , bacteriopheophytin derivative ubiquinone. Indeed, mechanics able reproduce very well not...

Here, the adsorption of alkanethiols (from ethane to dodecanethiol) on icosahedral gold nanocrystals with diameters up 10 nm is studied by molecular dynamics simulations in a vacuum. The surface coverage obtained good agreement experimental data. We show that average per adsorbed thiol does not markedly depend nanocrystal size and ligand only about 10% lower than value observed flat Au(111) surface. observe two different organizations thiolates edges centers facets. incompatibility between...

The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) in benzene increasing sizes, with water-to-surfactant number ratios ranging from W0 = 1 to 16. aggregation number, i.e., the DOPC molecules per micelle, is determined fit experimental light-scattering measurements micelle diameter. simulated found be approximately spherical. Larger (W0 > 4) exhibit a layered...

Constant pressure and temperature molecular dynamics techniques have been employed to investigate the changes in structure volumes of two globular proteins, superoxide dismutase lysozyme, under pressure. Compression (the relative proteins' volumes), computed with Voronoi technique, is closely related so-called protein intrinsic compressibility, estimated by sound velocity measurements. In particular, compression predicts, agreement experimental estimates, a negative bound water contribution...

This Letter is the first attempt at studying self-aggregation of AOT reverse micelles from first-principles. It focuses on predicting aggregation number, radius gyration, and hydrodynamic a low water content micelle by theoretical means. We show that molecular dynamics simulation in μs time range combined with atomistic potentials capable reproducing explaining, to convenient degree, experimental results size dimensions content, [H2O]/[AOT] ≈ 5.

We introduce a novel method to simulate hydrated macromolecules with dielectric continuum representation of the surrounding solvent. In our approach, interaction between solvent and molecular degrees freedom is described by means polarization density free energy functional which minimum at electrostatic equilibrium. After pseudospectral expansion discretization functional, we construct equations motion for system based on Car–Parrinello technique. limit adiabatic evolution field variables,...

We apply density functional theory in the gradient-corrected local-density approximation to determination of structural properties and harmonic vibrational modes trehalose gas phase monohydrate crystal. analyze local conformation relative strength intra- intermolecular hydrogen bonds, we discuss effects crystal environment on molecular geometry frequencies. The results are used assess quality a recent mechanics model. This simplified scheme provides fairly good description ground-state...