Search

The infrared spectroscopy of the transient H5O2+species in liquid water is studied. The potential energy surface of the system is modeled by a two-state Empirical Valence Bond (EVB) model. The quantization of the central proton of the dimer H5O2+is described by a three-dimensional time-dependent gaussian wavefunction within an adiabatic molecular dynamics simulation, or by using an effective parameterization of the EVB model, using a preliminary path-integral calculation. It is shown that the H5O2+complex in solution displays a strong absorption between 1000 and 2000cm−1. We demonstrate that the contribution of the asymmetric O–H+stretch cannot be unambiguously assigned, due to its close coupling to the other modes of the dimer. The oxygen–oxygen stretching mode of the dimer strongly modulates the infrared spectrum of the central proton while the effect of the solvent is mainly to induce an asymmetry of the central O–H–O+bond of H5O2+leading, partly, to absorption at higher frequencies.

As a model for understanding hydrophilic-hydrophobic interactions in aqueous solutions, the potential of mean force for Cl−···Ar and Na+···Ar pairs in water was computed by molecular dynamics simulations. The Cl−···Ar potential is slightly modified by the solvent, with the appearance of a shallow secondary minimum associated to the stabilization of a solvent separated pair in addition to the stable contact pair. The Na+···Ar potential is considerably modified from the gas to the liquid. The depth of the attractive well is divided by a factor 3. At short distances, the repulsive part of the potential is dominated by the solvent-induced electrostatic repulsion rather than by the direct Pauli repulsion. The difference of the solvation properties of the two pairs is explained by a simple electrostatic model and is attributed to a size rather than a charge effect.

Following Kramers, we describe the dynamics of an isomerization reaction A ⇆ B as a diffusion process in a bistable intramolecular potential. In order to calculate the chemical relaxation time tr, we rely on a purely equilibrium approach, introduced by Chandler, and we focus on the properties of the time correlation function C(t) = 〈δNA(0) δNA(t)〉, and of its derivatives. A plateau formalism permits the extraction of the long relaxation time tr from the short time dynamics of a molecule which starts at t = 0 from the activated region between A and B. The calculation makes it possible to encompass in a unified way the low and high friction limits, which are usually treated differently. It involves the definition of a species specification function σA, which indicates microscopically if a molecule is A or B. Most of the time, σA is taken as a Heaviside function, although its definition should be experiment-dependent. We examine the possibility of taking a wide species specification, presenting a smooth variation in the activated region.

The classical and quantum dynamics of an excess proton in water is studied by molecular dynamics simulations. The electronic structure of the system is described by an extended multistate valence-bond Hamiltonian that allows for the breaking and formation of O−H⁺ bonds. The proton quantum character is treated by means of an effective (path-integral) proton-transfer surface. Whereas classical simulations predict that the hydrated proton appears in a mixture of %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% and %@mt;sys@%H%@sb@%9%@sbx@%O%@sx@%4%@be@%+%@sxx@%%@mx@% structures, inclusion of proton quantization leads to the prevalence of %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% . The proton-transfer mechanism can be described mostly as the translocation of a transient %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% structure across the water hydrogen-bond network. The computed lifetime of a particular %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% is close to 2 ps, a value compatible with experimental estimates.

We study a stochastic theory of the two-cell model of the Schlögl reaction beyond the bistability threshold. We restrict ourselves to the case of a small diffusional coupling, where inhomogeneous steady states occur, and where a nucleationlike behavior is expected. Our analysis agrees with the deterministic analysis in the thermodynamic limit, and permits to calculate the long time evolution of the probability distribution function. We compare our results with a recent Monte Carlo simulation of this problem.

The theory of homogeneous nucleation is developed for a model nonlinear bistable chemical reaction driven far from equilibrium (trimolecular Schlögl model). The theory is restricted to the vicinity of the stable/unstable transition, where the nucleation barrier is small but nonvanishing. The nucleation rates are derived for two types of fluctuations: first, fluctuations due to a homogeneous external white noise source, and second, internal chemical fluctuations, described by a reastion-diffusion multivariate master equation. In the white noise case, a Landau-Ginzburg potential can be defined, and the standard nucleation formalism can be applied; this is not true for the internal case and a new result is used. The inhomogeneous chemical fluctuations, due to the coupling between the nonlinear reaction and diffusion, are shown to have an influence on the nucleation rate. Quantitative conditions are also given to evaluate the possibility of homogeneous nucleation in nonlinear chemical systems.

Abstract: The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a ‘Car–Parrinello’ dynamical approach. In this latter, the induced dipoles are calculated at each time step of the dynamics through the dynamics of additional degrees of freedom associated with the dipoles. This method saves computer time and allows to study polarized solvated proteins at a very low CPU cost. The program is written in C-language and runs on LINUX machines. A detailed manual of the code is given. The main features of the package are illustrated taking on examples of proteins in the gas phase or immersed in liquid water. Program summary: Program title: MDVRY Catalogue identifier: AEBY_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBY_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 39 156 No. of bytes in distributed program, including test data, etc.: 277 197 Distribution format: tar.bz2 Programming language: C Computer: Linux machines with FFTW Fourier Transform package installed Operating system: Linux machines, SUSE & RedHat distributions Classification: 3, 16.13, 23 External routines: FFTW (http://www.fftw.org/) Nature of problem: Molecular Dynamics Software package. Solution method: Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are associated to the induced dipoles so that a modified Hamiltonian of the dynamics is written. This allows to calculate the induced dipoles with a very fast ‘Car–Parrinello’ type of dynamics. Running time: The test run provided takes approximately 6 minutes to run. [Copyright &y& Elsevier]