Bertrand Guillot

Bio: Bertrand Guillot is an academic researcher from University of Paris. The author has contributed to research in topics: Absorption spectroscopy & Molecular dynamics. The author has an hindex of 28, co-authored 63 publications receiving 3554 citations. Previous affiliations of Bertrand Guillot include Pierre-and-Marie-Curie University.

A computer simulation study of the liquid–vapor coexistence curve of water

Abstract: The liquid–vapor coexistence curve of a model water (the extended simple point charge model, SPCE) is evaluated by molecular dynamics simulation in the (N,V,E) ensemble. It is shown that the simulated system (N=256 water molecules) is too small to present a spinodal decomposition and, hence, can be described by a classical equation of state whose the critical parameters (Tc=651.7 K, ρc=0.326 g/cm3, and Pc=189 bar) are found to be very close to that of real water (Tc=647.13 K, ρc=0.322 g/cm3, and Pc=220.55 bar). The critical parameters for SPCE water in the thermodynamic limit are deduced from the simulation data employing Wegner type expansions for the order parameter and the coexistence curve diameter; here also the values of the critical parameters (Tc=640 K, ρc=0.29 g/cm3, and Pc=160 bar) are close to that of real water. The temperature dependence of the dielectric constant for water and steam at orthobaric densities is next evaluated between ambient and Tc; the agreement with the experimental data is quite remarkable (e.g., eSPCE=81.0 at 300 K and eSPCE=6. at Tc instead of 78.0 and 5.3, respectively, in real water). The modifications experienced by water’s architecture with the temperature are deduced from the evaluation of the atom–atom correlation functions. It is shown that a structural change occurs in the temperature range 423–473 K. This important reorganization is characterized by a shift of the second shell of neighbors from 4.5 to 5.5 A and the loss of almost all angular correlations beyond the first solvation shell. Moreover, it is observed that the average number of hydrogen bonds per molecule nHB scales with the density all along the saturation curve. In the same way the values of nHB for orthobaric densities seems to follow a law analogous to the law of rectilinear diameter for orthobaric densities.

A molecular dynamics study of the far infrared spectrum of liquid water

Abstract: The far infrared spectrum of liquid water at room temperature is calculated by molecular dynamics simulation over the spectral range 0.5–1000 cm−1. It is shown that the experimental absorption intensity can be reproduced satisfactorily provided that the dipole induced dipole mechanism is conveniently implemented in the calculation and the classical profile corrected for quantum effects. The contribution due to exchange overlap dipoles between O and H atoms is also investigated but its role in the genesis of the far infrared (FIR) spectrum is negligible. Although the dipole induced dipole (DID) mechanism is found to be responsible for the peculiar band shape near 200 cm−1 by revealing the intermolecular oscillations of the hydrogen bond network, no other translational band is detected in the region 10–60 cm−1, a result in contradistinction with data put forward recently. Moreover, it is shown that the absorption spectrum is the seat of various cancellation effects between permanent and induced dipoles, eff...

How to build a better pair potential for water

Abstract: With the objective of improving the effective pair potentials for water, we develop a potential model that employs diffuse charges, in addition to the usual point charges, on the oxygen and hydrogen atoms, to account for charge penetration effects. The potential has better transferability from the liquid to gaseous phases since, unlike many existing models, it does not require an enhanced dipole moment. As a result it accurately reproduces the structural and thermodynamic properties of water over a wide range of conditions. Moreover, by allowing for electronic polarization when evaluating the total dipole moment of the simulated fluid, the model leads to the correct value of the dielectric constant for virtually any state point. At room temperature the calculation produces an average dipole moment of 3.09 D, in accord with recent theoretical and experimental evaluations. This supports the idea that induction effects in water are more important than previously expected.

Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications

Abstract: Approaches, Derivatives and Applications Vasilios Georgakilas,† Michal Otyepka,‡ Athanasios B. Bourlinos,‡ Vimlesh Chandra, Namdong Kim, K. Christian Kemp, Pavel Hobza,‡,§,⊥ Radek Zboril,*,‡ and Kwang S. Kim* †Institute of Materials Science, NCSR “Demokritos”, Ag. Paraskevi Attikis, 15310 Athens, Greece ‡Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo naḿ. 2, 166 10 Prague 6, Czech Republic

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Abstract: Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.

A general purpose model for the condensed phases of water: TIP4P/2005

Abstract: A potential model intended to be a general purpose model for the condensed phases of water is presented. TIP4P/2005 is a rigid four site model which consists of three fixed point charges and one Lennard-Jones center. The parametrization has been based on a fit of the temperature of maximum density (indirectly estimated from the melting point of hexagonal ice), the stability of several ice polymorphs and other commonly used target quantities. The calculated properties include a variety of thermodynamic properties of the liquid and solid phases, the phase diagram involving condensed phases, properties at melting and vaporization, dielectric constant, pair distribution function, and self-diffusion coefficient. These properties cover a temperature range from 123to573K and pressures up to 40000bar. The model gives an impressive performance for this variety of properties and thermodynamic conditions. For example, it gives excellent predictions for the densities at 1bar with a maximum density at 278K and an aver...

Force fields for protein simulations

Abstract: Publisher Summary The chapter focuses on a general description of the force fields that are most commonly used at present, and it gives an indication of the directions of current research that may yield better functions in the near future. After a brief survey of current models, mostly generated during the 1990s, the focus of the chapter is on the general directions the field is taking in developing new models. The most commonly used protein force fields incorporate a relatively simple potential energy function: The emphasis is on the use of continuum methods to model the electrostatic effects of hydration and the introduction of polarizability to model the electronic response to changes in the environment. Some of the history and performance of widely used protein force fields based on an equation on simplest potential energy function or closely related equations are reviewed. The chapter outlines some promising developments that go beyond this, primarily by altering the way electrostatic interactions are treated. The use of atomic multipoles and off-center charge distributions, as well as attempts to incorporate electronic polarizability, are also discussed in the chapter.