Philippe Bopp

THEORETICAL INVESTIGATIONS ON 1,2-ETHANEDIOL : THE PROBLEM OF INTRAMOLECULAR HYDROGEN BONDS

The conformational space of 1,2‐ethanediol is studied on the basis of ab initio and semiempirical calculations. All possible conformers are treated. The relative energies of the conformers are systematically studied using various basis sets up to 6–311 + G(3df, 3pd) in order to perform calculations as accurate as possible within a reasonable amount of computer time. Electron correlation is included using Møller‐Plesset perturbation theory. We propose two methods to evaluate the basis set superposition error associated with the intramolecular hydrogen bond appearing in some of the conformers. The results of semiempirical calculations are compared with these ab initio calculations.

Computer simulation studies of a model system for liquid crystals consisting of semiflexible molecules

A simple steric model of so‐called rfr (rigid–flexible–rigid) molecules is developed. It consists of two rigid spherocylindrical fragments linked by a flexible alkyl chain. Molecular dynamics simulations of 128 model molecules are carried out in a periodic box, and the influence of density and alkyl chain length on the molecular order and the self‐diffusion is studied. Different liquid crystalline phases are found which are stable within the time scale of the simulations. In agreement with experimental results the nematic order parameters and the stability of the phase, as indicated by the location of the isotropic/liquid crystalline phase transition, show an odd–even effect with respect to the number of methylene groups in the alkyl chain. A separation of rigid and flexible fragments is observed leading to smectic liquid crystalline phases.

Molecular dynamics studies of the interface between a model membrane and an aqueous solution.

Molecular Dynamics (MD) computer simulation studies are reported for a system consisting of two model membranes in contact with an aqueous solution. The influence of the membrane on the adjacent liquid is of main interest in the present study. It is therefore attempted to make the system sufficiently large to encompass the entire region between bulk liquid and the membranes. The latter are modeled by two-dimensional arrays of COO- groups with rotational and translational degrees of freedom. The water molecules are represented by the well-tested TIP4P model. The intermolecular potentials are parametrized in terms of Coulomb interactions between partial charges on the molecular frames and empirical, mostly Lennard-Jones (12-6), interactions centered at the atomic positions. A strong layering of the liquid accompanied by an increase in average water density is found in the vicinity of the membrane. The structural perturbation reaches approximately 8 A into the liquid. We discuss the static structure in these layers in terms of atom-atom distance distribution functions and study the average orientation of the water molecule dipoles with respect to the membrane. From the distribution of the ions, we find that less than 50% of the surface charge of the membrane is neutralized by Na+ ions in the first layer above the membrane. A simplified model of the adsorption site of the ion on the membrane is developed from the distance distributions. Finally the hydration of the Na+ in the first adsorbed layer is discussed.

The permeation of methane molecules through silicalite-1 surfaces.

The permeation of methane molecules through the silicalite-1 surfaces with and without silanol groups has been studied by nonequilibrium molecular dynamics computer simulations. A newly fitted intermolecular potential between the methane molecules and the silanol is used. A control volume provides a nearly stationary gas phase close to the membrane. The nonequilibrium process of filling the (initially empty) membrane with methane molecules until saturation is considered, and the surface permeability has been evaluated. It turns out to be strongly influenced by the presence of silanol groups. Additionally it was found that for a large part of the loading process the particle stream into the zeolite membrane was nearly independent upon the deviation from equilibrium. This means that far from equilibrium the decay of this deviation does not follow an exponential law.

Ab initio studies on tetramethylurea and tetramethylthiourea

Abstract Ab initio molecular orbital theory at the HF and MP2 levels was applied to study the structures of tetramethylurea and tetramethylthiourea and to carry out a conformational analysis of these molecules. The calculated structural parameters are in good agreement with the experimental observations and correctly describe the deviations of the molecular geometries from the planar structures. Conformational analysis shows that the rotational motions about the Csp2-N bond are less hindered than the analogous motions in dimethylformamide and dimethylthioformamide. The methyl groups can rotate quite freely around the C-N bond in both the molecules studied here.

Molecular Dynamics Simulations of Aqueous Ionic Solutions

The general principles of Molecular Dynamics (MD) computer simulations are briefly sketched. Models used in simulations of aqueous ionic solutions are reviewed and static and dynamic results obtained from such simulations are discussed and compared with experimental ones.

The Hitchhiker’s guide to molecular dynamics

This lecture aims at advanced (master’s, PhD) students in physics, chemistry, physical chemistry, biochemistry, engineering (and possibly biology) who use, or plan to use, molecular dynamics (MD) computer simulations in the course of their research work. This lecture is, however, neither (or only in a very limited way) a course on the scientific background of this method (quantum mechanics, statistical mechanics, computational methods), nor is it a pragmatics tutorial (‘how-to’ guide) which button to click on some graphical interface or other. We rather aim at pointing out to the aspiring user of any kind of simulation software some of the important choices that must be made as well as some of the problems and pitfalls that he or she may encounter on the way to reliable and meaningful scientific results. This includes a few reminders what not to forget to avoid such mistakes and possibly where to look to correct them if they have, unavoidably, been made.

Molecular Dynamic Simulation of the Interface Aqueous Ionic Solution / Lipid Membrane

The interface between an ionic solution and a membrane, modelled by an ensemble of COO− groups with translational and rotational degrees of freedom, is studied by molecular dynamics (MD) computer simulations. The charged membrane leads to a layering of the ions and the water molecules. Several water layers can be distinguished with structural properties very different from those found in the bulk phase.

The Determination of Vibrational Frequencies in H-Bonded Liquids from Molecular Dynamics Simulations

Molecular Dynamics (MD) computer simulations have become an increasingly important method in the field of liquid studies. In these simulations the atoms and molecules of a chemical system are represented by point masses and rigid bodies moving under the influence of their mutual interactions according to the laws of classical mechanics. The primary input to a simulation is of course the set of potentials (usually called the model) describing the microscopic interactions between the particles in the system. Many such models have been developed in recent years, especially for water and other hydrogen bonded systems.

Lokale Wechselwirkungspotentiale zur Simulation von Wasser und wässrigen Lösungen

Klassisch konnen die hier angesprochenen Monte Carlo- (MC) und Molekular-dynamische- (MD) Simulationsmethoden aus zwei Grunden genannt werden: Zum einen sind sie die altesten Simulationsmethoden in der chemischen Forschung. Sie gehen zuruck auf die Arbeiten von Metropolis und Mitarbeitern [1] sowie von Alder und Wainwright [2] in den funfziger Jahren. Ihre Weiterentwicklung erfolgte parallel zur Entwicklung moderner Grosrechner und waren teilweise auch Ansporn und Motivation zu deren Weiterentwicklung., insbesondere zur Steigerung der Rechengeschwindigkeit.