Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina.

ReaxFF is a computationally efficient model for reactive molecular dynamics simulations that has been applied to a wide variety of chemical systems. When ReaxFF parameters are not yet available for a chemistry of interest, they must be (re)optimized, for which one defines a set of training data that the new ReaxFF parameters should reproduce. ReaxFF training sets typically contain diverse properties with different units, some of which are more abundant (by orders of magnitude) than others.

Comparisons of Molecular Structure Generation Methods Based on Fragment Assemblies and Genetic Graphs.

The use of quantitative structure-property relationships (QSPRs) helps in predicting molecular properties for several decades, while the automatic design of new molecular structures is still emerging. The choice of algorithms to generate molecules is not obvious and is related to several factors such as the desired chemical diversity (according to an initial dataset's content) and the level of construction (the use of atoms, fragments, pattern-based methods). In this paper, we address the problem of molecular structure generation by revisiting two approaches: fragment-based methods (FMs) and genetic-based methods (GMs).

Inverse-QSPR for de novo Design: A Review.

The use of computer tools to solve chemistry-related problems has given rise to a large and increasing number of publications these last decades. This new field of science is now well recognized and labelled Chemoinformatics. Among all chemoinformatics techniques, the use of statistical based approaches for property predictions has been the subject of numerous research reflecting both new developments and many cases of applications.

Simulations of Interfacial Tension of Liquid-Liquid Ternary Mixtures Using Optimized Parametrization for Coarse-Grained Models.

In this work, liquid-liquid systems are studied by means of coarse-grained Monte Carlo simulations (CG-MC) and Dissipative Particle Dynamics (DPD). A methodology is proposed to reproduce liquid-liquid equilibrium (LLE) and to provide variation of interfacial tension (IFT), as a function of the solute concentration. A key step is the parametrization method based on the use of the Flory-Huggins parameter between DPD beads to calculate solute/solvent interactions.

Chemoinformatics at IFP Energies Nouvelles: Applications in the Fields of Energy, Transport, and Environment.

The objective of the present paper is to summarize chemoinformatics based research, and more precisely, the development of quantitative structure property relationships performed at IFP Energies nouvelles (IFPEN) during the last decade. A special focus is proposed on research activities performed in the "Thermodynamics and Molecular Simulation" department, i. e.

Prediction of Alternative Gasoline Sorption in a Semicrystalline Poly(ethylene).

In this work, we first report the acquisition of new experimental data and then the development of quantitative structure-property relationships on the basis of sorption values for neat compounds and up to quinary mixtures of some hydrocarbons, alcohols, and ethers, in a semicrystalline poly(ethylene). Two machine learning methods (i.e.

Surface photografting of acrylic acid on poly(dimethylsiloxane). Experimental and dissipative particle dynamics studies.

This work includes both experimental and theoretical studies of the wetting property changes of water on a surface of poly(dimethylsiloxane) (PDMS) modified with different amounts of acrylic acid (AA). The default surface properties of PDMS were changed from hydrophobic to hydrophilic behavior which was characterized with contact angle measurements by two approaches: (i) experimental tests of samples subjected to a photografting polymerization procedure to obtain a functionalized surface and (ii) DPD (dissipative particle dynamics) simulations which also involve the calculation of sets of repulsive parameters determined following two methods: the use of the "Blends" module in the Materials Studio software and the calculation of cohesive energy density with molecular simulations. Changes of contact angle values observed from both experimental and numerical simulation results provide qualitative and quantitative information on the wetting behavior of photografted surfaces.

Extension of a charged anisotropic united atoms model to polycyclic aromatic compounds.

A new potential model for polycyclic aromatic hydrocarbons has been developed on the basis of a charged anisotropic united atoms (AUA) potential with six AUA force centers and three electrostatic point charges per aromatic ring. Using quantum mechanical calculations, quadrupolar moments of several aromatic molecules were computed and a correlation has been observed that links the magnitude of the point charges with respect to the number of aromatic rings. The Lennard-Jones parameters of quaternary carbon atoms bridging two aromatic rings have been optimized with the minimization of a dimensionless error criterion incorporating various thermodynamic data of naphthalene.

Molecular dynamics study of hydrated imogolite. 2. Structure and dynamics of confined water.

The behaviour of water confined in an imogolite nanotube was studied by means of molecular dynamics simulations. The results of the study show an important difference between the interaction of water molecules with the internal and external surfaces of the nanotube. The analysis of the density profiles of confined molecules, of their spatial organisation, of the size of molecular clusters, of the lifetime of H-bonds in the system and of dynamical characteristics of molecules permits us to qualify the external imogolite surface as hydrophobic, whereas the internal surface reveals a hydrophilic character.