Manuel F. Ruiz-López

Ab initio SCF calculations on electrostatically solvated molecules using a deformable three axes ellipsoidal cavity

The analytical expression of the free energy of solvation of a molecule interacting with a dielectric continuum through a three axes ellipsoidal cavity is used to derive the SCF equations of such a solvated molecule. In this paper, the shape of the cavity is defined after the principal values of the electronic polarizability tensor. Applied to two sets of rotational isomers (trans and gauche 1,2 difluoroethane, and E and Z N methyl formamide), this method confirms that the electronic structure, the molecular geometry, and the equilibrium constant are influenced by the solvent. The energy of solvation depends strongly on the shape of the cavity although the electronic structure appears to be less influenced by a modification of the geometrical characteristics of the boundary surface at constant volume of cavity. Therefore, the computation of the electronic wave function of a molecule interacting with a solvent by electrostatic and induction forces appears to be quite feasible.

A COUPLED DENSITY FUNCTIONAL-MOLECULAR MECHANICS MONTE CARLO SIMULATION METHOD : THE WATER MOLECULE IN LIQUID WATER

A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solutes electronic distribution and of its fluctuations. We present the results for isothermal‐isobaric constant‐NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double‐zeta quality basis set with polarization orbitals and nonlocal exchange‐correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom‐atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed.

MOLECULAR DYNAMICS SIMULATIONS OF ELEMENTARY CHEMICAL PROCESSES IN LIQUID WATER USING COMBINED DENSITY FUNCTIONAL AND MOLECULAR MECHANICS POTENTIALS. I. PROTON TRANSFER IN STRONGLY H-BONDED COMPLEXES

The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional translation and reorientation of water molecules in water. The proton transfer takes place in 20–30 fs whereas the solvent response is delayed by about 50 fs. Therefore, the reaction occurs in an essentially frozen-solvent configuration. In principle, this would produce a barrier increase with respect to the equilibrium react...

Liquid state quantum chemistry : A cavity model

Abstract A cavity model for quantum chemical calculations on physically solvated molecules is described. The cavity is defined by a surface on which the electronic contribution to the electrostatic potential is constant and the value of this quantity is fixed by the volume of the cavity which is equal to the molecular volume in the liquid. The solvent is represented by its static dielectric constant. Although the thermodynamic quantities computed with this model are strongly dependent on the shape of the cavity, the electronic structure can be obtained with a good accuracy by approximating the surface by an ellipsoid which allows an analytical calculation of the electrostatic term and even the dispersion term of the interaction free energy. A general scheme is proposed for a liquid state quantum chemistry.

Electrostatic component of solvation: Comparison of SCRF continuum models

We report a systematic comparison of the electrostatic contributions to the free energy of solvation from three different kinds of quantum mechanical self‐consistent reaction field (SCRF) methods. We also compare the liquid‐phase dipole moments as a measure of the solutes response to the reaction field of the solvent. In particular, we compare these quantities for the generalized Born model as implemented in the SM5.42R method, the multipolar expansion model developed at Nancy, and the MST version of the polarizable continuum model. All calculations are carried out at the HF/6‐31G(d) level. The effects of various choices of solute cavities and representations of the charge density are examined. The test set consists of 18 molecules containing prototypical polar groups, and three different values of the dielectric permittivity are considered.

Theoretical Kinetic Study of Thermal Unimolecular Decomposition of Cyclic Alkyl Radicals

Whereas many studies have been reported on the reactions of aliphatic hydrocarbons, the chemistry of cyclic hydrocarbons has not been explored extensively. In the present work, a theoretical study of the gas-phase unimolecular decomposition of cyclic alkyl radicals was performed by means of quantum chemical calculations at the CBS-QB3 level of theory. Energy barriers and high-pressure-limit rate constants were calculated systematically. Thermochemical data were obtained from isodesmic reactions, and the contribution of hindered rotors was taken into account. Classical transition state theory was used to calculate rate constants. The effect of tunneling was taken into account in the case of CH bond breaking. Three-parameter Arrhenius expressions were derived in the temperature range of 500-2000 K at atmospheric pressure, and the CC and CH bond breaking reactions were studied for cyclic alkyl radicals with a ring size ranging from three to seven carbon atoms, with and without a lateral alkyl chain. For the ring-opening reactions, the results clearly show an increase of the activation energy as the pi bond is being formed in the ring (endo ring opening) in contrast to the cases in which the pi bond is formed on the side chain (exo ring opening). These results are supported by analyses of the electronic charge density that were performed with Atoms in Molecules (AIM) theory. For all cycloalkyl radicals considered, CH bond breaking exhibits larger activation energies than CC bond breaking, except for cyclopentyl for which the ring-opening and H-loss reactions are competitive over the range of temperatures studied. The theoretical results compare rather well with the experimental data available in the literature. Evans-Polanyi correlations for CC and CH beta-scissions in alkyl and cycloalkyl free radicals were derived. The results highlight two different types of behavior depending on the strain energy in the reactant.

Deamidation of Asparagine Residues : Direct Hydrolysis versus Succinimide-Mediated Deamidation Mechanisms

Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been carried out at the density functional level (B3LYP/6-31+G**). Comparisons of free energy profiles show that the most favorable reaction mechanism goes through formation of a succinimide intermediate and involves tautomerization of the asparagine amide to the corresponding imidic acid as the initial reaction step. Another striking result is that direct water-assisted hydrolysis is competitive with the succinimide-mediated deamidation routes even in the absence of acid or base catalysis. The rate-determining step for the formation of the succinimide intermediate is cyclization, regardless of the mechanism. The rate-determining step for the complete deamidation is the hydrolysis of the succinimide intermediate. These results allow clarification of some well-known facts, such as the isolation of succinimide or the absence of iso-Asp among the reaction products observed in some experiments.

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water.

Improvement of the modeling of the low-temperature oxidation of n-butane: study of the primary reactions.

This paper revisits the primary reactions involved in the oxidation of n-butane from low to intermediate temperatures (550-800 K) including the negative temperature coefficient (NTC) zone. A model that was automatically generated is used as a starting point and a large number of thermochemical and kinetic data are then re-estimated. The kinetic data of the isomerization of alkylperoxy radicals giving (•)QOOH radicals and the subsequent decomposition to give cyclic ethers has been calculated at the CBS-QB3 level of theory. The newly obtained model allows a satisfactory prediction of experimental data recently obtained in a jet-stirred reactor and in rapid compression machines. A considerable improvement of the prediction of the selectivity of cyclic ethers is especially obtained compared to previous models. Linear and global sensitivity analyses have been performed to better understand which reactions are of influence in the NTC zone.

Basic ideas for the correction of semiempirical methods describing H-bonded systems

Abstract In this Letter, we show how semiempirical methods may be improved to describe hydrogen-bonded systems and proton transfer reactions. The approach consists in a redefinition of the core–core interaction terms that, as previously shown, are at the origin of spurious artifacts in standard methods. The parameterization of the new core–core functions is done using ab initio data of the intermolecular potential energy surfaces (PESs), which permits reaching the correct behavior at short and long interatomic distances. Here we report the parameters for O–O, O–H and H–H interactions. Extension to other atom pairs seems feasible, so the development of a semiempirical method adapted to the study of intermolecular interactions might be envisaged.