Pedro C. Gómez

Variation with the intermolecular distance of properties dependent on the electron density in hydrogen bond dimers

The variation with the intermolecular distance of features in hydrogen bond (HB) dimers dependent on the electron density ρ(r) are studied in four complexes representative of weak/medium HB interactions. Topological properties, energy densities and integrated atomic properties are obtained with ρ(r) of dimers at B3LYP/6-311++G(d,p) optimized structures obtained upon fully relaxing the geometry of monomers. The dependence of A–H⋯B bond properties on intermolecular R(H⋯B) distances allows to characterize the nature of the interaction as monomers move nearer from infinite separation. At long distances the interaction is only electrostatic while for separations about 1 A larger than the equilibrium distance Req, quantum effects arising from ρ(r) begin to dominate. In the immediate neighborhood of Req the interaction is mainly led by the stabilization of the H-donor due in turn to energy lowerings in A and B atoms associated to polarization effects. The mutual penetration of electron densities of donor and acc...

Variation with the intermolecular distance of properties dependent on the electron density in cyclic dimers with two hydrogen bonds

The variation with the intermolecular distance of geometries, energies, and other properties dependent on the electron density ρ(r) are studied in three cyclic dimers linked by two hydrogen bonds: formic acid and formamide homodimers and the heterodimer formamide/formic acid complex. Topological features, energy densities and integrated atomic properties provided by AIM theory are calculated with ρ(r) obtained at B3LYP/6-311++G(d,p) optimized geometries for a number of intermonomer distances covering large separations, equilibrium, and short distances. The variation with these distances of properties studied allows to characterize the nature of the interaction in A–H⋯B (A=N, O and B=O) hydrogen bonds. Whereas at large distances the attraction is purely electrostatic, quantum effects associated with redistributions of ρ(r) mainly around H and B atoms dominate the interaction in the neighborhood of equilibrium. Mutual penetration of the electron densities of these atoms leads to considerable reductions of t...

Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine

Ab initio calculations at the MP2/6‐311++G** level of theory led recently to the identification of 13 stable conformers of gaseous glycine with relative energies within 11 kcal/mol. The stability of every structure depends on subtle intramolecular effects arising from conformational changes. These intramolecular interactions are examined with the tools provided by the Atoms In Molecules (AIM) theory, which allows obtaining a wealth of quantum mechanics information from the molecular electron density ρ(r). The analysis of the topological features of ρ(r) on one side and the atomic properties integrated in the basins defined by the gradient vector field of the density on the other side makes possible to explore the different intramolecular effects in every conformer. The existence of intramolecular hydrogen bonds on some conformers is demonstrated, while the presence of other stabilizing interactions arising from favorable conformations is shown to explain the stability of other structures in the potential energy surface of glycine.

Approximate kinetic energy density for intermolecular regions in hydrogen bond dimers

Abstract In a recent paper, Abramov [Y.A. Abramov, Acta Cryst. A53 (1997) 264] has proposed an approximation to compute the kinetic electron density G( r ) from any electron density ρ( r ) in the form of a truncated gradient expansion. This approach was known to provide accurate estimates of G( r ) at the bond critical points of ρ( r ) . We show that Abramovs approach can be reliably used in spatial intermolecular regions in hydrogen fluoride and water dimers to obtain accurate estimates of the kinetic electron density. The study shows the usefulness of this approximated G( r ) for quantum studies of intermolecular interactions in terms of ρ( r ) .

Variation of geometries and electron properties along proton transfer in strong hydrogen-bond complexes

Proton transfer in hydrogen-bond systems formed by 4-methylimidazole in both neutral and protonated cationic forms and by acetate anion are studied by means of MP26-311++G(d,p) ab initio calculations. These two complexes model the histidine (neutral and protonated)-aspartate diad present in the active sites of enzymes the catalytic mechanism of which involves the formation of strong hydrogen bonds. We investigate the evolution of geometries, natural bond orbital populations of bonds and electron lone pairs, topological descriptors of the electron density, and spatial distributions of the electron localization function along the process N-H...O-->N...H...O-->N...H-O, which represents the stages of the H-transfer. Except for a sudden change in the population of electron lone pairs in N and O at the middle N...H...O stage, all the properties analyzed show a smooth continuous behavior along the covalent --> hydrogen bond transit inherent to the transfer, without any discontinuity that could identify a formation or breaking of the hydrogen bond. This way, the distinction between covalent or hydrogen-bonding features is associated to subtle electron rearrangement at the intermolecular space.

Radial behavior of gradient expansion approximation to atomic Fukui function and shell structure of atoms

An approximation to the Fukui function in atoms recently proposed in the form of a gradient correction to the local density approximation expression is here investigated. The spatial behavior of this function is analyzed, focusing on the gradient correction term. Physical information on the shell structure of atoms is shown to be conveyed by the radial distribution of that term. The analytically modeled densities (AMD) procedure is also implemented, and global atomic hardnesses are calculated with Hartree‐Fock and AMD representations of atomic electron densities. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 488–503, 1998

Ab initio rotational energy levels and internal rotation splittings in protonated acetylene C2H3

The C2H3+ ion has an unusual internal-rotation tunneling degree of freedom in which the three protons rotate around the C2 core with the molecule remaining planar. We have used our semirigid bender Hamiltonian (R. Escribano and P.R. Bunker, J. Mol. Spectry. 122 (1987) 325), with the results of an ab initio calculation of this tunneling potential (R. Lindh et al., Chem. Phys. Letters 139 (1987) 407), to calculate the rotational energy levels and internal-rotation splittings.

A theoretical study on the formation of iodine oxide aggregates and monohydrates

Biotic and abiotic emissions of molecular iodine and iodocarbons from the sea or the ice surface and the intertidal zone to the coastal/polar marine boundary layer lead to the formation of iodine oxides, which subsequently nucleate forming iodine oxide particles (IOPs). Although the link between coastal iodine emissions and ultrafine aerosol bursts is well established, the details of the nucleation mechanism have not yet been elucidated. In this paper, results of a theoretical study of a range of potentially relevant aggregation reactions of different iodine oxides, as well as complexation with water molecules, are reported. Thermochemical properties of these reactions are obtained from high level ab initio correlated calculations including spin-orbit corrections. The results show that the nucleation path most likely proceeds through dimerisation of I2O4. It is also shown that water can hinder gas-to-particle conversion to some extent, although complexation with key iodine oxides does not remove enough of these to stop IOP formation. A consistent picture of this process emerges from the theoretical study presented here and the findings of a new laboratory study reported in the accompanying paper (Gomez Martin et al., 2013).

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates

Monohydrates of halogen monoxides ClO·H2O and BrO·H2O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug‐cc‐pVnZ basis sets ranging from triple‐ up to quintuple‐ζ. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO…HOH hydrogen bond and OX…OH2 halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX…O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the OX…O halogen bond with respect to the O…HO hydrogen bond.

Environmental effects on proton transfer in a strong hydrogen bond dimer: The 4-methyl-imidazole-aspartate case

Proton transfer in hydrogen bond dimers formed by acetate anion plus 4-methyl-imidazole, in both neutral and protonated forms, is studied by means of ab initio correlated calculations at the MP2/6-311++G(d,p) level of theory. These two dimers are selected as systems displaying a short and strong hydrogen bond with possible low barriers to proton transfer, also these systems resemble the dyad formed by histidine aspartate which is present in a variety of enzymes whose catalytic mechanisms involve the formation of short hydrogen bonds in the active site. The purpose of this job is twofold: we focus here on the effect of the polarity of the surrounding medium on the hydrogen bond, and on the other hand we analyse the relevance of the intermonomeric distance for the low barrier to proton transfer between the partners of the dimer. We have carried out an investigation for a number of intermonomeric distances and it was found that polar solvents and short intermonomeric distances lower the barrier, enhancing in that way the proton transfer between neutral imidazole and acetate. However, the binding energy of the dimer does not follow necessarily the same pattern. In the case of protonated imidazole no double well is found at all in the potential energy curve (not even in polar media) and barrierless proton transfer to acetate occurs at the shortest intermonomeric distances.