Luis Rincón

Hydrogen bond cooperativity and electron delocalization in hydrogen fluoride clusters

We investigate the energetic, structural, electronic and thermodynamics properties of hydrogen fluoride cluster, (HF)n, in the range n=2–8, by ab initio methods and density functional theory (DFT). The ab initio methods chosen were Hartree–Fock (RHF) and second-order Mo/ller–Plesset perturbation theory (MP2). The DFT calculations were based on Becke’s hybrid functional and the Lee–Yang–Parr correlation functional (B3LYP). We found that symmetric cyclic clusters are the most stable structure, and that large cooperative effects, particularly from trimer to tetramer are present, in binding energy, and hydrogen bond distance. An analysis of the topology of the electron density reveals a linear correlation between the binding energy per hydrogen bond and the density at the hydrogen bond critical point and the Cioslowski covalent bond order. Based on these correlations, hydrogen bond cooperativity is associated with the electronic delocalization between monomers units. Analysis of the thermodynamics properties ...

Molecular Mechanism for the Denaturation of Proteins by Urea

Understanding protein-solute interactions is one of the sizable challenges of protein chemistry; therefore, numerous experimental studies have attempted to explain the mechanism by which proteins unfold in aqueous urea solutions. On the basis of kinetic evidence at low urea concentrations, (1)H NMR spectroscopic analysis, and molecular orbital calculations, we propose a mechanistic model for the denaturation of RNase A in urea. Our results support a direct interaction between urea and protonated histidine as the initial step for protein inactivation followed by hydrogen bond formation with polar residues, and the breaking of hydrophobic collapse as the final steps for protein denaturation. With the proposed model, we can rationalize apparently conflicting results in the literature about the mechanism of protein denaturation with urea.

Is the Hammett's constant free of steric effects?

In this work, we have explored the validity of the hypotheses on which rest the Hammetts approach to quantify the substituent effect on a reaction center, by applying two DFT energy decomposition schemes. This is performed by studying the change in the total electronic energy, ΔΔE, associated with a proton transfer isodesmic equilibrium. For this reaction, two sets of substituted benzoic acids and their corresponding benzoate anions have been considered. One of these sets contains para- and meta-substitutions, whereas the other one includes ortho-substituted benzoic acids. For each case, the gas phase change in the total electronic energy has been calculated, and two DFT energy decomposition schemes have been applied. The experimental σ(X) was found to be nearly proportional to the computed ΔΔE. The results for the para- and meta-substituted benzoic acids lead to the conclusion that it is possible to treat separately and, in an additive manner, the electrostatic and steric contributions; and also that the Hammett constant depends mainly on the electronic contributions to the free energy, while the steric contribution is negligible. However, the results for the ortho-substituted cases lead to the conclusion, as was assumed by Hammett, that there are significant qualitative differences between the effects on a reaction site of substituents in the meta- and para-positions and those in the ortho-position.

The role of H-bonding in the structure of the 4-piperidinecarboxylic acid monohydrate

AbstractIn this work we have investigated the hydrogen bond scheme of 4-piperidinecarboxylic (isonipecotic) acid by means of X-raydiffraction, NMR spectroscopy and semi-empirical calculations. The 4-piperidinecarboxylic acid displays a three-dimensionalassembly of hydrogen bonds. Hence, infinite chains of amino acid molecules linked by amino–carboxylate intermolecularhydrogen bonds run parallel to the b and c axes; additionally, chains of amino acid molecules intercalated with water moleculesheld together by water–carboxylate hydrogen bonds run parallel to the a axis. The theoretical calculations show largecooperative effects for the first of the amino acid chains mentioned above, which is manifested as shortening on the amino–carboxylate hydrogen bond distances and decreasing of the hydrogen bond enthalpies per monomer of the hydrogen bondedclusters, with increment of monomers in the chain. q 2002 Elsevier Science B.V. All rights reserved. Keywords: Piperidinecarboxylic acids; Hydrogen bond; X-ray structure; Semi-empirical calculations

On the energetic and structure of 2-piperidinic acid

In this paper we investigate, by means of ab initio (RHF) and density functional theory calculations, the energetic, electronic and structural properties of the 2-piperidinic acid, in gas phase and explicitly interacting with a number of water molecules. We find that two water molecules, placed in the vicinity of the amino acid, are needed in order to stabilize the zwitterionic structure. These two water molecules and the amino acid form a cyclic structure that maximizes the hydrogen bond cooperativity. These results are compared with the crystal structure of the 2-piperidinic acid.

Identification of Active Sites of Biomolecules. 1. Methyl-α-mannopyranoside and FeIII

Car-Parrinello molecular dynamics (CPMD) simulations, DFT chemical reactivity index calculations, and mass spectrometric measurements are combined in an integrated effort to elucidate the details of the coordination of a transition-metal ion to a carbohydrate. The impact of the interaction with the FeIII ion on the glycosidic linkage conformation of methyl-alpha-d-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that FeIII interacts with specific hydroxyl oxygen atoms of the carbohydrate, affecting the ground state carbohydrate conformation. These conformational details are discussed in terms of a set of supporting experiments involving electrospray ionization mass spectrometry, and CPMD simulations clearly indicate that the specific conformational preference is due to intramolecular hydrogen bonding. Classical MD simulations proved insensitive to these important chemical properties. Thus, we demonstrate the importance of chemical reactivity calculations and CPMD simulations in predicting the active sites of biological molecules toward metal cations.

Electron density, exchange-correlation density, and bond characterization from the perspective of the valence-bond theory. II. Numerical results

In this work we have analyzed the bond character of a series of representative diatomic molecules, using valence bond and the atoms in molecules points of view. This is done using generalized valence-bond calculations. We have also employed more exigent levels, as configuration interaction with single and double excitations and complete active space self-consistent field calculations, in order to validate the generalized valence-bond results. We have explored the possibility that the known delocalization index, and a parameter that measures the excess or defect population within a given atomic basin, can be considered as indicators of the character of bond interaction. We conclude that for a proper description of the bond character, the global behavior of both the charge and two-electron densities should be considered.

Electron density, exchange-correlation density, and bond characterization from the perspective of the valence-bond theory. I. Two simple analytical cases

In this work, using a valence-bond wave function we obtain analytical expressions for the first- and second-order reduced density matrices of two simple, but quite representative, cases of diatomic molecular systems, namely, H2 and LiH. A detailed study of their exchange-correlation density is performed for both equilibrium and nonequilibrium internuclear distances, discriminating the parallel- and antiparallel-spin contributions. The results show that the behavior of the exchange-correlation density clearly changes with the character of the bond, making it possible to obtain a good deal of information regarding the type of the bond interaction.

Basis set and correlation effects in configuration analysis of reactive systems

A methodology for the configuration analysis of multi-configurational wave-functions of a closed-shell system is presented. The molecular system is partitioned in interacting fragments, the molecular orbitals are expanded in fragment orbitals and each Slater determinant is expanded in localized reactant electronic structures. Finally, to reduce the number of relevant coefficients, a transformation of orbitals is performed. The main advantage of employing configuration analysis lays in its simplicity and compactness, specially when extended basis sets are used. As a test, the wave-function at the transition state for some nucleophilic substitution reactions is analyzed. q 2000 Elsevier Science B.V. All rights reserved.

Haptotropic rearrangements in heterocycles–MLn complexes. I. [Thiophene–Rh(PH3)3]+

Abstract A theoretical analysis of the haptotropic rearrangements involving thiophene and [Rh(PH3)3]+ is presented. This haptotropic rearrangement is involved in the C–S bond activation of thiophene by d8-ML3 fragments. In this study, two theory levels, the second order Moller–Plesset perturbation theory (MP2) and density-functional theory (DFT-B3LYP), are employed. The pathway discussed in this paper connects an η4 coordination mode with an η3 one. The results suggest that for the fragment studied in this work, an η3 precursor of the C–S cleavage is preferred over the other one proposed in the literature.