F. Javier Torres

A theoretical study of the conformational preference of alkyl- and aryl-substituted pyrogallol[4]arenes and evidence of the accumulation of negative electrostatic potential within the cavity of their rccc conformers

We report a theoretical study of the structural and electronic properties of the rccc and rctt conformers of several pyrogallol[4]arenes, R-Pyg[4]arenes (i.e. R = fluoroethyl, methyl, t-butyl, phenyl, tolyl and p-fluorophenyl) carried out by employing the HF-DFT hybrid B3LYP functional. Comparison of the B3LYP energies of the two stereoisomers showed that the rccc conformer is more stable than its rctt counterpart for all the derivatives considered. However, calculations made with the double-hybrid Grimmes B97D functional confirmed the experimental observation that the relative stability depends on the type of the R substituents. These results clearly suggest that the B97D functional together with large enough basis sets (i.e. split-valence plus polarisation and diffuse functions) is sufficiently accurate for the purpose of describing the conformational features of these compounds. Computed electrostatic potential maps of the rccc of the different R-Pyg[4]arenes showed that a negative potential is present within the cavity of these compounds. In addition, it is observed that the size of this negative electrostatic potential depends on the electron-donating or electron-withdrawing character of the R substituents.

Generalized Molecular Descriptors Derived From Event-Based Discrete Derivative

In the present study, a generalized approach for molecular structure characterization is introduced, based on the relation frequency matrix (F) representation of the molecular graph and the subsequent calculation of the corresponding discrete derivative (finite difference) over a pair of elements (atoms). In earlier publications (22- 24), an unique event, named connected subgraphs, (based on the Kier-Halls subgraphs) was systematically employed for the computation of the matrix F. The present report is a generalization of this notion, in which eleven additional events are introduced, classified in three categories, namely, topological (terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sachs subgraphs), fingerprints (MACCs, E-state and substructure fingerprints) and atomic contributions (Ghose and Crippen atom-types for hydrophobicity and refractivity) for F generation. The events are intended to capture diverse information by the generation or search of different kinds of substructures from the graph representation of a molecule. The discrete derivative over duplex atom relations are calculated for each event, and the resulting derivatives, local vertex invariants (LOVIs) are finally obtained. These LOVIs are subsequently employed as the basis for the calculation of global and local indices over groups of atoms (heteroatoms, halogens, methyl carbons, etc.), by using norms, means, statistics and classical algorithms as aggregator (fusion) operators. These indices were implemented in our house software DIVATI (Derivative Type Indices, a new module of TOMOCOMDCARDD system). DIVATI provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http: //www.tomocomd.com. Factor analysis shows that the presented events are rather orthogonal and collect diverse information about the chemical structure. Finally, QSPR models were built to describe the logP and logK of 34 furylethylenes derivatives using the eleven events. Generally, the equations obtained according to these events showed high correlations, with the Sachs sub-graphs and Multiplicity events showing the best behavior in the description of logK (Q2 LOO value of 99.06%) and logP (Q2 LOO value of 98.1 %), respectively. These results show that these new eventbased indices constitute a powerful approach for chemoinformatics studies.

Is the Pauli exclusion principle the origin of electron localisation

ABSTRACT In this work, we inquire into the origins of the electron localisation as obtained from the information content of the same-spin pair density, γσ, σ(r2∣r1). To this end, we consider systems of non-interacting and interacting identical Fermions contained in two simple 1D potential models: (1) an infinite potential well and (2) the Kronig–Penney periodic potential. The interparticle interaction is considered through the Hartree–Fock approximation as well as the configuration interaction expansion. Morover, the electron localisation is described through the Kullback–Leibler divergence between γσ, σ(r2∣r1) and its associated marginal probability. The results show that, as long as the adopted method properly includes the Pauli principle, the electronic localisation depends only modestly on the interparticle interaction. In view of the latter, one may conclude that the Pauli principle is the main responsible for the electron localisation.

On the separation of the information content of the Fermi and Coulomb holes and their influence on the electronic properties of molecular systems

ABSTRACT In this paper, two information-based functions are employed as a real space measure of the Fermi and Coulomb holes for same-spin electrons. The first one is the information content of the Exchange-Correlation hole, calculated from the Kullback–Leibler divergence of the same-spin conditional pair density respect to the marginal probability (). As reported previously, , can be used to reveal the regions of the space associated to the classical electron pair model. Here, correlated wave-functions, such as CISD, MP2, and CCSD, are considered for the calculation of . This is achieved by introducing an approximated method based on employing natural orbitals and their occupancy numbers. In addition to , in this work we propose a measure of the information content of the same-spin correlation hole, which is computed in terms of the Kullback–Leibler divergence of a correlated same-spin conditional pair density respect to the uncorrelated Hartree–Fock pair density (). The proposed methodology is discussed in the light of the result derived from noble gas atoms, the molecule and some non-covalently bonded systems. GRAPHICAL ABSTRACT

Understanding the role of Zn2+ in the hydrolysis of glycylserine: a mechanistic study by using density functional theory

ABSTRACT The hydrolysis mechanism of glycylserine in the presence of Zn2+ was theoretically studied by means of density functional theory calculations. Two possible reaction mechanisms are proposed for the hydrolysis reaction: (1) the first one involves a stepwise reaction with an initial attack of the serine –OH to the amide carbonyl group through a general base catalysis of a water molecule, which undergoes to a proton transfer to the carboxylate group to give a cyclic intermediate. Its further rearrangement finally forms an ester that hydrolyses to yield products. (2) The second mechanism involves a general base catalysis by the carboxylate group for the water attack to the amide carbonyl group to generate a tetrahedral intermediate. Upon comparison of both mechanisms, it is observed that the former is favoured; furthermore, its first step is the rate-limiting step in a bicyclic asynchronous transition state with evolution of 86% in C(1)–O(2) bond. The crucial role of Zn2+ in this hydrolysis process can be rationalised in terms of the inductive effect and the formation of a rigid structure that increases the electrophilicity of the amide carbonyl group. The calculations presented in this report are in good agreement with reported values for the activation barrier.