Jesús Hernández-Trujillo

Chemical bonding: From Lewis to atoms in molecules

The Lewis electron pair concept and its role in bonding are recovered in the properties of the electron pair density and in the topology of the Laplacian of the electron density. These properties provide a bridge with the quantum mechanical description of bonding determined by the Feynman, Ehrenfest, and virial theorems, bonding being a consequence of the electrostatic forces acting within a molecular system.

MP2 ab initio calculations of the hexafluorobenzene—benzene and —monofluorobenzene complexes

Interaction energies for the C6F6C6H6 and C6F6C6H5F supermolecules have been investigated through pseudopotential SCF-MP2 calculations. For both systems, a minimum in the interaction energy curve was found. For C6F6C6H6 this is in agreement with experimental evidence for the formation of a complex, while for C6F6C6H5F the calculated interaction energy suggests the existence of this less symmetric complex. Well defined minima were obtained for the interaction energy curves only after the inclusion of electron correlation. However, the difference between the stabilization energies of the two complexes is determined by the electrostatic contribution.

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Quadrupole interactions in pure non-dipolar fluorinated or methylated benzenes and their binary mixtures

Quadrupole–quadrupole interaction energies for benzene (Bn), 1,3,5-trimethylbenzene or mesitylene (M), hexamethylbenzene (HMB), 1,3,5-trifluorobenzene (TFB) and hexafluorobenzene (HFB) and their binary mixtures have been calculated. The equations to obtain these energies, which were previously wrongly identified in terms of the pairwise interactions involved (N. M. D. Brown and F. L. Swinton, J. Chem. Soc., Chem. Commun., 1974, 770), are presented. Three molecular pair orientations were considered: face-to-face, edge-to-edge and mutually perpendicular. It is found that the preferred orientation for the pure components is that where both molecules are mutually perpendicular. For the equimolar mixtures the preferred orientation is determined by the sign of the product of the quadrupole moments of the two components. For the mixtures of HFB with Bn, M or HMB the quadrupole–quadrupole interaction energies are large and the preferred orientation is that where the molecules are oriented face-to-face. For the other mixtures the interaction energies are small and the stable orientation is either face-to-face or mutually perpendicular. The results are in agreement with available solid–liquid phase equilibria and X-ray studies which indicate the existence of 1 : 1 complexes for this type of mixture. It is concluded that quadrupole–quadrupole interactions are responsible for the existence and molecular orientation of such complexes.

Theoretical analysis of hydrogen bonding in catechol–n(H2O) clusters (n = 0…3)

The electronic structure and hydrogen bonding of the stable isomers of catechol and its complexes with one to three water molecules is studied by means of theoretical methods. A conformational analysis based on a simulated annealing search on the potential energy surface of each complex was carried out previous to the quantum chemical energy minimization. Twenty three stable conformers were found including some involving a pi-interaction between the catechol moiety and a water molecule. The topological properties of the electron density reveal the presence of an intramolecular hydrogen bond only in the case of one complex with three water molecules. The infrared spectra of these molecules were computed and compared to available experimental results. An alternative assignment of the experimental vibrational spectrum within the range 3340-3750 cm(-1) of the catechol-3(H(2)O) complex (M. Gerhards, C. Unterberg, and K. Kleinermanns, Phys. Chem. Chem. Phys. 2000, 2, p. 5538) is proposed. The red-shift observed for the stretching vibrational frequency of the catechol hydrogen donor hydroxyl group in the presence of water molecules is rationalized in terms of the properties of the electron distribution and a Darwinian family tree is proposed to classify the diverse structural and energetic characteristics of the stable complexes found.

Application of the additivity of group energies to understand conformational preference: the anomeric effect

The conformational preference in normal and reverse anomeric effects is analyzed by taking advantage of the known additivity and transferability of functional group energies defined by the gradient of the electron density. As the anomeric effect has an energetic origin and every change in the electron density produces an energetic change, an explanation of this phenomenon should be based on the density changes taking place in a conformational equilibrium. The total energy of substituted cyclohexanoids is partitioned into ring and substituent contributions and the preferred conformation is the result of a balance between them. This new alternative approach allows understanding of the anomeric effect in terms of group energy contributions. In general, the most stable conformer in both the anomeric and reverse anomeric effects is that where the ring transfers charge to the heteroatom in the substituent during the process.

Properties of atoms in molecules: Construction of one-density matrix from functional group densities

The demonstrated transferability of functional groups defined as proper open systems within the theory of atoms in molecules is used to iteratively construct a one-electron density matrix P and its derived electron density distribution. The initial guess at the density used in the fitting procedure is obtained from the addition of the density distributions of groups defined in parent molecules by the maximal matching of their interatomic surfaces. The method thus takes advantage of the observation that the “zero-flux” boundary condition defining a proper open system maximizes the transferability of the density distribution of a given group between molecules, one that is accompanied by a paralleling transferability in all of its properties. The construction is subject to the constraints that P be idempotent and normalized. The method is applied to the construction of P for the molecules HCH2|CH2X, with X=CH3, NH2, OH, and F, where the vertical bar denotes the new C–C interatomic surface, the new zero-flux ...

Quantum molecular dynamics of the topological properties of the electron density: charge transfer in H3(+) and LiF.

This paper presents a method to analyze the time evolution of electron density descriptors defined by the quantum theory of atoms in molecules. The wave packet nuclear dynamics was followed solving the time-dependent Schrödinger equation. The time evolution of the nuclear wave packets was combined with the electronic wave functions to follow the time dependence of the average values of topological electron density descriptors. The method was applied to the reactive collision of H(+) + H(2) under different initial conditions and the photodissociation of LiF for either diabatic or adiabatic processes, with emphasis on the information provided by the time evolution of the atomic charges. These examples illustrate how this approach allows for a detailed analysis of the electronic structure in the time domain.

Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective

This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H2 taken as a prototype for a covalent bond, excimer formation of He2 to analyze non‐covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C2H4. The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one‐ and two‐electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states.

Energetic analysis of conjugated hydrocarbons using the interacting quantum atoms method

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clars sextet rules devised for aromatic systems. In addition, the H ⋯ H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms.