Fernando Cortés-Guzmán

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.

Intercalation processes of copper complexes in DNA

The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.

Structural Evolution : Mechanism of Olefin Insertion in Hydroformylation Reaction

Hydroformylation is the transformation of an alkene to an aldehyde via the addition of both hydrogen and carbon monoxide. The final aldehyde has one more carbon atom than the precursor alkene. Two isomeric products can result. The regiochemistry of the hydroformylation reaction is believed to be controlled by the olefin insertion step. A reaction mechanism is usually studied by finding the reactants, products, intermediates, and transition states. Alternatively, a chemical reaction can be studied from the redistribution of the electron density along the reaction path connecting the stationary points. The aim of this work is to describe the reaction mechanism of the insertion process by the structural evolution defined by the changes in the electron density during the reaction.

Properties of atoms in electronically excited molecules within the formalism of TDDFT.

The topological analysis of the electron density for electronic excited states under the formalism of the quantum theory of atoms in molecules using time‐dependent density functional theory (TDDFT) is presented. Relaxed electron densities for electronic excited states are computed by solving a Z‐vector equation which is obtained by means of the Sternheimer interchange method. This is in contrast to previous work in which the electron density for excited states is obtained using DFT instead of TDDFT, that is, through the imposition of molecular occupancies in accordance with the electron configuration of the excited state under consideration. Once the electron density of the excited state is computed, its topological characterization and the properties of the atoms in molecules are obtained in the same manner that for the ground state. The analysis of the low‐lying π→π⋆ singlet and triplet vertical excitations of CO and C6H6 are used as representative examples of the application of this methodology. Altogether, it is shown how this procedure provides insights on the changes of the electron density following photoexcitation and it is our hope that it will be useful in the study of different photophysical and photochemical processes.

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.

Preparation of telluro- and selenoalumoxanes under mild conditions.

Syntheses of the heavy chalcogen-containing alumoxanes [(Me)LAl(SeH)]2(μ-O) (4) and ((Me)LAl)2(μ-Te)(μ-O) (7) were accomplished by the reaction of ((Me)LAlH)2(μ-O) (2; (Me)L = HC[(CMe)N(2,4,6-Me3C6H2)]2(-)) with either red selenium or metallic tellurium. The aluminum hydrogenselenide [(Me)LAl(SeH)]2(μ-Se) (3) was also prepared from the reaction of red selenium and (Me)LAlH2 (1). All compounds were characterized by spectroscopic methods and X-ray diffraction studies. Density functional theory calculations were performed on 4 and 7.

The role of induced current density in Steroelectronic effects: Perlin effect

The normal and reverse Perlin effect is usually explained by the redistribution of electron density produced by hyperconjugative mechanisms, which increases the electron population within axial or equatorial proton in normal or reverse effect, respectively. Here an alternative explanation for the Perlin effect is presented on the basis of the topology of the induced current density, which directly determines the nuclear magnetic shielding. Current densities around the CH bond critical point and intra‐atomic and interatomic contributions to the magnetic shielding explain the observed Perlin effect. The balance between intra‐atomic and interatomic contributions determines the difference in the total atomic shielding. Normal Perlin effect is dominated by intra‐atomic part, whereas reverse effect is dominated by interatomic contribution.

Valence Shell Charge Concentration (VSCC) Evolution: A Tool to Investigate the Transformations within a VSCC Throughout a Chemical Reaction

Theoretical studies about reaction mechanisms are usually limited to the determination of the energetic paths that connect reactants, transition states, and products. Recently, our group proposed the structural evolution, which has provided insights about the molecular structure changes occurring along a reaction path. Structural evolution may be defined as the development of a chemical reaction system across the partitioning of the nuclear configuration space into a finite number of structural regions defined on account of the topology of a scalar field, e.g., the electron density. In this paper, we present a tool to investigate within the framework of the Quantum Theory of Atoms in Molecules the evolvement of the Valence Shell Charge Concentration, the VSCC evolution, which is the description of the changes of electron density concentrations and depletions around the bonding area of an atom. The VSCC evolution provides supplementary information to the structural evolution because it allows the analysis of valence shells within a structural region, i.e., a subset of R(Q) with the same connectivity among the atoms forming a molecule. This new approach constitutes also a complement to the Valence-Shell Electron Pair Repulsion (VSEPR) model because it gives an account of the adjustments of electron pairs in the valence shell of an atom across a chemical reaction. The insertion reaction in the hydroformylation reaction of ethylene, the reduction of cyclohexanone with lithium aluminum hydride, the oxidation of methanol with chlorochromate, and the bimolecular nucleophilic substitution of CH(3)F with F(-) are used as representatives examples of the application of the VSCC evolution. Overall, this paper shows how the VSCC evolution through an analysis of the modifications of local charge concentrations and depletions in individual steps of a chemical reaction gives new insights about these processes.

Is hexachloro-cyclo-triphosphazene aromatic? Evidence from experimental charge density analysis.

Experimental charge density studies of hexachloro-cyclo-triphosphazene (1) and the boat conformation of octachloro-cyclo-tetraphosphazene (2 a) were performed to unambiguously describe the origin of the electron delocalization in the P3 N3 ring in 1. The obtained results were compared to DFT studies in the solid state and the gas phase. Electron density analysis revealed a highly polarized nature of the P-N bonds and a modular structure of the P3 N3 and P4 N4 rings, which can be separated into independent Cl2 PN units with a perfect transferability between the compounds. Further analysis of the source function experimentally proves the presence of negative hyperconjugation involving both out-of-plane and in-plane nitrogen electrons as well as electrons of the chlorine atoms. Finally, these results discard the presence of pseudoaromatic delocalization in the nearly planar P3 N3 ring.

The Role of the DNA Backbone in Minor‐Groove Ligand Binding

Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.