Alberto Vela

Recent advances in planar tetracoordinate carbon chemistry

We summarize our contributions on the quest of new planar tetracoordinate carbon entities (new carbon molecules with exotic chemical structures and strange bonding schemes). We give special emphasis on the rationalization why in this type of molecules the planar configuration is favored over the tetrahedral one. We will concentrate on the latter and will show that molecules containing planar tetracoordinate carbons have a stabilizing system of delocalized π electrons, which shows similar properties as π systems in aromatic molecules.

The Implications of Symmetry of the External Potential on Bond Paths

The concept of the chemical bond is of paramount importance to the modern chemical language. Similar to other unicorns in the chemical world, like aromaticity, reactivity, or covalency, the chemical bond is a fuzzy entity eluding a precise numerical definition. Guided by the leading role played by the electron density in the Hohenberg and Kohn theorems, Bader proposed a way to use this observable to generate lines connecting atoms that generally are very well aligned with common chemical sense. Avoiding the highly controversial issue about the interpretation of the zero flux basins that are obtained from the least action principle as the “atoms” of chemistry, one cannot raise any doubt regarding the existence of the saddle points (critical points) in the region between some nuclei and the corresponding gradient path connecting the nuclei. This is an experimental fact that in the last 25 years has been widely used to gain a deeper and alternative knowledge about the essence of chemical bonding or, paraphrasing Pauling, the nature of the chemical bond. Despite the uncontroversial physical existence of the gradient paths and critical points, their interpretation as direct manifestations of true chemical interactions has been the source of controversy in the chemical community. The set of critical points and gradient paths, the molecular graph, is a beautiful representation of the structure of the electron density but, its identification with genuine chemical concepts (like a chemical bond) is an interpretation, which like all interpretations, has a degree of subjectivity and, consequently, any inference drawn from it should be taken with judicious care. An illustrative example is the interaction between two helium atoms. He2 is a prototype of a van der Waals dimer, that is, the potential-energy surface of He2 is repulsive, except for the van der Waals minimum. In this entity, there are two maxima of the electron density at the position of the nuclei, a (3, 1) critical point in halfway between both centers, and a bond path connecting the maxima. Since a minimum always exists between two maxima, this bond path will survive even if the nuclei are separated by 2 or by 20 . Certainly, the electron-density value at the (3, 1) critical point is negligible in the latter situation. The central question is the following: Is the existence of a bond path a sufficient condition that proves that two atoms are connected by a bond in the chemical sense of the word? To answer this question, we selected a set of molecules where the number of gradient paths terminating at an atom is chemically meaningless. Consider the He@C8H8 complex. [21] This endohedral system with Oh symmetry is a local minimum on the corresponding potential-energy surface. Using B3LYP/6-311++ GACHTUNGTRENNUNG(d,p) calculations, we found eight bond paths that connect each carbon atom to helium (Figure 1, top left). As expected, the He C distances are short (1.480 ) and, consequently, the value of the electron density at the He C (3, 1) critical points is relatively high (0.140 a.u., see Table 1). However, the dissociation energy associated to the reaction He@C8H8!He+C8H8 is negative ( 322.4 kcalmol ), which indicates that the helium–cubane interaction is destabilizing overall. Note that stability is not the decisive point to define a chemical bond, since also in metastable molecules one can find chemical bonds. The situation is stranger when a noble gas (Ng) is confined in the C20H20 cage. Evidently, in this case the cavity is larger than in cubane, allowing the inclusion in silico of heavier noble gas atoms than helium. Experimentally, only the helium complex has been characterized, adopting an Ih symmetry, despite the fact that the energy to put the He atom inside dodecahedrane is 35.5 kcalmol . No calculation is necessary to predict that the number of bond paths [a] E. Cerpa, Prof. G. Merino Facultad de Qu mica Universidad de Guanajuato Noria Alta s/n C.P. 36050, Guanajuato, Gto. (M xico) Fax: (+52) 473-732-0006/-8120 E-mail : gmerino@quijote.ugto.mx [b] Dr. A. Krapp Senter for teoretisk og beregningsorientert kjemi Kjemisk institutt Universitetet i Oslo Postboks 1033 Blindern, 0315 Oslo (Norway) [c] Prof. A. Vela Departamento de Qu mica Centro de Investigaci n y de Estudios Avanzados A. P. 14-740, M xico, D.F., 07000 (M xico)

Troubleshooting time-dependent density-functional theory for photochemical applications: oxirane.

The development of analytic-gradient methodology for excited states within conventional time-dependent density-functional theory (TDDFT) would seem to offer a relatively inexpensive alternative to better established quantum-chemical approaches for the modeling of photochemical reactions. However, even though TDDFT is formally exact, practical calculations involve the use of approximate functional, in particular the TDDFT adiabatic approximation, the use of which in photochemical applications must be further validated. Here, we investigate the prototypical case of the symmetric CC ring opening of oxirane. We demonstrate by direct comparison with the results of high-quality quantum Monte Carlo calculations that, far from being an approximation on TDDFT, the Tamm-Dancoff approximation is a practical necessity for avoiding triplet instabilities and singlet near instabilities, thus helping maintain energetically reasonable excited-state potential energy surfaces during bond breaking. Other difficulties one would encounter in modeling oxirane photodynamics are pointed out.

Nonlocal correlation functional involving the Laplacian of the density

Abstract The gradient-free correlation functional derived in a previous work is extended to a nonlocal scheme beyond the gradient-corrected ones. It involves the Laplacian of the density and the self-consistent (SCF) Kohn-Sham kinetic energy density. Using two additional parameters, the correlation contribution to the binding energy is adjusted to compensate the error from a chosen exchange functional. When combined with the exchange functionals of Becke and Perdew the new scheme gives improved results for the binding energies and geometries of test molecules.

Non-empirical improvement of PBE and its hybrid PBE0 for general description of molecular properties

Imposition of the constraint that, for the hydrogen atom, the exchange energy cancels the Coulomb repulsion energy yields a non-empirical re-parameterization of the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) exchange-correlation energy functional, and of the related PBE hybrid (PBE0). The re-parameterization, which leads to an increase of the gradient contribution to the exchange energy with respect to the original PBE functional, is tested through the calculation of heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies, for some well known test sets designed to validate energy functionals. The results for the re-parameterized PBE GGA, called PBEmol, give substantial improvement over the original PBE in the prediction of the heats of formation, while retaining the quality of the original PBE functional for description of all the other properties considered. The results for the hybrids indicate that, although the PBE0 functional provides a rather good description of these properties, the predictions of the re-parameterized functional, called PBEmolβ0, are, except in the case of the ionization potentials, modestly better. Also, the results for PBEmolβ0 are comparable to those of B3LYP. In particular, the mean absolute error for the bond distance test set is 17% lower than the corresponding error for B3LYP. The re-parameterization for the pure GGA (PBEmol) differs from that for the hybrid (PBEmolβ0), illustrating that improvement at the GGA level of complexity does not necessarily provide the best GGA for use in a hybrid.

Comparison of static polarizabilities of Cun,Nan, and Lin(n⩽9) clusters

This paper presents the first study of static polarizabilities and polarizability anisotropies of copper clusters up to nine atoms calculated in the framework of density functional theory. The calculations were of all-electron type and have been performed by using a finite field approach implemented in the density functional program ALLCHEM. A newly developed first-order field induced copper basis set for density functional calculation was employed. A gradient-corrected exchange-correlation functional has been used. All cluster structures were fully optimized. The calculated polarizabilities of copper clusters are compared with experimental polarizabilities of sodium and lithium clusters. This comparison shows that the size dependency of the static polarizabilities per atom of copper clusters posseses the same trend as that observed in sodium clusters. However, the absolute polarizabilities of the copper clusters are considerably smaller as those of the sodium clusters.

An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfaces

We introduce a method to compute atomic properties according to the “quantum theory of atoms in molecules.” An integration grid in real space is partitioned into subsets, ωi. The subset, ωi, is composed of all grid points contained in the atomic basin, Ωi, so that integration over Ωi is reduced to simple quadrature over the points in ωi. The partition is constructed from deMon2ks atomic center grids by following the steepest ascent path of the density starting from each point in the grid. We also introduce a technique that exploits the cellular nature of the grid to make the algorithm faster. The performance of the method is tested by computing properties of atoms and nonnuclear attractors (energies, charges, dipole, and quadrupole moments) for a set of representative molecules.

Local softness and chemical reactivity of maleimide: nucleophilic addition

Abstract The local softness and the Fukui function of maleimide are determined through a finite differences scheme in order to show the usefulness of these concepts for rationalizing the inherent chemical reactivity of a given molecule. The local softness surface diagram of maleimide indicates that soft nucleophiles interact with the a carbon atoms, whereas hard nucleophiles interact with the carbonyl carbon atoms, in agreement with the experimental evidence.

Chemically controlled self-assembly of [2]pseudorotaxanes based on 1,2-bis(benzimidazolium)ethane cations and 24-crown-8 macrocycles

Cations derived from 1,2-bis(benzimidazolium)ethane can penetrate the cavity of dibenzo-24-crown-8 macrocycles to produce a new family of [2]pseudorotaxanes. These supramolecular structures are held together by a series of charge-assisted hydrogen bonds (+)N-H[dot dot dot]O, ion-dipole and pi-stacking interactions. These new adducts were fully characterised by NMR spectroscopy, ESI mass spectrometry and single-crystal X-ray diffraction. The effect of electron-donating and electron-withdrawing groups on the association constants was also analyzed. Chemical control of the threading/unthreading process was acheived by the alternate addition of acid and base.

Spectroscopic and electronic structure studies of copper(II) binding to His111 in the human prion protein fragment 106-115: evaluating the role of protons and methionine residues.

The prion protein (PrP(C)) is implicated in the spongiform encephalopathies in mammals, and it is known to bind Cu(II) at the N-terminal region. The region around His111 has been proposed to be key for the conversion of normal PrP(C) to its infectious isoform PrP(Sc). The principal aim of this study is to understand the role of protons and methionine residues 109 and 112 in the coordination of Cu(II) to the peptide fragment 106-115 of human PrP, using different spectroscopic techniques (UV-vis absorption, circular dichroism, and electron paramagnetic resonance) in combination with detailed electronic structure calculations. Our study has identified a proton equilibrium with a pK(a) of 7.5 associated with the Cu(II)-PrP(106-115) complex, which is ascribed to the deprotonation of the Met109 amide group, and it converts the site from a 3NO to a 4N equatorial coordination mode. These findings have important implications as they imply that the coordination environment of this Cu binding site at physiological pH is a mixture of two species. This study also establishes that Met109 and Met112 do not participate as equatorial ligands for Cu, and that Met112 is not an essential ligand, while Met109 plays a more important role as a weak axial ligand, particularly for the 3NO coordination mode. A role for Met109 as a highly conserved residue that is important to regulate the protonation state and redox activity of this Cu binding site, which in turn would be important for the aggregation and amyloidogenic properties of the protein, is proposed.