Alejandro Toro-Labbé

Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies

AbstractWe describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules. FigureCalculated electrostatic potential (left) and average local ionization energy (right) on the molecular surface of Tetryl. Yellow and black circles indicate the positions of the local minima and maxima, respectively.

An electrostatic interaction correction for improved crystal density prediction

Recent work by others has shown that the densities of C,H,N,O molecular crystals are, in many instances, given quite well by the formula M/Vm, in which M is the molecular mass and Vm is the volume of the isolated gas phase molecule that is enclosed by the 0.001 au contour of its electronic density. About 41% of the predictions were in error by less than 0.030 g/cm3, and 63% by less than 0.050 g/cm3. However, this leaves more than one-third of the compounds with errors greater than 0.050 g/cm3, or in some instances, 0.100 g/cm3. This may indicate that intermolecular interactions within the crystal are not being adequately taken into account in these cases. Accordingly, the effectiveness of including a second term that reflects the strengths, variabilities and degree of balance of the positive and negative electrostatic potentials computed on the surfaces of the isolated molecules, has been included. The database was selected such that half of the densities predicted by M/Vm had errors larger than 0.050 g/cm3. The introduction of the electrostatic interaction correction produced a marked improvement. Overall, 78% of the predictions are within 0.050 g/cm3 of experiment, with 50% within 0.030 g/cm3. Among those that originally all had errors larger than 0.050 g/cm3, 67% are now less. The reasons for the better performance of the dual-variable formula are analysed.

Characterization of copper clusters through the use of density functional theory reactivity descriptors

In this paper we study nine neutral copper clusters through the theoretical characterization of their molecular structures, binding energy, electronic properties, and reactivity descriptors. Geometry optimization and vibrational analysis were performed using density functional theory calculations with a hybrid functional combined with effective core potentials. It is shown that reactivity descriptors combined with reactivity principles like the minimum polarizability and maximum hardness are operative for characterizing and rationalizing the electronic properties of copper clusters.

A new perspective on chemical and physical processes: the reaction force

The reaction force F(R) of a chemical or physical process is the negative derivative of the systems potential energy V(R) along the reaction coordinate. The features of F(R) – its maxima, minima and zeroes – divide the process into well-defined stages which can, in general, be characterized in terms of changes in structural and/or electronic properties. This has been demonstrated for bond dissociation/formation and for reactions that have activation barriers in both forward and reverse directions. An important aspect of the reaction force is that it naturally and unambiguously divides activation energies into two components, one corresponding to the preparative structural stage of the process and the other to the first phase of the transition to products. It is shown how this can help to elucidate the effect of a solvent or a catalyst upon an activation barrier.

Density-functional theory (hyper)polarizabilities of push-pull π-conjugated systems: Treatment of exact exchange and role of correlation

The performance of the optimized effective potential procedure for exact exchange in calculating static electric-field response properties of push-pull pi-conjugated systems has been studied, with an emphasis on NO2-(CH=CH)n-NH2 chains. Good agreement with Hartree-Fock dipole moments and (hyper)polarizabilities is obtained; particularly noteworthy is the chain length dependence for beta/n. Thus, the problem that conventional density-functional theory functionals dramatically overestimate these properties is largely solved, although there remains a significant correlation contribution that cannot be accounted for with current correlation functionals.

Comparative study of the electrocatalytic activity of cobalt phthalocyanine and cobalt naphthalocyanine for the reduction of oxygen and the oxidation of hydrazine

Abstract Cobalt phthalocyanine (CoPc) and cobalt naphthalocyanine (CoNPc) exhibit different redox and electronic properties. Redox processes on CoPc are more reversible than on CoNPc. The pH dependence of those processes is also different for these complexes, which could indicate that in the case of CoNPc, the redox couples observed involve the macrocyclic ligand and not the metal as with CoPc. This seems to explain the different redox properties and kinetics for O2 reduction and N2H4 oxidation of these two macrocyclics. In this study we compare the electrocatalytic activity of these two phthalocyanines, adsorbed on glassy carbon, for the electrochemical reduction of O2 and for the oxidation of hydrazine.

The reaction force and the transition region of a reaction

The reaction force F(R) and the position-dependent reaction force constant κF(R) are defined by F(R)=-∂V(R)/∂R and κ(R)=∂2V(R)/∂R2, where V(R) is the potential energy of a reacting system along a coordinate R. The minima and maxima of F(R) provide a natural division of the process into several regions. Those in which F(R) is increasing are where the most dramatic changes in electronic properties take place, and where the system goes from activated reactants (at the force minimum) to activated products (at the force maximum). κ(R) is negative throughout such a region. We summarize evidence supporting the idea that a reaction should be viewed as going through a transition region rather than through a single point transition state. A similar conclusion has come out of transition state spectroscopy. We describe this region as a chemically-active, or electronically-intensive, stage of the reaction, while the ones that precede and follow it are structurally-intensive. Finally, we briefly address the time dependence of the reaction force and the reaction force constant.

The reaction force : Three key points along an intrinsic reaction coordinate

The concept of the reaction force is presented and discussed in detail. For typical processes with energy barriers, it has a universal form which defines three key points along an intrinsic reaction coordinate: the force minimum, zero and maximum. We suggest that the resulting four zones be interpreted as involving preparation of reactants in the first, transition to products in the second and third, and relaxation in the fourth. This general picture is supported by the distinctive patterns of the variations in relevant electronic properties. Two important points that are brought out by the reaction force are that (a) the traditional activation energy comprises two separate contributions, and (b) the transition state corresponds to a balance between the driving and the retarding forces.

Reaction electronic flux: a new concept to get insights into reaction mechanisms. Study of model symmetric nucleophilic substitutions.

The present work is focused on studying chlorine and fluorine identity SN2 substitutions on a methyl center, within the framework of the newly introduced reaction electronic flux J(xi), that allows one to identify charge transfer and polarization mechanisms that take place along the reaction coordinate. The main results concern the discovery of different charge transfer mechanism, despite both reactions have the same energetic pattern with simultaneous bond breaking and formation. It turns out that the chlorine substitution is mainly driven by polarization effects and characterized by through bond interactions while intermolecular charge transfer dominates the fluorine exchange reaction, that is characterized by through space interactions.

Designing 3-D molecular stars.

We have explored in detail the potential energy surfaces of the Si(5)Li(n)(5-6) (n = 5-7) systems. We found that it is feasible to design three-dimensional star-like silicon structures using the appropriate ligands. The global minimum structure for Si(5)Li(7)(+) has a perfect seven-peak star-like structure. The title compounds comprise, essentially, the Si(5)(6-) ring interacting with lithium cations. The ionic character of the Si-Li interactions induces the formation of a bridged structure. Concomitantly, our calculations show that the reduction of the Pauli repulsion and the maximization of the orbital contribution are also significant for the star-like structure formation. Additionally, the MO analysis of the systems suggests that the role of the lithium atoms is to provide the precise number of electrons to the central Si(5) unit. This is confirmed by the magnetic properties, which show that electron delocalization enhances the stability of the star-like structures proposed here.