Doris Guerra

Structural Characterization of the (Methanol)4 Potential Energy Surface

In this paper, we report the geometries and properties of the structural isomers obtained from a random walk of the potential energy surface (PES) of the methanol tetramer. Thirty-three structures were obtained after B3LYP/6-31+g* optimization of 94 candidate structures generated from a stochastic search of the PM3 conformational space. The random search was carried out using a recently proposed modified Metropolis acceptance test in the simulated annealing (SA) procedure. Corrections for the basis set superposition error (BSSE) show improvements on the binding energies of the clusters in an average of approximately 2.0 kcal/mol, while geometries are predicted to be less sensitive to BSSE corrections. MP2/aug-cc-pvdz calculations on representative structures did not change the geometries but predicted better binding energies. Highly correlated CCSD(T) energies were calculated on the B3LYP and MP2 stationary points and used to establish relative stabilities. We report several new conformations and group the structures into six distinct geometrical motifs. Only the cyclic tetramers with four primary hydrogen bonds in the same plane are predicted to have significant populations. Secondary hydrogen bonds, those for which the donated proton comes from an alkyl group, lead to a rich conformational space.

Structures, energies, and bonding in the water heptamer

In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency.

Structure and Reactivity of the 1Au6Pt Clusters

In this paper we report the geometries, properties, and reactivity descriptors of 12 structural isomers located on the MP2/SDDALL potential energy surface of the (1)Au(6)Pt binary clusters. A nonplanar, D(3d) symmetry, cyclohexane chairlike structure is predicted to be the global minimum. Binding energies per atom in the range ≈44-51 kcal/mol account for very stable clusters. The relative stability of the clusters is directly related to all global and local reactivity descriptors. All structures are predicted to have large electron affinities. The chemical environment of the Pt atom on the structures plays a central role in the resulting relative stabilities and global and local reactivities. Our results show that more peripheral Pt atoms are more likely to be involved in electron-accepting processes.

The Jahn-Teller effect: a case of incomplete theory for d4 complexes?

We present relativistic calculations at the four-component Dirac-DFT level for the geometries of the series of group 9 monoanionic hexafluorides MF(6)(-), M = Co, Rh, Ir. Highly correlated four-component relativistic CCSD(T) energies were also calculated for the optimized geometries. Spin-orbit coupling effects influence the geometrical preferences for molecular structures: relativistic calculations predict ground states with octahedral symmetries O(h)* for all hexafluorides in this study, while at the nonrelativistic limit, a structural deviation toward D(4h) ground state symmetries is predicted. Our findings suggest that relativistic effects have an important role in molecular structure preferences for the title hexafluorides.

Structural characterization of the (MeSH) 4 potential energy surface

AbstractA random walk on the PES for (MeSH)4 clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted. FigureTwo distinct types of hydrogen bonds are predicted for the Methanethiol tetramers

Electronic Structure Calculations on Helical Conducting Polymers

We present a study of the electronic structure and derived properties of polyfurane (PFu), polypyrrol (PPy), and polythiophene (PTh). Two spatial arrangements are considered: trans chain (tc-PFu, tc-PPy, tc-PTh) and cis α-helical (α-PFu, α-PPy, α-PTh). Even at the small sizes considered here, helical conformations appear to be stable. Band gaps of pure, undoped oligomers fall into the semiconductor range. Density of states (DOS) analysis suggest dense valence and conduction bands. Bond length alternation analysis predicts almost complete delocalization of the π clouds in all spatial arrangements. Doping with electron donors or electron-withdrawing impurities reduces all band gaps close to the metallic regime in addition to increasing the DOS for the valence and conduction bands.

A detailed look at the reaction mechanisms of substituted carbenes with water.

Two competitive reaction mechanisms for the gas-phase chemical transformation of singlet chlorocarbene into chloromethanol in the presence of one and two water molecules are examined in detail. An analysis of bond orders and bond order derivatives as well as of properties of bond critical points in the electron densities along the intrinsic reaction coordinates (IRCs for intermediates → transition state (TS) → products) suggests that, from the perspective of bond breaking/formation, both reactions should be considered to be highly nonsynchronous, concerted processes. Both transition states are early, resembling the intermediates, yielding rate constants whose magnitudes are mostly influenced by structural changes and to a lesser degree by bond breaking/formation. For the case of one water molecule, most of the energy in the reactants region of the IRC is used for structural changes, while the transition state region encompasses the majority of electron activity, except for the formation of the C-O bond, which extends well into the products region. In the case of two water molecules, very little electron flux and comparatively less work required for structural changes is noticed in the reactants region, leading to an earlier transition state and therefore to a smaller activation energy and to a larger rate constant. This, together with evidence gathered from other sources, allows us to provide plausible explanations for the observed difference in rate constants.

Very weak interactions: structures, energies and bonding in the tetramers and pentamers of hydrogen sulfide

Potential energy surfaces (PESs) for the hydrogen sulfide tetramers and pentamers are shown to be very complex. 11 and 15 different isomers were located on the MP2/6-311++G(d,p) PES of (H2S)4 and (H2S)5 respectively. CCSD(T) energy calculations on the MP2 optimized geometries suggest that all tetramers are within 2.0 kcal mol−1 of the lowest energy structure, while for the pentamers, all structures are found in a 3.5 kcal mol−1 range. To the best of our knowledge, we report and analyze here for the first time in the scientific literature, a newly found type of very weakly stabilizing intermolecular H2S⋯SH2 interaction. In conjunction with traditional H2S⋯H–S–H hydrogen bonds, these previously unreported H2S⋯SH2 intermolecular contacts dictate cluster structures and energies. Our results reveal a very complicated scenario, where a number of different tetramers and pentamers are very close in energy, rendering impossible the unequivocal identification of the global minimum in each case, and as a consequence, suggesting that the properties of these systems would have contributions from many different structures.

Reactivity of δ-substituted α,β-unsaturated cyclic lactones with antileishmanial activity

The present study examines a set of 43 compounds for their antileishmanial activities and cytotoxicities. Negative lowest unoccupied molecular orbitas and similar values for the electrophilic Fukui function condensed at the β-position for a subset of δ-substituted α,β-unsaturated cyclic lactones classify them as strong Michael acceptors. There was a well-defined trend of increasing antileishmanial activity with increasing cytotoxicity and large selectivity indices for the most active compounds. Softer compounds were more active than harder ones as observed from the experimental data and rationalised by calculated reactivity indices.

Competitive Substituent Effects on the Reactivity of Aromatic Rings

We performed second order perturbation theory calculations of gas phase proton affinities for o, m, p-nitroaniline at all positions and attempted correlations of the thermodynamic stability of the products with several reactivity indices: inductive effects from resonance, partial charges, and frontier orbital related indices such as local nucleophilic and electron-donating powers, global hardness of the products, and the substituent push-pull effect. All protonation reactions at ring positions are predicted to be exothermic. Resonance and charge analysis give inconsistent correlations with proton affinities, while the condensed nucleophilic Fukui function, electron-donating power, global hardness, and push-pull effect show promising trends.