Theoretical study on the molecular mechanism for the reaction of VO2+ with C2H4

The complex reaction between VO2+ ((1)A(1)/(3)A) and C2H4 (Ag-1(g)/(3)A(1)) to yield VO+ ((1)Delta/(3)Sigma) and CH3CHO ('A'/(3)A) has been studied by means of B3LYP/6-31G* and B3LYP/6-311G(2d,p) calculations. The structures of all reactants, products, intermediates, and transition structures of this reaction have been optimized and characterized at the fundamental singlet and first excited triplet electronic states. Crossing points are localized, and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate approach. Relevant stationary points along the most favorable reaction pathways have been studied at the CCSD/6-311G(2d,p)//B3LYP/6-311G(2d,p) calculation level. The theoretical results allow the development of thermodynamic and kinetic arguments about the reaction pathways of the title process. In the singlet state, the first step is the barrierless obtention of a reactant complex associated with the formation of a V-C bond, while in the triplet state a three-membered ring addition complex with the V bonded to the two C atoms is obtained. Similar behavior is found in the exit channels: the product complexes can be formed from isolated products without barriers. The reactant and product complexes are the most stable stationary points in the singlet and triplet electronic states. From the singlet state reactant complex, two reaction pathways are posssible to reach the triplet state product complex. (i) A mechanism in which a hydrogen transfer process is the first and rate limiting step and the second step is an oxygen transfer between vanadium and carbon atoms with a concomitant change in the spin state. The crossing point between singlet and triplet spin states is not kinetically relevant because it takes place at a later stage occurring in the exit channel. (ii) A mechanism in which the first stage renders a four-membered ring between vanadyl cation and the ethylene fragment and an oxygencarbon bond is formed; on going from this minimum to the second transition structure, associated with a carbon-vanadium bond breaking process, the crossing point between singlet and triplet spin states is reached. The final step is the hydrogen transfer between both carbon atoms to yield the product complex. In this case the spin change opens a lower barrier pathway. The transition structures with larger values of relative energies for both reactive channels of VO2+ ((1)A(1)) + C2H4 (Ag-1) --> VO+ ((3)Sigma) + CH3CHO ((1)A') present similar energies, and the two reaction pathways can be considered as competitive.

The generator coordinate method for a reaction coordinate coupled to a harmonic oscillator bath

This paper investigates the usefulness of the generator coordinate method (GCM) for treating the dynamics of a reaction coordinate coupled to a bath of harmonic degrees of freedom. Models for the unimolecular dissociation and isomerization process (proton transfer) are analyzed. The GCM results, presented in analytical form, provide a very good description and are compared to other methods Like the basis set method and multiconfiguration time dependent self-consistent field. (C) 1998 American Institute of Physics. [S0021-9606(98)50934-8].

The Origin of Nonmonotonic Complex Behavior and the Effects of Nonnative Interactions on the Diffusive Properties of Protein Folding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

MNDO theoretical study of ethanol decomposition process on SnO2 surfaces

An MNDO study has been carried out to analyze the decomposition process of the ethanol molecule on a SnO2 surface. A (SnO2)(7) (110) model has been selected to represent the surface. The decomposition process has been monitored by selection of a hydrogen-alpha-carbon distance of the ethanol molecule as reaction coordinate, This minimum energy pro file shows a maximum of 186 kJ mol(-1), and in the transition state there is a transfer of hydrogen-alpha-carbon to the SnO2 surface. There is also the interaction between the alcohol hydroxyls and the two oxygens of the oxide.

Smooth landscape solvent dynamics in electron transfer reactions

Solvent effects play a major role in controlling electron-transfer reactions. The solvent dynamics happens on a very high-dimensional surface, and this complex landscape is populated by a large number of minima. A critical problem is to understand the conditions under which the solvent dynamics can be represented by a single collective reaction coordinate. When this unidimensional representation is valid, one recovers the successful Marcus theory. In this study the approach used in a previous work [V. B. P. Leite and J. N. Onuchic; J. Phys. Chem. 100, 7680 (1996)] is extended to treat a more realistic solvent model, which includes energy correlation. The dynamics takes place in a smooth and well behaved landscape. The single shell of solvent molecules around a cavity is described by a two-dimensional system with periodic boundary conditions with nearest neighbor interaction. It is shown how the polarization-dependent effects can be inferred. The existence of phase transitions depends on a factor y proportional to the contribution from the two parameters of the model. For the present model, γ suggests the existence of weak kinetic phase transitions, which are used in the analysis of solvent effects in charge-transfer reactions. © 1999 American Institute of Physics.

Estudo do coeficiente de difusão no enovelamento de proteínas na rede

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estudo da interação não-nativa no enovelamento de proteínas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

NH3+N2O3 reaction. High level calculations

We have undertaken a comprehensive study of the NH3 + N2O3 reaction in gas phase. Total energies of reactants, intermediates, transition states, and products have been calculated at CBS-QB3 level of theory. The corresponding BSSE analysis were performed at the highest level of theory, i.e. MP2 using the complete basis set (CBS) extrapolation at CBS-QB3 optimized geometries. A detailed mechanism was proposed for 2NH(3) - N2O3 -> 2N(2) - 3H(2)O with Delta H-r= - 170.08 kcal/mol N-2. (c) 2005 Elsevier B.V. All rights reserved.

Bronsted Acid Catalyzed Morita-Baylis-Hillman Reaction: A New Mechanistic View for Thioureas Revealed by ESI-MS(/MS) Monitoring and DFT Calculations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Low-energy muon-transfer reaction from hydrogen isotopes to helium isotopes

Direct muon transfer in low-energy collisions of the muonic hydrogen H-mu and helium (He++) is considered in a three-body quantum-mechanical framework of coordinate-space integro-differential Faddeev-Hahn-type equations within two- and six-state close coupling approximations. The final-state Coulomb interaction is treated without any approximation employing appropriate Coulomb waves in the final state. This procedure of treating Coulomb interaction leads to much improved results for low-energy transfer rates. The present results agree reasonably well with previous semiclassical calculations. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Gaussian basis sets by generator coordinate Hartree-Fock method to ab initio calculations of electron affinities of enolates

The Generator Coordinate Hartree-Fock (GCHF) method is employed to generate uncontracted 15s and 18s11p gaussian basis sets for the H, C and O atoms, respectively. These basis sets are then contracted to 3s and 4s H atom and 6s5p, for C and O atoms by a standard procedure. For quality evaluation of contracted basis sets in molecular calculations, we have accomplished calculations of total and orbital energies in the Hartree-Fock-Roothaaii (HFR) approach for CH, C(2) and CO molecules. The results obtained with the uncontracted basis sets are compared with values obtained with the standard D95, 6-311G basis sets and with values reported in the literature. The 4s and 6s5p basis sets are enriched with polarization and diffuse functions for atoms of the parent neutral systems and of the enolates anions (cycloheptanone enolate, 2,5-dimethyleyelopentanone enolate, 4-heptanone enolate, and di-isopropyl ketone enolate) from the literature, in order to assess their performance in ab initio molecular calculations, and applied for calculations of electron affinities of the enolates. The calculations were performed at the DFT (BLYP and B3LYP) and HF levels and compared with the corresponding experimental values and with those obtained by using other 6-3 1 + +G((*)) and 6-311 + +G((*)) basis sets from literature. For the enolates studied, the differences between the electron affinities obtained with GCHF basis sets, at the B3LYP level, and the experimental values are -0.001, -0,014, -0.001, and -0.001 eV. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)