Journal of Theoretical and Computational Chemistry

We introduce a new quantum mechanics/molecular mechanics based method to drive electron transfer reactions. Our approach uses the dynamically restrained electrostatic potential derived charges of the quantum atoms¹ as a reaction coordinate, and allows an estimation of the free energy barrier of the electron transfer process. Moreover, it provides an accurate description of the electronic structure changes and of the nuclear reorganization associated with the reaction. We use the method to describe the electron-transfer induced dissociation of the m-chloro-cyano-benzene radical anion in aqueous solution. The reaction is triggered by solvent reorganization by a change in the coordination water shell around the cyano nitrogen atom. At the onset of the reaction, charge-spin segregation is observed. The negative charge is transferred to the leaving Cl, while the spin density localizes on the non-saturated carbon atom of the benzene ring. The calculated free energy barrier of dissociation is in good quantitative agreement with the experimental data.

The conductance properties of the thiophene bithiol molecular wire, a nano-wire connecting two metallic electrodes, were investigated using quantum-mechanical based methods such as Density Functional Theory, in conjunction with non-equilibrium Green's function formalism. Using the quantum mechanics methods, the Hamiltonians of the three main parts of system, i.e. the right lead, the device, the left lead and conductance properties of this molecular wire such as I-V curve, were calculated.

A Comparative computational analysis of ordering in higher homologous series of p-n-alkylbenzoic acids (nBAC), having 7(7BAC); 8(8BAC) and 9(9BAC) carbon atoms in the alkyl chain, has been carried out based on quantum mechanics and intermolecular forces. The evaluation of atomic charge and dipole moment at each atomic centre has been carried out through an all-valence electron (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory, along with multicentered-multipole expansion method, has been employed to evaluate long-range intermolecular interactions, while a "6-exp" potential function has been assumed for short-range interactions. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at room temperature, nematic-isotropic transition temperature and above transition temperature using the Maxwell-Boltzmann formula. A comparative picture of molecular parameters such as total energy, binding energy and total dipole moment has been given. A model has been developed to describe the nematogenicity of these acids in terms of their relative order with molecular parameter introduced in this paper.

A detailed computational study is performed on the radical-molecule reactions between HCO/HOC and ethylene (C₂H₄) at the Gaussian-3//B3LYP/6-31G(d) level. For the HCO + C₂H₄ reaction, the most favorable pathway is the direct C-addition forming the intermediate H₂CCH₂CHO, followed by a 1,2-H-shift leading to H₃CCHCHO. Subsequently, there are two highly competitive dissociation pathways for H₃CCHCHO: one is the formation of the direct H-extrusion product H₂CCHCHO + H, and the other is the formation of C₂H₅ + CO via the intermediate H₃CCH₂CO. The overall reaction barrier is 14.1 and 14.6 kcal/mol respectively, at the G3B3 level. The quasi-direct H-donation process to produce C₂H₅ + CO with the barrier 16.5 kcal/mol is less competitive. Thus, only at higher temperatures, the HCO + C₂H₄ reaction could play a role. In contrast, the HOC + C₂H₄ reaction just need to overcome a small barrier 2.0 kcal/mol to generate C₂H₅ + CO via the quasi-direct H-donation mechanism. This is suggestive of the potential importance of the HOC + C₂H₄ reaction in combustion processes. However, the direct C-addition channel is much less competitive. The present kinetic data and orbital analysis show that the HCO radical has much higher reactivity than HOC, although the latter is more energetic. Till now, no kinetic study on the HOC radical has been reported, the present study can provide useful information on understanding the reactivity and depletion mechanism of the energetic HOC radical.

In this work, I present a practical way to obtain the vibration-rotation kinetic energy operator for an N-atomic molecule in an arbitrary body-frame . The body-frame need not be orthogonal or rigid. In practice, I derive the explicit form of the measuring vectors associated with the body-frame components of the internal angular momentum. Their inner products with the vector derivatives of the shape coordinates give the "Coriolis" part of the metric tensor appearing in the Hamiltonian, and their inner products among themselves give the "rotational" part. As a simple example, the measuring vectors are explicitly derived in an oblique bond-vector body-frame. The metric tensor elements are also derived for a tetra-atomic pyramidal molecule, whose shape is parametrized in bond-angle coordinates.

The formalism of density functional theory (DFT) with Perdew and Wang exchange-correlation functional, has been employed to study the electronic and geometric structures of silver cation and the neutral dimer bonded with carbon monoxide and oxygen. A charge state study of the use of and Ag₂, for the catalytic oxidation of CO, has been performed and compared with our previous results for . Different possible structures for , Ag₂CO⁺, Ag₂O₂ and Ag₂CO have been investigated in detail. An all electron 6-311 ++ G** basis set for carbon and oxygen, and a pseudopotential basis set for silver have been used for performing the calculations. Using silver cation and neutral dimer as catalysts, full catalytic cycles producing two carbon dioxide molecules have been presented. Also, the presence of intermediate states, and Ag₂CO₃, which can be detected experimentally, are predicted. The presence of an energy barrier for certain reactions from the catalytic cycle have been observed. This is noteworthy since no reaction barrier has been observed using silver anion dimer as a catalyst, for the same catalytic cycle. Analyzing the charge state effects, it is concluded that silver anion dimer performs better as a catalyst, compared with silver cation and neutral dimers.

This paper develops a new semiclassical mechanics from an exact quantum prescription. In this formulation, a zeroth order propagation, rather than Hamiltonian, is specified. The exact, full evolution operator is then given from a specific interaction representation of the evolved "perturbation" Hamiltonian. We then investigate a variety of approximate, semiclassical, and mixed Quantum/Classical methods, along with exact methodologies to evaluate this time dependent interaction Hamiltonian. The approximate full evolution operator can be described in a variety of ways including an iterated Lippman-Schwinger like equation, and an expansion of the perturbation propagator generated from the time evolved Hamiltonian.

The reaction mechanisms and kinetics for DMS + O₃ ⇒ DMSO + O₂ in water vapor are studied using density functional theory. A series of reaction pathways are determined with molecular clusters containing the reacting species and up to three water molecules. The results show that the energy barrier, defined as the energy difference between the reactant complex and the transition state, decreases progressively as each water molecule is added to the reacting system. A decreasing energy barrier is attributed to favorable electrostatic interactions between the reacting species and water at the transition state and at the more polar product. Rate constants for the second-order reactions, involving different combinations of hydrated reactants up to three water molecules, are calculated using transition state theory with Eckart tunneling corrections. Effective rate constants for DMS + O₃ ⇒ DMSO + O₂ are obtained using the calculated second-order rate constants and the concentrations of hydrated reactants present in saturated water vapor. The results show that the rate of reaction for DMS + O₃ ⇒ DMSO + O₂ increases dramatically in the presence of water vapor, by up to seven orders of magnitude for reactions involving three water molecules. The study implies that the gas-phase reaction of DMS with ozone is significant in the troposphere and can greatly influence the global climate.

Si_n clusters in the size range n = 4–30 have been investigated using a combination of global structure optimization methods with DFT and ab initio calculations. One of the central aims is to provide explanations for the structural transition from prolate to spherical outer shapes at about n = 25, as observed in ion mobility measurements. Firstly, several existing empirical potentials for silicon and a newly generated variant of one of them were better adapted to small silicon clusters, by global optimization of their parameters. The best resulting empirical potentials were then employed in global cluster structure optimizations. The most promising structures from this stage were relaxed further at the DFT level with the hybrid B3LYP functional. For the resulting structures, single point energies have been calculated at the LMP2 level with a reasonable medium-sized basis set, cc-pVTZ. These DFT and LMP2 calculations were also carried out for the best structures proposed in the literature, including the most recent ones, to obtain the currently best and most complete overall picture of the structural preferences of silicon clusters. In agreement with recent findings, results obtained at the DFT level do support the shape transition from prolate to spherical structures, beginning with Si₂₆ (albeit not completely without problems). In stark contrast, at the LMP2 level, the dominance of spherical structures after the transition region could not be confirmed. Instead, just as below the transition region, prolate isomers are obtained as the lowest-energy structures for n ≤ 29. We conclude that higher (probably multireference) levels of theoretical treatments are needed before the puzzle of the silicon cluster shape transition at n = 25 can safely be considered as explained.

Using the generalized Keldysh theory, we investigate the quantum interference and the laser pulse phase effects by tunneling photoionization of an excited hydrogen atom. We assume that its initial state be a linear combination of 1s, 2s, 2p Stark-shifted atomic states. It is found that within the Keldysh approximation, quantum interference can take place among the 1s, 2s, and 2pz states, while this is not the case among 1s, 2s, 2pz and 2px, 2py, or 2px and 2py themselves. From the numerical calculations, we predict that the prominent destructive quantum interference takes place between 2s and 2pz atomic orbitals. In addition, we have found that in general, the laser pulse phase does not affect the individual photoionization rates while it does affect the quantum interference terms.

This paper presents dipole moments, static isotropic polarizabilities and polarizability anisotropies of 20 molecules calculated in the framework of a new natural orbital functional method. All calculations have been performed using a finite field approach. Comparison with other correlated methods (CCSD(T), B3LYP) shows a reasonable agreement in the prediction of electric response properties by this new functional.