Journal of Theoretical and Computational Chemistry

Tirapazamine is a radiosensitizer, whose biological activity is associated to its electron affinity (EA). The electron affinity can be divided in two main processes: Vertical and Adiabatic. In this work, we calculated the EAs of nitroimidazoles (Fig. 2) using HF and DFT methods and evaluated solvent effects (water and carbon tetrachloride) on EAs. For water, we combined the Polarized Continuum Model (PCM) and free energy perturbation (Finite Difference Thermodynamic Integration, FDTI) methods. For carbon tetrachloride, we used the FDTI method. The values of adiabatic EA obtained are in agreement with experimental data (deviations of 13.25 meV). The vertical EA were calculated according to Cederbaum's Outer Valence Green Function (OVGF) method. This study, which relays on theoretical aspects of free energy calculations on charged molecules in solution, could be helpful in the rational design of new and more selective bioreductive anticancer drugs.

Nonadditive three- and four-body interaction energies have been calculated for HF tetramer at the MP2/aug-cc-pVTZ level and for H₂ tetramer at the MP4(SDTQ)/aug-cc-pVTZ level using the so-called fifteen-point method. Calculated results show that with intermolecular distances decreasing from 3.0 to 1.7 Å the nonadditive three- and four-body interactions may be: (a) more and more attractive; (b) more and more repulsive; or (c) extremely weak. Strangely the minimum point of nonadditive three- and four-body interaction potentials has not been found up to now. For both H₂ and HF tetramers the nonadditive four-body interaction energy makes a negligible contribution to total binding energy when intermolecular distances are compressed from 3.0 to 1.7 Å.

We have calculated the structures, the heats of hydrogenation and the resonance energies of benzene isomers. All structures and energies were calculated by using the MMX force fields. Using PC model, the calculated structure parameters of benzene's 8 isomers are generally in good agreements with the experimental data. The heats of hydrogenation and resonance energy of benzene isomers are parallel to those experimental data and need a systematic adjustment of 4.5 kJ/mol.

We have obtained the enthalpies of formation from elements of a representative set of 158 coordination compounds resorting to the QSPR theory. The basic variables to determine the regression equations are the correlation weights of the nearest neighboring codes. Both linear and quadratic fitting relationships were determined as well as an optimal exponent method. Statistical parameters are quite satisfactory and they show the suitability of this sort of methodology to predict molecular enthalpies of formation.

A method to perform full quantum mechanical (ab initio) calculation of interaction energy involving a macromolecule like protein has recently been developed. This new scheme, named molecular fractionation with conjugate caps (MFCC), decomposes a protein molecule into amino acid-based fragments. These individual fragments are properly treated to preserve the chemical property of the bonds that are cut. Through proper combination of interaction energies between the molecule and individual fragments and their conjugate caps, the full protein-molecule interaction energy can be obtained to a high degree-of-accuracy by full ab initio calculations. Here we report a benchmark full ab initio calculation of interaction energy between a HIV-1 gp41 protein (with 982 atoms) and a water molecule at various geometries using HF (Hartree Fock), DFT (density functional theory) and MP2 (second-order Moller-Plesset perturbation theory) methods on a standard workstation.

Although there are tremendous studies about the conformational feature of calix[4]arenes and its analogies, no theoretical study has been done systematically about why some structural modifications could completely lead to a change of conformational preference. For example, calix[4]arene 1 adopts a cone conformation while its analogue calix[4]pyrrole 7 only adopts a 1,3-alternate conformation. So if this is only because of the effect of OH—OH hydrogen bonds, then why does O-methyl substituted calix[4]arene 2 still has cone conformation? In this paper, the conformational features of a series of seven calix[4]aromatics, calix[4]arene and calix[4]pyrrole related structures, have been investigated at BLYP/6–31G* level both in the gas phase and in CH₂Cl₂ solution. The calculations demonstrated that three main factors influence the conformational preference of these calix[4]aromatics, i.e. the intramolecular hydrogen bond, the adjacent ring-ring electrostatic interaction and the intrinsic flexibility of the [1₄] metacyclophane framework. Calix[4]benzene 3 and calix[4]pyridine 4 have little conformational preferences due to their flexible [1₄] metacyclophane framework, the lack of hydrogen-bonding interactions and weak ring-ring electrostatic interactions. In contrast, calix[4]aromatics 1 and 5–7 have either intramolecular hydrogen bonds (1) or ring-ring electrostatic interactions (5–7). Consequently, calix[4]arene 1 has the cone preference and calix[4]pyrrole, calix[4]furan, and calixthiophene (5–7) have the 1,3-alternate preference. Methoxy calix[4]arene prefers a cone or partial cone conformation, because the 1,3-alternate and 1,2-alternate conformations are destabilized by electrostatic repulsions involving the methoxy group and the adjacent phenyl ring.

Viscosity and diffusion coefficients for five equimolar binary gas mixtures of SF₆ with O₂, CO₂, CF₄, N₂ and CH₄ gases are determined from the extended principle of corresponding states of viscosity by the inversion technique. The Lennard–Jones 12-6 (LJ 12-6) potential energy function is used as the initial model potential required by the technique. The obtained interaction potential energies from the inversion procedure reproduce viscosity within 1% and diffusion coefficients within 5%.

This paper presents a numerical method which locates caustics of classical trajectories on-the-fly. The method is conceptually simple and is applicable to a system of arbitrary dimensions. The efficiency of the method is demonstrated by determining caustics of trajectories in the 2-D Henon–Heiles potential and of trajectories used to simulate a triatomic reaction process for J (total angular momentum) = 0.

Based on the Franck–Condon principle, vertical ionization energies regarding the inner-shell valence electrons of alkyl halides and their unsaturated analogues were evaluated with a designated single-configuration complete active self-consistent field (CASSCF) approach as well as the advanced correction with configuration interaction. Excitations corresponding to the elimination of one electron from a specific molecular orbital of these species were calculated by the deviation between the energy of the SCF-optimized neutral structure and of its cation. The freezing over the outer orbitals with identical symmetry was achieved while performing the CASSCF ionization calculation for the inner orbitals. These energy evaluations utilized Pople's 6-31G*, 6-311G** and Roos' ANO basis sets. Computed results agreed well with the experimental data. The characters for the molecular orbitals of corresponding vertical ionizations could be qualitatively assigned by the MOLDEN visualization program.

This article reviews microscopic development of time dependent functional method and its application to chemical physics. It begins with the formulation of density functional theory. The time dependent extension is discussed after the equilibrium formulation. Its application is explained by solvation dynamics. In addition, it reviews studies of nonlinear effects on polar liquids and simple mixtures.