Journal of Theoretical and Computational Chemistry

An energy-dependent partitioning scheme is explored for extracting a small number of eigenvalues of a real symmetric matrix with the help of a serial as well as parallel genetic algorithm (GA). The proposed method is tested on two matrices (up to 2000 × 2000) with an increasing number of processors in a master–slave architecture. A comparison is made with the Jacobi–Davidson method in serial mode as implemented in the JDQZ-package. Different partition sizes are used. Traditionally used Löwdin's method is also tested in both serial and parallel modes. The advantages and disadvantages of the parallel GA-based method in solving the partitioned eigenvalue problem are analyzed.

The kinetics and mechanism of the modification of adenosine deaminase with N-ethyl-5-phenyl isoxazoliom-3′-sulfonate (WR-K) are investigated using molecular dynamics simulations, QM and QM/MM minimization methods. Two methodological algorithms are employed. In the first algorithm, a glutamate residue is dissected from ADA and its reaction with WR-K is studied by employing minimization and frequency calculations under the B3LYP method. Results obtained show that ketoketenimine is produced from the interaction of WR-K with OH^- in an exergonic two-step reaction. In this process, an intermediate is consumed in the rate-determining step. Next, the dissected residue is modified using ketoketenimine in a three-step reaction. This reaction is accompanied by the production of two intermediates, with the first intermediate produced in the rate-determining step.

For the second algorithm, modification of glutamate residue in the presence of water molecules and ions is investigated using conformational sampling, MM and QM/MM minimization. Stability of species in the reaction is evaluated using a combination of the B3LYP method and the WASA model. It is proved that the stability of an intermediate which is initially produced in the reaction of glutamate residue with ketoketenimine must be considered crucial when the reactivity of the different residues is compared. Results obtained indicate that these reactions have energetic features qualitatively similar to the glutamate-dissected case. It is also clear that protein structure plays a basic role in the formation of the product that arises from the reaction of ADA with ketoketenimine.

The theoretical studies on the electronic structure, DNA-binding, and absorption-spectral properties of "light switch" complex [Ru(phen)₂(taptp)]²⁺ (phen = 1,10-phenanthroline; taptp = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene) in aqueous solution have been carried out using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. The results show the following: (i) The solvent effect makes all the frontier molecular orbital energies of complex to increase to a certain extent; however, the energies (ε_{LUMO + x}) of some frontier unoccupied molecular orbitals (MOs) in aqueous solution are still negative and rather lower than those of the energies (ε_{HOMO - x}) of some frontier-occupied MOs of DNA-base pairs, and thus the complex in aqueous solution is still an excellent electron-acceptor in its DNA-binding. (ii) The solvent effect further shows that simply increasing the conjugative planar area of intercalative ligand may be ineffective on the improvement of DNA-binding of the resulting complex because of going along with the increase in the LUMO (and LUMO + x) energy. It is the reason why the DNA-binding affinity of "light switch" complex [Ru(phen)₂(taptp)]²⁺ is not better than that of the well-known complex [Ru(phen)₂(dppz)]²⁺ yet. (iii) The three main experimental bands (~450 nm, ~360 nm, and ~290 nm) of the studied complex in aqueous solution were further well calculated, simulated, and explained by the TDDFT computations.

The interference of dissociating wave packets for the Br₂ molecule in femtosecond laser field is studied theoretically using time-dependent quantum wave packet method. The interference of dissociating wave packets can be determined by the spectrum of laser field. By shaping laser pulses in frequency domain, the corresponding R- and v-dependent density functions can be effectively controlled. Compared with the 2-pulse excitation scheme, the resolution of the interference patterns can be improved by using 3- and 4-pulse excitation schemes. The dissociating velocity can be steered by varying laser parameters.

Hydrogen bonding interactions between trimethylamine (TMA) and a series of para substituted phenols (X–C₆H₄OH, X = H, CH₃, NH₂, Cl, CN, and NO₂) are studied by using density functional theory with the hybrid B3LYP functional and the 6-31++G(d,p) basis set. Both electron donor and acceptor substituents (X) are chosen to study systematically the relation between the proton donor ability of the phenols and the strength of the OH…N hydrogen bond. The effect of hydrogen bonding on spectral and structural parameters and their inter relation are discussed. The natural bond orbital (NBO) analysis (occupation of σ* orbitals, hyperconjugative energies and atomic charges) is also carried out to elucidate the reason behind the spectral and structural changes due to hydrogen bond formation. Several correlations between hydrogen bond strength and bond properties are discussed.

Based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), the intermolecular potential for transition metal ion Fe²⁺, Co²⁺, and Ni²⁺ cations in water has been derived. Parameters for the effective interaction between a cation and a water molecule were determined by reproducing the ab initio results. Many structural and dynamic properties of Fe²⁺(aq.), Co²⁺(aq.), and Ni²⁺(aq.) were studied using these potential parameters. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of alkali metal and alkaline-earth metal cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of transition metal cations in water.

Ab initio calculations show that, for the P_n(CH)_4-nPH with n = 0 - 4, the fully optimized structures have decreasing pyramidality at the tri-coordinated phosphorus atom with n. The interaction between the tri-coordinated phosphorus and the carbons–phosphorus π-system with different n, the differences of the structure, electron properties and energy among the phospholes indicate that the ring strain and the delocalization of the lone pair electron of tri-coordinated phosphorus should be responsible for this phenomena. Various aromatic criteria such as geometry, magnetism, and energy show that these molecules are aromatic, and their aromaticities increase with the number of phosphorus atoms in the nonplanar pentagons. The electron circulation in the aromatic molecules can promote the delocalization of the lone pair. In contrast to the B3LYP prediction, we draw some similar conclusions, but the planarity and aromaticity of molecules increase largely at the MP2 lever due to the consideration of electron correlation.

The present work concerns the analytical and numerical development of three-center molecular integrals over Slater-type functions (STFs) and B functions of the second order involving in the operator. These integrals appear in the analytic expression of the nuclear magnetic shielding tensor.

The basis set of STFs is used to represent atomic orbitals. These STFs are expressed in terms of B functions, which are better suited to apply the Fourier transform method thoroughly developed by Steinborn group.

Analytic expressions are obtained for the integrals of the second order involved in nuclear magnetic resonance shielding tensor over B functions. These expressions turned out to be similar to those obtained for the usual molecular multi-center integrals. Consequently, the numerical evaluation of the integrals under consideration will benefit from the work previously done on the molecular multi-center integrals.

Kinetics and mechanism of the reaction between cyclohexyl isocyanide and 1,1,1,5,5,5-hexafluropentane-2,4-dione has been investigated by utilizing transition state theory and using B3LYP/6-31G* method. Based on previous experimental studies, two paths namely direct attack and conjugate addition have been proposed. Energy changes vs intrinsic reaction coordinate (IRC) along these paths have been studied both in the gas phase and considering nonspecific solvent effect under Onsager's model while all intermediate and possible transition states' geometries obtained and optimized. Small differences have been observed between gas phase and solution phase results. Taking advantage of the thermodynamic and kinetic calculated parameters, observed reaction rate constants and activation energies have been acquired. Computational results suggest that the conjugate addition path is totally unacceptable, while a new path has been proposed, which is both energetically and kinetically preferred to direct attack path. This new path undergoes the Michael addition along with a Cope–Claisen-type rearrangement. In this path, a new intermediate has been encountered for the first time, which contains a five-membered ring of four carbon atoms and one oxygen atom. NBO analysis has revealed that in such intermediate, oxygen lone pair has resonance with C–C π bond inside and C–N π bond outside of the ring leading to this species special stability. Molecular orbital calculations satisfy NBO findings.

The structures and conformational stability of vinylphosphonic and vinylthiophosphonic acids were investigated using calculations mostly at DFT/6-311G** level and ab initio ones at MP2/6-311G** level. From the calculations the molecules were predicted to exist in a nonplanar near-cis (nc) to trans -gauche (tg) conformational equilibrium with nc (phosphonic oxygen or sulfur nearly eclipses the vinyl group) being the predominant conformer at ambient temperature, at least on the basis of Gibbs free energy (in the case of the thio compound the potential energy of tg is slightly lower than that of nc). The antisymmetric potential function for the internal rotation was determined for each one of the molecules. However, when starting optimizations from a structure too close to the full cis symmetry, the cis form results as an extremum on the potential hyper-surface. Consequently cis was reported in the literature several times as minimum. However, when we calculated the vibrational frequencies the cis form turned out to have an imaginary frequency, and thus cis is a local maximum along one of the normal coordinates. The true minimum, with only real frequencies, actually is an nc one with a very low barrier to rotation. The rotational angle out of cis is rather small; however, HOPX dihedral angles are quite away from real cis. This holds true not only with DFT but also with MP2. The vibrational frequencies were computed and the spectra were plotted as a prediction. Normal coordinate calculations were carried out and potential energy distributions were calculated for the molecules in the nc and the tg conformations. From our results and their analysis, we conclude, in agreement with results from the literature based on localized orbitals, that conjugation effects are absent – or at least negligible – as compared with electrostatic or steric ones in determining the structures of the stable conformers in the vinyl derivatives.

The gas phase reaction thermodynamics in the chemical vapor deposition (CVD) process of preparing boron carbides via the precursors of BCl₃–C₃H₆(propene)–H₂ is investigated with a set of 325 gaseous species, in which the data for 135 species are evaluated in this work. The thermochemistry data are calculated with accurate model chemistry at G3(MP2) and G3//B3LYP levels. The concentration distribution of all of the 325 species is obtained with the principle of chemical equilibrium. The thermochemistry data include the heat capacities, entropies, enthalpies of formation, and Gibbs free energies of formation. The heat capacities and entropies at temperatures in 298.15–2000 K are evaluated with the standard statistical thermodynamics. The Gibbs free energies of formation in 298.15–2000 K are calculated with the classical thermodynamics based on the developed heat capacities and entropies. By including the crystal B₄C, C(graphite), and B, the results for an example of the 3:1:2 precursors of BCl₃:C₃H₆:H₂ show that the crystal B₄C can be produced at temperatures higher than 700 K while the graphite has a higher molar value and can be produced at lower temperatures. It is also examined that the production of graphite can be controlled by changing the ratio of the injected reactants or pressure. It is interesting that BHCl₂, BCH₃Cl₂, BH₂Cl, and B₂Cl₄ are found to be the most effective species in the CVD process, which is similar to those in the BCl₃–CH₄–H₂ system. The results predicted in this work are consistent with the experiments.