Journal of Theoretical and Computational Chemistry

We propose a high-temperature expansion for thermodynamic functions. As an example we calculate the free energy for a restricted plane rigid rotor and compare present approach with perturbation theory.

In addition to four isomers of N₁₄ cluster previously reported, one new isomer was investigated. The decomposition and isomerization pathways of these five N₁₄ isomers were studied using the density functional theory (DFT) method. Relative energies were refined at the B3LYP/6-311+G(3df, 2p)//B3LYP/6-31G* level of theory. The present study shows that the decomposition barrier heights for the isomers 1, 2, and 3 are all much lower than 20 kcal/mol, which hints the fact that it may be possible to observe these three isomers only as short-lived species at room temperature. The barrier height for the cis-trans isomerization reaction of the isomers 4 and 5 is about 43.3 kcal/mol at the B3LYP/6-113+G(3df, 2p)//B3LYP/6-31G* level of theory. Unfortunately, however, the decomposition barrier height for the isomer 4 is about 17.9 kcal/mol. For the isomer 5, one barrier height corresponding to the -N₄ side chain breaking to lose the N₂ molecules is about 32.9 kcal/mol, however, the other barrier height corresponding to the -N₅ side chain breaking to lose a N₂ molecule is about 17.1 kcal/mol. From the study presented here, it seems that these five N₁₄ isomers are not kinetically stable enough to serve as high energy density materials (HEDMs).

The dissociation and isomerization reactions of N₁₁ isomers, including the two structures 1 and 3 previously studied as well as the three new structures 2, 4, and 5, were investigated by the density functional theory (DFT) at the B3LYP/6-31G(d), B3LYP/6-311G(d), and B3LYP/6-311+G(3df)//B3LYP/6-311G(d) levels of theory. The results indicate that, similar to previous results on N₉ and N₁₀ isomers, the barrier heights for structures 1 and 2 to lose N₂ are about 10–15 kcal/mol whereas the barrier heights for structures 1–3 to lose N₃ are about 25–30 kcal/mol. Therefore, it seems that N₂ is easier to be eliminated than is N₃ from the relatively larger nitrogen isomers. In addition, for structures 1 and 3, both dissociation and isomerization can occur in the N8–N9 bond, due partly to its character in having an aromatic bond. Moreover, the isomerization is preferred compared with dissociation because of its relatively lower energy barrier height.

The potential energy surfaces of dissociations and isomerizations for butyrophenone and its α-substituted derivative in low-lying electronic states have been studied with use of the CASSCF and DFT methods. A three-surface (S₁, T₁ and T₂) intersection was found in the present work and this plays an important role in the S₁ → T₁ process for butyrophenone and related aromatic carbonyl compounds. Examination of these results provides some new insights into the mechanistic photochemistry of aromatic ketones. The most probable mechanism leading to formation of a cyclopropane moiety was obtained on the basis of the calculated potential energy surfaces and their intersections. The selection of a suitable α-substituent was found to be a key step for cyclopropanation to occur by photoexcitation of butyrophenone derivatives.

Critical temperatures and critical pressures are calculated within the framework of the QSPR theory for a set of normal alkanes and a set of branched alkanes. The chosen molecular descriptors are the simplest topological properties: number of atoms, coordination numbers and chemical bonds. Predictions are quite satisfactory when compared with the available experimental data. These results are in line with other similar ones for a set of diverse organic compounds. Some possible future extensions are pointed out.

We have carried out computational sensitivity analysis to analyze the interactions between the inhibitor PD173074 and FGFR1 in order to identify the determinants of their recognition and generate insights into further refining the inhibitor. The analysis has identified the parts of the inhibitor that are already useful for binding, e.g. the part that recognizes the linker connecting the N-terminal and C-terminal lobes of the kinase domain. These parts are profitably kept during a lead optimization process. The analysis has also pointed out regions of the inhibitors that may be useful to modify to improve its binding affinity, e.g. the dimethoxyphenyl ring. Comparative structural analysis of the binding pocket of almost 400 protein kinases also suggests that modifying the dimethoxyphenyl moiety might improve selective binding. Selectivity may be achieved not only by introducing groups to the 3 and 5 positions but also to the 1 and 6 positions. Replacing the tertiary amines by hydrocarbon might also improve binding affinity.

The adsorption of N₂O at regular and defect sites of MgO (001) surface has been studied systematically using cluster models embedded in a large array of point charges by density functional method. The calculated results show that the MgO (001) surface with oxygen vacancies exhibits high catalytic reactivity toward N₂O adsorptive-decomposition at variance with the regular MgO surface or the surface with magnesium vacancies. Much elongation of O–N bond of N₂O after adsorption at oxygen vacancy site with O end of N₂O down indicates that O–N bond has been broken with concurrent production of N₂, leaving a regular site instead of the original oxygen vacancy site (F center). Besides, the MgO (001) surface with magnesium vacancies hardly exhibits catalytic reactivity. It can be concluded that N₂O dissociation is likely occurred at MgO (001) surface oxygen vacancy sites, which is consistent with the generally accepted viewpoint in the experiment.

A customizable, orthonormal basis for solving the multidimensional Schrödinger equation is constructed using modified Wilson–Daubechies wavelets, and a simple phase space truncation scheme. Unprecedented numerical efficiency is achieved, enabling a ten-dimensional direct calculation of nearly 600 eigenvalues to be performed. Higher dimensionalities are possible using more sophisticated linear algebra techniques. The new approach is ideally suited to rovibrational spectroscopy applications, but can be used in any context where elliptic partial differential equations are involved.

We present a new method for treating the dynamics of molecular systems. The method has been named "quantum dressed" classical mechanics and is based on an expansion of the wave function in a time-dependent basis-set, the Gauss–Hermite basis-set. From here it is possible to proceed in two ways, one is in principle exact and the other approximate. In the exact approach one constructs a discrete variable representation (DVR) in which the grid points are defined by the Hermite part of the Gauss–Hermite basis set. In the approximate method a second order expansion of the potential around the classical trajectories is introduced and the quantum dymamics solved in a second quantization rather than a wave-function representation.

Cytochrome oxidase (COX) is the terminal component of electron transport chain of the respiratory system in mitochondria, and one of the key enzymes responsible for energy generation in cells. COX functions as a proton pump that utilizes free energy of oxygen reduction for translocation of protons across the mitochondrion membrane. The proton gradient created in the process is later utilized to drive synthesis of ATP. Although the structure of COX has been recently resolved, the molecular mechanism of proton pumping remains unknown. In this paper, general principles and possible molecular mechanisms of energy transformations in this enzyme will be discussed. The main question is how exactly chemical energy of oxygen reduction and water formation is transformed into a proton gradient; or, how exactly electron transfer reactions are utilized to translocate protons across the mitochondrion membrane against the electrochemical gradient. A key to the solution of this problem is in understanding correlated transport of electrons and protons. Here, theoretical models are discussed for coupled electron and proton transfer reactions in which an electron is tunneling over long distance between two redox cofactors, and a coupled proton is moving along a proton conducting channel in a classical, diffusion-like random walk fashion. Such reactions are typical for COX and other enzymes involved in biological energy transformations.