Journal of Theoretical and Computational Chemistry

The reaction mechanisms of HNCS with CH₂CH radical have been investigated by density functional theory (DFT). The geometries and harmonic frequencies of the reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311++G(d,p) level. The results show that the reaction is very complicated. Nine possible reaction pathways were identified. The results show that the most feasible reaction channel is the hydrogen-transfer pathway CH₂CH + HNCS → IMA1 → TSA1 → CH₂CHH + NCS. The pathway VIC C-S addition channel (CH₂CH + HNCS → TSD5 → IMD4 → TSD9 → CH₂CHS + CNH) can also occur easily. Ethene and radical NCS is the main product of the studied reaction, and product P8 (CH₂CHS and CNH) may also be observed. Compared with our previous study on the reaction HNCS + CH₂CH, the present reaction is easier to proceed.

A simple expression for the distance between two electrons, (δr₁₂)_ab, has been defined from one-electron expectation values. This value is calculated for triplet and singlet systems of two electrons, and closed-shell molecules of up to 58 electrons. When (δr₁₂)_ab is compared to the corresponding coulomb integral, J_ab, an interesting relationship is observed. The relationship is followed extremely closely by all pairs of electrons, except for some deviations involving delocalized core–core electron pairs.

The electronic structures of S-doped TiO₂ have been carried out by first-principles calculations based on density functional theory with plane-wave ultrasoft pseudopotential method. Comparing anion doping with cation doping in anatase and rutile, we found different energy band structures and origins of photoactivity of S-doped TiO₂. For anion-doped TiO₂, new S–3p bands appear and which lie slightly above the top of the O–2p valence band. It plays a significant role in increasing absorbance in the visible region, resulting in improvement in photocatalytic activity under visible-light irradiation. For cation-doped TiO₂, the potential of the O–2p valence band shift much downwards, yielding the stronger oxidative power than that of undoped and S anion-doped TiO₂. Nevertheless, the deep impurity states in BG (bond gap) that originate from the S-dopant have negative effects on the recombination of the photoexcited electrons and holes. From our calculated results, we can explain their differences in photocatalytic activity under visible-light irradiation.

The semiclassical path integral approach is undertaken to develop new definitions and atomic scales of electronegativity and chemical hardness. The considered quantum probability amplitude up to the fourth-order expansion provides intrinsic electronegativity and chemical hardness analytical expressions in terms of principal quantum number of the concerned valence shell and of the effective atomic charge including screening effects. The present electronegativity scale strikes on different orders of magnitude down groups of the periodic table, while still satisfying the main required acceptability criteria regarding the finite difference–based scale. The actual chemical hardness scale improves the trend across periods of the periodic system, avoiding the usual irregularities within the old-fashioned energetic picture. The current quest introduces the electronegativity of an element as the power by which the frontier electrons are attracted to the center of the atom being a stability measure of the atomic system as a whole.

Ab initio molecular dynamics simulations of SiO₂ in supercritical water at temperatures of 900 K and 1200 K and a pressure of 1.5 GPa at concentrations of 5 wt% and 16 wt% have been carried out. The different polymeric forms SiO₄H₄, Si₂O₇H₆, and Si₃O₁₀H₈ are found to be energetically similar within the statistical error, suggesting that all three polymeric forms play an important role in solutions at the above conditions. However, neither spontaneous polymerization nor depolymerization has been observed during the 10-ps time span of the simulations. The dynamic and structural properties of the supercritical solutions have been analyzed in terms of diffusion coefficients, vibrational spectra, and radial pair distribution functions.

MurF was considered as an attractive target for new antibacterial discovery. In this paper, three QSAR methods were employed, viz. comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram QSAR (HQSAR), to derive highly predictive QSAR models for designing novel MurF inhibitors and comparing different 3D-QSAR/alignment methods. QSAR models with high predictive ability for MurF inhibitors were successfully constructed in terms of cross-validation q², standard error and predictive coefficient r², which were around 0.70, 0.55 and 0.99, respectively. All the models from different methods were in good agreement with each other. Compounds with indeterminate activities were used as a test set; results showed that CoMSIA had the best predictive ability, followed by HQSAR and CoMFA. Based on these models, some key features for designing new MurF inhibitors were identified. A virtual database screen process was proposed based on the combination of these models.

Using a Morse type pair potential, molecular-dynamics simulations have been performed to investigate the atomic geometries, growing patterns, structural stabilities, energetics and magic sizes of Ti_n, V_n and Cr_n (n = 2-50) clusters. Following rearrangement collision of the atom–cluster system in fusion process, and absorbing their energies step by step down to 0 K, possible optimal equilibrium geometries of the clusters have been generated to tackle the structural determination problem. This approach serves an efficient alternative to the growing path identification and the optimization techniques. It has been found that titanium, vanadium and chromium clusters prefer to form three-dimensional compact structures in the determined configurations and the appearances of medium sizes are, in general, five-fold symmetry on the spherical clusters. Moreover, relevant relations between atomic arrangements in the clusters and the magic sizes have been observed.

In a recent series of papers,^1-3 a bipolar counter-propagating wave decomposition, Ψ = Ψ₊ + Ψ_-, was presented for stationary bound states Ψ of the one-dimensional Schrödinger equation, such that the components Ψ_± approach their semiclassical WKB analogs in the large action limit. The corresponding bipolar quantum trajectories are classical-like and well-behaved, even when Ψ has many nodes, or is wildly oscillatory. In this paper, the earlier results are used to construct an universal "black-box" algorithm, numerically robust, stable and efficient, for computing accurate scattering quantities of any quantum dynamical system in one degree of freedom.

Novel bioinformatic procedures and computational methods have been used to analyze, characterize and provide more detailed description of some selected fish antifreeze proteins (AFPs) retrieved from Swiss–Prot database. Analysis shows that AFPs are rich in non-polar residues and that the AFPs Q01758 and P05140 contain SS bonds. The aliphatic index computed by ExPasy's ProtParam infers that AFPs may be stable for a wide range of temperatures and the AFP P80961 is classified as an unstable protein. The very low GRAVY index of AFP P80961 infers its higher hydrosolubility. Secondary structure analysis shows that the flounder and sculpin fish AFPs are found to be of predominant ∝–helical structures and the rest of them are with mixed secondary structures. The average molecular weight of AFPs computed is 9584 Da. SOSUI server predicts one transmembrane region in P04002 (winter flounder fish) and two regions in P09031 (yellowtail flounder fish). The predicted transmembrane regions were visualized and analyzed using helical wheel plots generated by EMBOSS pepwheel tool. The residues A, L, G and N are identified as the antigenic sites by EMBOSS antigenic program. The presence of 11 Cys residues in AFPs Q01758 (rainbow smelt fish) and P05140 (sea raven fish) indicates the presence of disulfide bridges (SS bonds) in these AFPs, and it is also recognized by CYS_REC tool and well documented from the three dimensional structure using Rasmol tool.

With homology-modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of the human inosine triphosphatase (ITPase; EC 3.6.1.19) is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed, and the results indicate that Arg178, Lys19 and Glu44 are three important determinant residues in substrate binding because they have prominent interaction energies with ITP and form strong hydrogen bonds with ITP. In addition, we further find that the P32T substitution alters the α-helices of ITPase but the β-sheets are almost not changed, and the mutation induces the interaction energy between ITPase and ITP to increase, which are consistent with the conclusion predicted by Sumi et al.⁸ The results from the mutagenesis imply that Pro32 is vital for the catalytic activity.

Molecular dynamics simulation has been applied to study the adsorption process of PVDF/PCTFE copolymers on TATB (001) surfaces. The copolymers were formed by linking PVDF and PCTFE in 1:1 proportion as ABABAB pattern with the degree of polymerization N ranging from 10 to 200. The equilibrium time of each chain is several hundred picoseconds, and the adsorption energy E_a increases with the distance H between the chain and the increased surface. Adsorption process occurs when H is below 10 Å, and E_a tends to be zero as H becomes greater than 10 Å. Polymer's adsorbability is related to the length of the chain, and a longer chain is better than a short one. A short chain has more train conformation monomers than a long chain. Chain conformation changes greatly during the first hundred ps, and stabilizes after 150 ps. Monomers close to the TATB surface are easy to approach the surface, and the units far from the surface will approach the surface by chain torsion and bond rotation. The ratio of the number of train conformation monomers to the degree of polymerization N_t/N increases with the increasing MD simulation time.

A heuristic proposal is made in this communication that involves potentially unusual chemical bonding between the 3d transition series element Ni and the 3d transition series metals preceding it in the Periodic Table. The bonding in such mixed metal dimers, and their potential realizations as some simple three-dimensional (3D) extended structures in a one-to-one stoichiometry, as sphaelerite, rocksalt or CsCl structure-types, is proposed to include two principal components that involve either covalent or ionic contributions. Ordinary covalent contributions from a σ bond (or band) formed from overlap of singly occupied 4s atomic orbitals on each metal center are proposed to be operative in these molecules (or their extended realizations). However, in addition to this 4s–4s σ bond (band), an unprecedented transfer of a d electron from the incomplete, open 3d⁹ subshell of the transition metal involved in the bonding that precedes Ni in the Periodic Table, into the 3d⁹ subshell on the Ni center, which results in completion of this 3d subshell in Ni, is here implicated as a further driving force for the formation of these species. The resulting molecular and extended structures MNi, where M is a 3d transition metal preceding Ni in the Periodic Table (i.e. M = Sc, Ti, V, Cr, Mn, Fe and Co), are therefore proposed to be bonded together by a combination of covalent and ionic forces, such that the Ni center acts as an anion of charge 1-, a so-called nickelide anion Ni^-, while its counterpart is a univalent cation M⁺. This proposal is consistent with commonly employed electronegativity scales of chemical bonding, and with considerations of the relative orbital energies of the 3d subshells of the elements across the 3d transition series period, as well as with known trends in covalent and ionic bonding in the Periodic Table of the elements. It is also found to be in agreement with the spin multiplicities calculated in the nickel dimers MNi (M = Sc, Ti, V, Cr, Mn, Fe and Co) if Hund's rule is assumed to be operative.

The adsorptions of sulfur atom on the Ir(100) surface at p(2 × 2) and c(2 × 2) phases were investigated by the density functional calculations within the generalized gradient approximation. The adsorption energy, adsorption geometry, work function change, and charge density distribution were analyzed. The hollow site was found to be the most stable, followed by the bridge and the top sites. The calculated adsorption geometries were in good agreement with the observed results. Particularly, it was found that the adsorption of S on Ir(100) caused a work function decrease. A charge accumulation at the interface between the S layer and the Ir substrate, which centered closer to the S atom, suggests a polar covalent bonding. Density of states (DOS) analysis showed that the adsorption of S induces a reduction of the surface Ir d-orbital DOS around the Fermi level.

The mechanism of the isomerization of nitrosomethane to formaldoxime catalyzed by neutral molecule (H₂O and HCOOH) has been investigated at the level of B3LYP/6-311+G**. Calculated results indicate that the rearrangement from nitrosomethane to more stable trans-formaldoxime can proceed via two different reaction channels, but the favorable reaction pathway catalyzed by water and formic acid is different from the one in the catalyst-free reaction. It is more favorable that the tautomeric reaction involves the formation of cis-formaldoxime and a subsequent rotation about the N–O bond to form trans-formaldoxime in the catalyzed reaction. The activation energy of rate-determining step was reduced from 197.9 kJ/mol to 138.7 kJ/mol in the water-catalyzed reaction and 79.6 kJ/mol in the formic acid-catalyzed reaction, respectively, due to the catalysis of hydroxylic groups, but the catalysis of more acidic hydroxyl group in the latter system has been shown to be more efficient.