Journal of Theoretical and Computational Chemistry

The CO migratory insertion into M–O and M–C bonds of the new model (PMe₃)₂M(η² – CH₂CH₂O) (M = Ni, Pd and Pt) (model (d)) proposed in this work has been studied with the aid of density functional theory (DFT) calculations. It is found (1) when M = Ni, CO migratory insertion into Ni–C is thermodynamically and kinetically favored, and (2) when M = Pd and Pt, the insertion into M–O bond via a one-step process is preferred. Further investigation on CO migratory insertion using Pt(PMe₃)2(C₇H₁₀O) (R′-Pt) derived from the experimental compound Pt(PEt₃)₂(C₇H₁₀O) gives the same conclusions as model (d) with M = Pt. Results obtained from the reaction of model (d) (M = Pt) with CO are consistent with the experimental observation that CO prefers to insert into Pt–O bond of Pt(PEt₃)₂(C₇H₁₀O).

The electronic band structure, structural phase transition, metallization and superconducting transition of cubic zinc blende type indium phosphide (InP) and indium nitride (InN), under pressure, are studied using FP-LMTO method. These indium compounds become metals and superconductors under high pressure but before that they undergo structural phase transition from ZnS to NaCl structure. The ground state properties and band gap values are compared with the experimental and previous theoretical results. From our analysis, it is found that the metallization pressure increases with increase of lattice constant. The superconducting transition temperatures (T_c) of InP and InN are obtained as a function of pressure for both the ZnS and NaCl structures and these compounds are identified as pressure induced superconductors. When pressure is increased T_c increases in both the normal (ZnS) and high pressure (NaCl) structures. The dependence of T_c on electron–phonon mass enhancement factor λ shows that InP and InN are electron–phonon mediated superconductors. The non-occurrence of metallization, phase transition and onset of superconductivity simultaneously in InP and InN is confirmed.

Quasiclassical trajectory (QCT) calculations have been performed to investigate the reaction dynamics of the title reactions at a state-to-state level. The recently developed adiabatic potential energy surfaces (PESs) of the two triplet electronic states of 1³A″ and 1³A′ (Gómez-Carrasco S. et al., J Chem Phys121:4605, 2004; J Chem Phys123:114310, 2005) are employed in the present QCT calculations. Product vibrational and rotational state distributions have been calculated at three collision energies of 0.5, 0.7 and 0.9 eV. The product vibrational state distributions are found to be Gaussian distributions. Both the vibrational and rotational state distributions depend clearly on the isotope substitution, electronic PESs and collision energies. The observed phenomena are probably attributed to the competition of direct and indirect reactions.

More reaction pathways in the CVD process of preparing boron-carbides with BCl₃-C₃H₆(propene)-H₂ precursors were examined in addition to the "lowest" path proposed by Jiang et al. in Theor Chem Acc127:519–538, 2010. The new pathways investigated in this work involve 81 new transition states and 79 new intermediates. Geometries of the species were optimized with the density functional theory at B3PW91/6-311G(d,p) level. Intrinsic reaction coordinates were analyzed to confirm the correct reaction linkages. Energy barriers and reaction energies were calculated with the accurate model chemistry method G3(MP2) after a non-dynamical electronic correlation detection using CASSCF method. Heat capacities and entropies were obtained with the statistical thermodynamics and fitted as a function of temperature. Gibbs free energies at 298.15 K and 1200 K were used to examine the reaction paths. It was found that some steps in the new paths at both 298.15 K and 1200 K are different from the "lowest" path obtained previously and the pathways for the new products CB and C₂B were obtained.

Quasi-Classical Trajectory (QCT) calculations have been carried out to study the stereodynamics of the reactions N + NH → N₂ + H and isotopic effects on the product polarization at collision energies of 10.0 kcal/mol and 25.0 kcal/mol which proceed on the Double-Many-Body-Expansion (DMBE) potential energy surface. The distribution of dihedral angle P(ϕ_r), and the distribution of angle between k and j′, P(θ_r) are discussed in detail. Furthermore, four generalized polarization dependent differential cross sections (PDDCSs) (2π/σ)(dσ₀₀/dω), (2π/σ)(dσ₂₀/dω), (2π/;σ)(dσ₂₂₊/dω), and (2π/σ)(dσ_{21 -}∕dω) are presented. The results reveal that isotope effect plays an important role for P(ϕ_r) and P(θ_r) distribution, and the PDDCSs exhibit similar collision energy dependency relationship at low and high collision energies.

1,3-dipolar cycloaddition between acrylonitrile and methylmethacrylate with two N-(4-bromophenyl)-C-(4-substituted) nitrilimines which were generated in situ afforded the new pyrazoles. The regioselectivity and reactivity of these reactions has been investigated on the basis of density functional theory (DFT)-based reactivity indexes and activation energy calculations. The theoretical ¹³C NMR chemical shifts of the cycloadducts which were obtained by GIAO method were comparable with the observed values.

The influenza A (H5N1) virus attracts a worldwide attention and calls for the urgent development of novel antiviral drugs. In this study, explicitly solvated flexible docking and molecular dynamics (MD) simulations were used to study the interactions between the H5N1 sub-type hemagglutinin (HA) and various catechin compounds, including EC ([–]-epicatechin), EGC ([–]-epigallocatechin), ECG ([–]-epicatechin gallate) and EGCG ([–]-epigallocatechin gallate). The four compounds have respective binding specificities and their interaction energies with HA decrease in the order of EGCG (-133.52) > ECG (-111.11) > EGC (-97.94) > EC (-83.39). Units in kcal mol^-1. Residues IleA267, LysA269, ArgB68 and GluB78 play important roles during all the binding processes. EGCG has the best bioactivity and shows potential as a lead compound. Besides, the importance was clarified for the functional groups it was revealed that the C5′ hydroxyl and trihydroxybenzoic acid groups are crucial for the catechin inhibitory activities, especially the latter. Combined with the structural and property analyses, this work also proposed the way to effectively modify the functional groups of EGCG. The experimental efforts are expected in order to actualize the catechin derivatives as novel anti-influenza agents in the near future.

Quantitative structure–property relationship (QSPR) was used to predict melting points of 62 ionic liquids (ILs), which include ammonium, pyrrolidiniu, imidazolium, pyridiniu, piperidiniu, phosphonium ionic liquid salts. The structures of ionic liquids were optimized by Hyperchem software and MOPAC program, and stepwise multiple linear regression method was applied to select the relevant structural descriptors. The predicting models correlating selected descriptors and melting points were set up using multiple linear regressions (MLR) and multilayer perceptron neural network (MLP NN), separately. The obtained linear and nonlinear QSPR models were validated by internal and external test sets. According to the obtained results, the correlation coefficients between predicted and experimental melting points for training, test and validation sets were; 0.91, 0.86 and 0.79 for MLR model. These values for MLP NN model were; 0.97, 0.96 and 0.85, respectively. The results of this study revealed the high applicability of QSPR approach to melting point prediction of ILs.

Temperature dependence of the rate constant of the O(³P) + HCl → OH + Cl reaction was calculated for 200–700 K range within the quantum instanton approximation using the ³A″ potential energy surface. Curvature of the Arrhenius plot arising from quantum effects in the hydrogen exchange reaction was observed. Results of the present method were found to significantly improve upon those obtained within the ICVT/μOMT method. The errors pertaining to the present method were estimated.

The presence of aqueous solution is inevitable in complex systems involving biological and material components and could affect the interaction between them substantially. To properly simulate such an interaction system, it is necessary to quantitatively explore the effects and specific roles of the water environment on the material surface. In this work, a silica surface was adopted as an example to study the impact of water environment (144H₂O) on the structure and energetics using a self-consistent charge density functional tight binding/molecular dynamic method. First, we demonstrated that the silica surface in a vacuum involves a large deformation due to the formation of hydrogen bonds among the surface silanols; in contrast, the deformation is eased in water environment because water molecules could locate in between the silanols and form many hydrogen bonds with the silanols. Therefore, water molecules play an important role to maintain surface from not getting heavily deformed. Our work not only tested the feasible computational methodology of studying nanoscale large systems under water environment at a quantum-mechanical level of theory, but also provided clear evidence on the impact of water environment to the inorganic surface.

Charge preservation is a necessary condition in population analysis. However, one such constraint is not enough to solve the arbitrariness involved in the population analysis such as Hirshfeld population. This arbitrariness results in too small Hirshfeld charges and poor reproducibility of molecular dipolar moments. In this article, the preservation of the molecular dipole moment is imposed upon the Hirshfeld population analysis as another constraint to improve the original Hirshfeld charges. In the scheme each atomic dipolar moment defined by the deformation density is expanded as contributions from all atoms in the molecule. The corresponding correction charges are then accumulated for each atom together with the original Hirshfeld charge as the predicted charge. All computed charges are generally larger than Hirshfeld charges, independent of basis set, and have very good electrostatic potential reproducibility and high correlation with the charges derived from the electrostatic potential fitting.

The structures and stabilities of charged, copper-doped, small silicon clusters (n = 1–7) have been systematically investigated using the density functional theory method at the B3LYP/6-311+G* level. For comparison, the geometries of neutral CuSi_n clusters were also optimized at the same level, although most of them have been reported previously [see Xiao CY, Abraham A, Quinn R, Hagelberg F, Comparative study on the interaction of scandium and copper atoms with small silicon clusters, J Phys Chem A106:11380, 2002; Liu X, Zhao GF, Guo LJ, Wang XW, Zhang J, Jing Q, Luo YH, First-principle studies of the geometries and electronic properties of Cu_mSi_n (2 ≤ m + n ≤ 7) clusters, Chin Phys16:3359, 2007]. Our results for the ground state structures of neutral CuSi_n clusters agree well with those of Liu et al. and Xiao et al. except for CuSi₃ and CuSi₇. Removing or adding an electron greatly changes some ground state structures, i.e. for , , , , and ; others are almost unchanged, e.g. , , , , . The ground states of ionic are all singlet, except for the smaller CuSi^- and . Based on the optimized geometries, various energetic properties, including binding energies, second-order difference energies, the highest occupied molecular orbit and the lowest unoccupied molecular orbital (HOMO–LUMO) energy gaps, ionization potential and electron affinities, were calculated for the most stable isomers of . All the results indicate that anionic and cationic clusters are relatively stable. The higher stability of the latter has been confirmed by Beck's observations.

Applying relativistic density functional theory to isomers of C₇₈ and M₂@C₇₈(M = La, Ce), we calculate and analyze the relative energies and HOMO–LUMO gaps of neutral and hexaanion ( -6 charged) C₇₈ isomers. Our results indicate that the (5) isomer is the most stable, and it illustrate that electron transfer plays an important role in controlling the stability of endohedral metallofullerenes. We also calculate the electronic structures of there neutral isomers, and based on their LUMO + 2 and LUMO + 3 gaps, we explain why it is easier to encage two metal atoms in D_3h′ (78:5). To further elucidate this issue, we theoretically characterize M₂@C₇₈(M = La, Ce) and compare the relative energies and the HOMO–LUMO gap of the two isomers M₂@C₇₈ (4) and the M₂@C₇₈ (5) (M = La, Ce). The results indicate that M₂@C₇₈ (5) is more stable than M₂@C₇₈ (4). Furthermore, the good agreement between the experimental and computed ¹³C NMR chemical shift of the isomer M₂@C₇₈ (5) provided strong evidence that M₂@C₇₈ forms a D_3h′ (78:5) cage.

p-nitrophenylazoaniline (1) belongs to the family of compounds with conjugated bonds and delocalized π-electrons, structurally similar to the well known push-pull compound Disperse Red 1 (DR1).¹ Due to the assembly of the molecule, nonlinear optical (NLO) properties are expectable and can be more or less accurately predicted. To estimate the potential for second-order NLO properties, the electric dipole moment (μ), dispersion-free dipole polarizabilities (α) and first hyperpolarizabilities (β) have been determined by density functional theory (DFT) quantum chemical calculations at B3LYP/ 6-311 + G(d, p) level. According to the computation results, the synthesized compound exhibits non-zero β values and it might have second-order NLO behavior. Title compound has been synthesized and characterized by FT-IR, ¹H-NMR and UV-Vis spectroscopies. The maximum one-photon absorption (OPA) wavelengths were estimated to be shorter than 450 nm by quantum mechanical computations using the configuration interaction (CI) method. The same result was achieved by UV-Vis spectra measurements, whereas the compound exhibited good optical transparency to the visible light. Quantitative measurements of second harmonic generation (SHG) at 800 nm and 1064 nm have been performed. The relative efficiency comparable with that of KDP (kalium diphosphate) has been observed with the exciting wavelength of 1064 nm, while the other wavelength led to strong absorption of produced light by the sample. In the following more detailed study on frequency-dependent first hyperpolarizabilities using time-dependent Hartree–Fock (TDHF) method have been computed at the wavelengths used in SHG measurements.

In this paper some of the characteristic of Hückel method, were exploited in order to obtain some important results, through a new technique with which it is possible to obtain non-degenerate characteristic values as in the case of pyrrole and allowing the expression of conjugated ring systems (Pentalene) as function of a system of diene monomer (Cyclopentadienyl). The local similarity index based on the Hirshfeld partitioning in the framework of conceptual Density Functional Theory (DFT), was introduced in the secular determinant of the Hückel method and was applied to Pyrrole molecule in order to express their orbital energies as a function of the orbital energy of Cyclopentadienyl, to express the energies of molecular orbitals of the Cyclopentadienyl as a function of Pentalene, resolved by the Hückel method and applied to Cyclopentadienyl, by means of six local similarity index: Overlap, Overlap-Interaction, Coulomb, Coulomb-Interaction, with their respective Euclidean distances, using the Topo-Geometrical Superposition Approach (TGSA) as a method of alignment, which allowed us to obtain good results in local similarity indices.

This technique will permit the study of some molecular systems that differ in one atom in its molecular structure, resolving the Hückel method for the Pyrrole and Thiophene system without taking into account the considerations with its neighboring atoms. This proposed technique reduces the symmetry of fused ring systems which are Cyclopentadienyl derivatives, allowing to express the orbital energy of a diene dimmer (Pentalene) as a function of diene monomer systems, creating a tool of calculation to solve the problem of obtaining non-degenerate values in systems where the approximations in the Hückel method approximation provide degenerate values and providing a symmetry reduction technique.