Journal of Theoretical and Computational Chemistry

A global optimization scheme which utilizes the framework of replica-exchange simulation and replaces the system exchange probability for jumping between different temperature replicas with the kernel exchange probability is brought out. The kernel exchange probability is calculated by taking into account the kernel part interaction, including protein–protein interactions only, with protein–solvent and solvent–solvent interactions approximated by a continuum solvation model. All the configurations are sampled with potential energies explicitly considering water molecules during the simulation while the energies obtained from continuum solvation model play as a scoring function to rank the conformation during the exchange process. It is shown that this method gives nearly identical total potential energy distribution in the solvated alanine dipeptide system compared with the results of the standard replica-exchange simulation in which much more number of replicas has to be employed. This optimization method is highly demonstrated in successfully folding a β-hairpin peptide, C-terminus (residue 41-56) of protein G, from the extended structure to native conformation.

The reaction mechanism of SrO + CH₄ has been investigated on a singlet spin state potential energy surface at the B3LYP/SDD, AUG-cc-pVQZ//B3LYP/SDD, 6-311+G(2df, 2p) levels of theory. Initially, the reactants give two molecule–molecule complexes: (i) a collinear C–H approach to O-end of the Sr–O bond forming SrOCH₄ molecular complex with C_3v symmetry, and (ii) a side-on to side-on approach of C–H bond to Sr–O forming OSrCH₄ molecular complex with C₁ symmetry. From SrOCH₄, the SrOH + CH₃ radicals are formed by the direct abstraction of a hydrogen atom from CH₄ moiety. From OSrCH₄, the gas-phase methane to methanol conversion by SrO is suggested to involve the SrO insertion into a C–H bond of CH₄ to produce the hydroxy and methoxy intermediates, HOSrCH₃ and HSrOCH₃, and the reaction pathway via the hydroxy intermediate (HOSrCH₃) is energetically more favorable than the other one via the methoxy intermediate (HSrOCH₃). These channels to form (SrOH + CH₃) and (Sr + CH₃OH) are expected to compete with each other, and the formation of methyl radical via the direct Sr–C cleavage from HOSrCH₃ is energetically more preferable. On the other hand, the intermediates HSrOCH₃ and HOSrCH₃ are predicted to be the energetically preferred configuration in the reaction of Sr + CH₃OH, which is precisely the reverse reaction of methane hydroxylation. For the reaction of MO (M = Mg, Ca, Sr) with CH₄, the two main reaction pathways, methyl formation via a-TS1 and hydroxyl intermediate formation via b-TS1, are expected to compete with each other, and the preference of methyl formation pathway via a-TS1 would follow the sequence: MgO > CaO > SrO.

In this paper, we present a critical evaluation of the influence of geometry on the behavior of the transient current at all ultramicroelectrodes. The nonsteady-state chronoamperometric diffusion limited current of various microelectrodes (circular disc, circular ring, elliptical disc, elliptical ring, band, hemicylinder, hemisphere, hemioblate and hemiprolate electrodes) are compared. Here, the area of the entire electrode is fixed and time variables are also normalized with respect to area. The chronoamperometric current for short and long time for all microelectrodes are given in tabular as well as graphical form also.

The topological index of a graph G is a numeric quantity related to G which is invariant under automorphisms of G. In this paper, the vertex PI and Szeged indices of an infinite family of fullerenes are computed.

The formation mechanisms of pentafulvenone and azafulvenone were extensively investigated at the B3LYP/6-311++G** level and the potential energy surfaces were drawn out. Ketene pentafulvenone (A) and 3-carbonyl-3H-pyrrole (C) can be formed by eliminating N₂ from the diazo ketone via α elimination reaction and ketene 2-carbonyl-2H-pyrrole (B), 4-carbonyl-4H-imidazole (D), and 2-carbonyl-2H-imidazole (E) were formed by the elimination of water or methanol from pyrrole-2-carboxylic acid (rB) and carboxylate (rD and rE) via β elimination reaction. The structures of these monomers were compared and showed some information about the bond changed characters. The structure investigation indicated that the C=C bond is activated when the nitrogen atom locates in the ortho position of the C=C=O part, and therefore ortho-monomers are more facile to react. The difference of the amount and stability of the corresponding dimers are caused by differing the position and number of nitrogen atom and the variety of the ortho-dimer is complicated. In addition, the infrared spectra of the title species were also analyzed including the vibrational frequencies, IR relative intensities, and vibrational mode assignment.

A theoretical investigation about the cooperative effect on (HCN)_n homo and (HCN)_n ⋯ HF heterochains was performed in terms of structural parameters and topological properties obtained in concordance with the protocol of Bader's atoms in molecules theory. Initially, the hydrogen bonding distances, electronic densities, and Laplacian descriptors were used to characterize small (HCN)_n and (HCN)_n ⋯ HF chains formed by n = 2–4 units of HCN. Hydrogen bond distances and distribution of charge density have revealed that the cooperative effect on (HCN)_n ⋯ HF heterochains is ruled by the polarity of the extreme hydrofluoric acid species. Furthermore, we investigated larger homo and heterochain systems formed by n = 2–8 molecules of HCN. In this insight, the drastic polarized effect caused by HF molecule which was considered very substantial at prior, in fact is seriously limited by an excessive number of HCN molecules connected to the heterochain. This leads to a stabilization of the (N ⋯ HF) hydrogen bonds with invariable electronic density in the range of . In this stage and henceforth, the cooperative effect is re-established with n = 4 molecules of HCN. Thereby, the electronic density of the hydrogen bonds become unaltered within the (HCN)_n ⋯ HF heterochains.

Using one-center expansion relations for the Slater type orbitals (STOs) of noninteger principal quantum numbers in terms of integer nSTOs derived in this study with the help of ψ^a-exponential type orbitals (ψ^a-ETOs, a = 1, 0, -1, -2,…), the general formulas through the integer nSTOs are established for the unsymmetrical and symmetrical one-range addition theorems for STOs and Coulomb–Yukawa-like correlated interaction potentials (CIPs) with integer and noninteger indices. The final results are especially useful for the computations of arbitrary multicenter multielectron integrals that arise in the Hartree–Fock–Roothaan (HFR) approximation and also in the correlated methods based upon the use of STOs as basis functions.

The role of a surface oxygen vacancy in the N₂O dissociation over a Cu₂O surface was studied using density functional theory — generalized gradient approximation periodic calculations. To perform this study, surface slab model — surface cell was used. The results indicated that N₂O adsorption properties were associated with the surface oxygen vacancies. The presence of a surface oxygen vacancy, prepared by removing one O_SUF atom from supercell, makes the N₂O decomposition possible, which was believed to occur at a oxygen vacancy site. The N₂O decomposition at the surface oxygen vacant site depends on whether the molecule is adsorbed with the O- or N-end on a vacancy. For the first case, the reaction proceeds spontaneously, which leads to an ejection of N₂ from the surface and the rest of the oxygen atoms occupying the vacancy. In the second case, even though there is an elongation of both N–N and N–O bonds, the dissociation is unfeasible due to very small adsorption energy and high activation energy. The role of the defective surface with surface oxygen vacancy is to provide electrons to the adsorbed molecule.

Ab initio and density functional calculations are used to analyze the interaction between a molecule of fulminic acid with one, two, three, and four molecules of ammonia along with a 2:2 complex at B3LYP/6-311++G(d, p) and MP2/6-311++G(d, p) computational levels. Cooperative effect (CE) in terms of stabilization energy of clusters is calculated and discussed as well. For the studied clusters, the CE is increased with increasing cluster size. Red shifts of H–C stretching frequency for complexes involving HCNO as H-donor are predicted. Atom in molecules is used to analyze the cooperative effect on topological parameters.

Two-dimensional (2D) and three-dimensional (3D) quantitative structure–activity relationships (QSARs) of 23 analogs of 2-Methoxyestradiol with anticancer activity (expressed as pGI₅₀) against MCF-7 human breast cancer cells have been studied by using a combined method of the DFT, MM2 and statistics for 2D, as well as the comparative molecular field analysis (CoMFA) for 3D. The established 2D-QSAR model in training set shows not only significant statistical quality, but also predictive ability, with the square of adjusted correlation coefficient and the square of the cross-validation coefficient (q² = 0.779). The same model was further applied to predict pGI₅₀ values of the four compounds in the test set, and the resulting being as high as 0.827, further confirms that this 2D-QSAR model has high predictive ability for this kind of compound. The 3D-QSAR model also shows good correlative and predictive capabilities in terms of R²(0.927) and q²(0.786) obtained from CoMFA model. The results that 2D- and 3D-QSAR analyses accord with each other, suggest that the electrostatic interaction plays a decisive role in determining the anticancer activity of the studied compounds, and that increasing the negative charge of substituent R₂ and the positive charge of substituents linking to C₁₇ as well as decreasing the size of substituent R₁ are advantageous to improving the cytotoxicity. Such results can offer some useful theoretical references for directing the molecular design and understanding the action mechanism of this kind of compound with anticancer activity.