Showing papers in "Journal of Theoretical and Computational Chemistry in 2012"

Atomic dipole moment corrected hirshfeld population method

Abstract: 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.

A theoretical study on the antioxidant property of gallic acid and its derivatives

Abstract: We analyze the antioxidant property of four phenolic compounds i.e., gallic acid, methyl gallate, ethyl gallate, and 4, 5-dihydroxy 3-methoxy benzoic acid through the determination of bond dissociation enthalpy (BDE), vertical ionization potential (IPv) in gas phase as well as in six different solvent medium. The theoretical trends of these phenolic compounds, based on BDE and IP, is compared with the scavenging activity towards HOCl. In addition, we compute and analyze the values of the density-based reactivity descriptors such as chemical potential, hardness, electrophilicity, and local softness.

Theoretical studies on the mechanism of cyclic nucleotide monophosphate hydrolysis within phosphodiesterases

Abstract: As the only metabolizing enzyme for the degradation of second messenger cAMP and cGMP, phosphodiesterase (PDE) has been the clinical target of various human diseases. But the hydrolysis procedure of PDE is still unclear. To investigate the mechanism of PDE catalysis, three types of PDE (PDE4d, PDE5a and PDE10a) were selected and studied by using molecular dynamics (MD) simulation and quantum mechanics (QM) calculation methods. MD Simulation results indicate that different PDEs share a similar hydrolysis area in the active sites, and the phosphate parts of cyclic nucleotides take the same orientation and are partly surrounded by water molecules. Based on the statistical data of MD simulation, the QM calculation models were built. The calculation results indicate that in aqueous solution, the nucleophile hydroxide ion that attacks the phosphor atom of the cyclic nucleotide in the hydrolysis may migrate between the two metal ions in the active site. To help the ring-open reaction, it is the water molecule that provides proton to the O3′ atom of cyclic nucleotide, and generates another hydroxide ion complexed with the metal ion.

THEORETICAL CALCULATION OF pKb VALUES FOR ANILINES AND SULFONAMIDE DRUGS IN AQUEOUS SOLUTION

Abstract: In this work, calculations of pKb values have been performed for aniline and its substituted derivatives and sulfonamide drugs by using Gaussian 98 software package. Gas-phase energies were calculated with HF/6-31 G** and B3LYP/6-31 G** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor-like polarizable continuum model (CPCM) and the integral equation formalism-polarizable continuum model (IEFPCM) at the same levels which have been used for geometry determination in the gas-phase. The results show that the calculated pKb values using the B3LYP/6-31 G** are better than those using the corresponding HF/6-31 G**. At first, the correlation equation was found to determine the pKb values of the investigated anilines. Then, this correlation equation was used to calculate the pKb values of the sulfonamide drugs. The results obtained indicate that the PCM model is a suitable solvation model for calculating pKb values in comparison to the other solvation models. For the investigated compounds a good agreement between the experimental and the calculated pKb values was also observed.

Dft quantum chemical studies on 1-[n-(2-pyri̇dyl) ami̇nomethyli̇dene]-2(1h)-naphtalenone

Abstract: Quantum chemical calculations of the structure, molecular electrostatic potential and thermodynamic functions have been performed using the density functional (DFT/B3LYP) method with the 6-311++G(d,p) basis set for the title compound 1-[N-(2-pyridyl)aminomethylidene}-2(1H)-Naphtalenone. The energetic behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole μ, the polarizability α and the first hyperpolarizability β were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-311++G(d,p) basis set. According to our calculations, the title compound exhibits nonzero β value revealing second order NLO behavior. The changes of thermodynamic properties for the formation of the title compound with the temperature ranging from 200 K to 500 K have been obtained using the statistical thermodynamic method. The relationship between formation enthalpy and entropy changes has been investigated with the entropy–enthalpy compensation. Besides, natural bond orbital and frontier molecular orbital analysis of the title compound were investigated by theoretical calculations.

A dft study on the role of different oh groups in the radical scavenging process

Abstract: The molecular properties of robinetin and melanoxetin which are the two naturally occurring flavonoid compounds have been studied theoretically by means of density functional theory approach (DFT) at the level of B3LYP/6-311G(d,p). The analysis of computed bond dissociation enthalpy (BDE), proton dissociation enthalpy (PDE), proton affinity (PA), electron transfer enthalpy (ETE) values for both the flavonoid compounds indicate the role of B-ring for the significant antioxidant characteristics and the instability of the A-ring. It also concerns the dominant role of BDE mechanism for antioxidant activity than PDE, PA and ETE mechanisms. Ionization potential (IP) is also found to be trustworthy in the study of antioxidant activity and the computed IP magnitudes are in agreement with the values of synthetic food additives. Further, the various molecular descriptors along with the plot of frontier molecular orbitals and Mulliken spin population analysis have been obtained and the validity of Koopmans' theorem is also verified with reference to antioxidant behavior.

Size dependence of solvation structure and dynamics of ions in liquid n-methylacetamide: a molecular dynamics simulation study

Abstract: The solvation structure and dynamics of alkali metal (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions in liquid N-methylacetamide (NMA) are calculated at two different temperatures T = 313 K and 453 K, by using classical molecular dynamics simulations. We have also considered and some larger cations such as I+, Me4N+, and Et4N+ in this study to investigate the size dependence solvation structure and dynamics of ions in liquid NMA. With the increase of ion size, the self-diffusion coefficients of cations are found to increase and the maximum is observed at Me4N+, whereas for halide ions the increase of diffusion coefficient with ion size continues up to I- and no maximum is observed. However, the relative increase of the diffusion coefficients of larger ion compared to those of Li+ and F+ are found to be significantly higher at low temperature. Results are very good in agreement with experimental observation.

ADSORPTION STATES AND SITE CONVERSIONS OF PHENYLACETYLENE ON Si(100)2 × 1 CALCULATED BY DFT

Abstract: The adsorption on Si(100)2 × 1 of PhenylAcetilene (PA), a bifunctional molecule with a phenyl ring and a triple bond, may occur through each group, selectively, or both functional groups simultaneously. The most favorable adsorption sites upon adsorption were calculated by DFT. Furthermore, several energy barriers were calculated: The ones connecting the physisorbed to the chemisorbed states, as well as the interconversion barriers of different chemisorbed states. The conversion of physisorbed-to-chemisorbed states has barriers of 0.11–0.19 eV. The barriers of sites inter-conversions are all higher (1.11–1.36 eV) and suggest a difficult post-chemisorption surface rearrangement.

POTENTIAL ENERGY SURFACE, MICROWAVE AND INFRARED SPECTRA OF THE Xe–CO2 COMPLEX FROM AB INITIO CALCULATIONS

Abstract: We present a new three-dimensional potential energy surface for Xe–CO2 including the Q3 normal mode for the υ3 antisymmetric stretching vibration of the CO2 molecule. Two vibrationally adiabatic potentials with CO2 in both the ground (υ3 = 0) and the first excited (υ3 = 1) states are generated by the integration of this potential over the Q3 coordinate. Each potential is found to have a T-shaped global minimum. The radial DVR/angular FBR method and the Lanczos algorithm are employed to calculate the rovibrational energy levels. The calculated band origin shifts, microwave and infrared spectra based on the two averaged potentials are in good agreement with the available experimental data.

Evolutionary discovery of transition states in water clusters

Abstract: As a basic Aristotle element, water is the most abundant and more importantly crucial substance on earth. Without water, there would not be any form of life as we know. Understanding many phenomena in water such as water evaporation and ice melting and formation requires a deep understanding of hydrogen bond breaking and formation. In particular transition states play a key role in the understanding of such hydrogen bond behavior. Transition states, unlike other metastable states, are energy maxima along the minimum energy path connecting two isomers of molecular clusters. Geometry optimization of transition state structures, however, is a difficult task, and becomes even more arduous, especially when dealing with complex biochemical systems using first-principles calculations. In this paper, a novel molecular memetic algorithm (MOL-MA) composing of specially designed molecular-based water evolutionary operators coupled with a transition-state-local search solver and valley adaptive clearing scheme for the discovery of multiple precise transition states structures is proposed. The transition states of water clusters up to four water molecules uncovered using MOL-MA are reported. MOL-MA is shown not only to reproduce previously found transition states in water clusters, but also established newly discovered transition states for sizes 2–4 water molecules. The search performance of MOL-MA is also shown to outperform its compeers when pitted against those reported in the literature for finding transition states as well as recent advances in niching algorithms in terms of solution precision, computational effort, and number of transition states uncovered.

The effect of substitution on structure, intramolecular hydrogen bonding strength, electron density and resonance in 3-amino 2-iminomethyl acryl aldehyde

Abstract: B3LYP/6-311++G** calculations have been carried out to simulate the influence of substitutions in position R1 and R2 of 3-amino 2-iminomethyl acryl aldehyde on intramolecular hydrogen bond strength. The following substituents are taken into considerations: CN, NO2, Cl, F, CH3, CHO, NH2, C2H5, SH, SCH3, CF3 and CH3CO and their vibrational frequencies are calculated at the same level of theory. Quantum theory of "Atoms in Molecules" and Natural Bond Orbitals method were applied to analyzed H-bond interactions. The electron density (ρ) and Laplacian (∇2ρ) properties, estimated by AIM calculations, indicate that N⋯H bond possesses low ρ and positive ∇2ρ values which are in agreement with electrostatic character of the HBs, whereas N–H bonds have covalent character (∇2ρ < 0). Natural population analysis data, the electron density and Laplacian properties, as well as, ν(N-H) and γ(N-H) have been used to evaluate the hydrogen bonding interactions.

Hückel treatment of pyrrole and pentalene as a function of cyclopentadienyl using local quantum similarity index (lqsi) and the topo-geometrical superposition approach (tgsa)

Abstract: In this paper some of the characteristic of Huckel 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 Huckel 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 Huckel 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 Huckel 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 Huckel method approximation provide degenerate values and providing a symmetry reduction technique.

The investigation of second-order nonlinear optical properties of p-nitrophenylazoaniline: second harmonic generation and ab initio computations

Abstract: 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.

Effects and role of water environment on a geminal hydroxylated silica surface — self-consistent charge density functional tight binding theory based molecular dynamics simulation

Abstract: 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.

DENSITY FUNCTIONAL THEORY STUDIES OF CHARGED, COPPER-DOPED, SMALL SILICON CLUSTERS, ${\rm CuSi}_{n}^{+}/{\rm CuSi}_{n}^{-}$ (n = 1–7)

Abstract: 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 CuSin 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 CumSin (2 ≤ m + n ≤ 7) clusters, Chin Phys16:3359, 2007]. Our results for the ground state structures of neutral CuSin 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.

Theoretical study on cui-catalyzed ligand-free n-arylation of imidazole with bromobenzene

Abstract: The density functional theory (DFT) is used to investigate the mechanism of ligand-free CuI-catalyzed N-arylation of imidazole with aryl halide. The oxidative addition/reductive elimination mechanism is adopted via two different pathways to form the same Cu(III) intermediate. Comparing two pathways, the path 1 in which the imidazolyl coordination occurs prior to the oxidative addition is more favorable, because the free energy barrier of the rate-limiting step of path 1 is lower than the barrier of the other. In addition, it leads to a relative stable intermediate which can promote the reaction to process via path 1. And the overall free energy barrier of oxidative addition to imidazole-ligated Cu(I) complex is not high enough when comparing with the diamine-promote process, which can further prove that the N-arylation of imidazole is feasible in the absence of additional ligands. Nucleophile coordination and reductive elimination steps are facile, while the oxidative addition is the rate-limiting step.

In silico prediction of melting points of ionic liquids by using multilayer perceptron neural networks

Abstract: 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.

THE GEOMETRIES AND PROTON TRANSFER OF HYDRATED DIVALENT LEAD ION CLUSTERS [Pb(H2O)n]2+(n = 1–17)

Abstract: The low-lying candidates of hydrated divalent lead ion clusters [Pb(H2O)n]2+ with up to n = 17 have been extensively studied by using density functional theory (DFT) at B3LYP level. The optimized structures show that for n = 5–13 the lowest-energy structures prefer tetracoordinate with hemi-directed geometries, while the best candidates with n = 14–17 are hexacoordinate with holo-directed geometries, which is just consistent with the experimental observation. Furthermore, the origin of hemi-directed and holo-directed geometries has been revealed. It is found that in the hemi-directed geometries, the lone pair orbital has p character and fewer electrons are transferred from the water molecules to the Pb2+ ion. Contrarily, in the holo-directed geometries, the lone pair orbital has little or no p character and more electrons are transferred to the Pb2+ ion. On the other hand, the proton transfer reactions of the [Pb(H2O)n]2+(n = 2, 4, 8) complexes have been examined, from which the predicted products of these complexes are in good agreement with the experimental observation.

A dft study of co migratory insertion reactions with a new type of group 10 metal-alkyl and metal-alkoxide bonds

Abstract: 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).

Assessment of the performance of the m05-class and m06-class functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes

Abstract: The M05-class (M05 and M05-2X) and M06-class (M06, M06-2X, M06-HF, and M06-L) functionals, developed by Zhao and Truhlar, have shown better performance than popular older DFT functionals in obtaining accurate binding energies of noncovalent complexes. However, the reliability of these functionals for the structure and geometry of noncovalent systems was seldom assessed. Here, using the MP2/aug-cc-pVTZ values as a benchmark, we assessed the performance of the M05-class and M06-class functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes. The results clearly show that the M05, M06 and M06L functionals totally fail to predict the structure of the hydrogen-bonded complex formed between glycine and carbonic acid whereas the M05-2X, M06-2X, M06-HF, and even B3LYP succeed. For the geometries of a series of halogen-bonded complexes, it is found that the M05-2X functional performs slightly better than the M06-2X and M06-HF functionals and much better than the M05, M06 and M06-L functionals on average. Based on these tests, we concluded that the M05, M06 and M06-L functionals are not good for the study of the structure and geometry of the hydrogen-bonded and halogen-bonded complexes and the density functional M05-2X is the best choice. In addition, we have also assessed the integration grid errors arising from the numerical integration of these functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes.

Erratum: "computational studies of squalene synthase from panax ginseng: homology modeling, docking study and virtual screening for a new inhibitor"

Abstract: Through a reductive dimerization of two farnesyl diphosphate (FPP) molecules, Squalene synthase from Panax ginseng (P. ginseng) (PgSS) catalyzes the biosynthesis of squalene, a key cholesterol precutsor, and hence is an attractive site of therapeutic intervention. Thus, the 3D structure of PgSS has been firmly established by homology modeling and was used to relax by MD simulation to get the reliable structure. It is well known that Mg2+ plays an important role in substrate binding. Understanding how PgSS recruits the FPP substrate through Mg2+ is the first and foremost step toward further mechanistic investigations and the design of effective PgSS inhibitors. Quantum mechanical calculation method is used to determine the Mg2+ binding mode. In the first binding motif, the Mg2+ ion is coordinated to D77, D81, and one oxygen atom from the α- and β-phosphates of FPP. In order to determine the important residue of the substrate (FPP) binding, we dock the one FPP to the protein. Arg113 may be an important residue because they form a salt bridge with PgSS. After virtual screening technique of PgSS, a novel natural compound (8002215) has been found with the lowest affinity energy. Then we identify that His266 is the most important anchoring residue for binding with 8002215 because it has strong edge-to-face interaction with inhibitor. Leu205 and Gln206 are important residues for they make hydrogen bonds with inhibitor. Our results may be helpful for further experimental investigations.

Elemental and mixed actinide dioxides: an ab initio study

Abstract: We present a systematic study of the electronic, geometric, and magnetic properties of the actinide dioxides, UO2, PuO2, AmO2, U0.5Pu0.5O2, U0.5Am0.5O2 and Pu0.5Am0.5O2. For UO2, PuO2 and AmO2, both density functional and hybrid density functional theory (DFT and HDFT) have been used. The fractions of exact Hartree–Fock (HF) exchange chosen were 25% and 40% for the hybrid density functional. For U0.5Pu0.5O2, U0.5Am0.5O2 and Pu0.5Am0.5O2, only HDFT with 40% exact HF exchange was used. Each compound has been studied at the nonmagnetic, ferromagnetic and anti-ferromagnetic configurations, with and without spin–orbit coupling (SOC). The lattice parameters, magnetic structures, bulk moduli, band gaps and density of states have been computed and compared to available experimental data and other theoretical results. Pure DFT fails to provide a satisfactory qualitative description of the electronic and magnetic structures of the actinide dioxides. On the other hand, HDFT performs very well in the prediction and description of the properties of the actinide dioxides. Our total energy calculations clearly indicate that the ground-state structures are anti-ferromagnetic for all actinide dioxides considered here. The lattice constants and the band gaps expand with an increase of HF exchange in HDFT. The influence of SOC is found to be significant.

INTERACTIONS OF THE NUCLEOTIDES WITH THE METAL IONS Mg2+, Ca2+, Mn2+, Na+, AND K+

Abstract: The interactions of the four typical nucleotides with the metal ions Mg2+, Ca2+, Mn2+, Na+, and K+ were studied by using the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) calculations in the PCM model. A lot of initial binding sites of the metal ions were designed and optimized to determine the most stable structures of the metal ion nucleotide compounds. It has been shown that the metal ions tend to attach at the center of the negatively charged atoms of the nucleotides. Furthermore, the vertical excitation energies of the metal ion nucleotide compounds were calculated at the same level with the TDDFT method, and also NBO charges were analyzed to understand the bonding characteristics between the metal ions and the nucleotides. That was also compared with the conclusion in the gas phase.

FIRST-PRINCIPLES STUDY OF OXYGEN-VACANCY Cu2O (111) SURFACE

Abstract: Geometric and electronic properties and vacancy formation energies for two kinds of oxygen-vacancy Cu2O (111) surfaces have been investigated by first-principles calculations. Results show that the relaxation happens mainly on the top three trilayers of surfaces. Two vacancies trap electrons of -0.11e and -0.27e, respectively. The effects of oxygen vacancies on the electronic structures are found rather localized. The electronic structures suggest that the oxygen vacancies enhance the electron donating ability of the surfaces to some extent. The energies of 1.75 and 1.43 eV for the formation of oxygen vacancies are rather low, which indicates the partially reduced surfaces are stable and easy to produce.

Effect of cation radical formation on reactivity and acidity enhancement of cytosine nucleobase: natural bond orbital and atom in molecule analysis

Abstract: The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The influence of cation radical formation on acidities of multiple sites in cytosine molecule was investigated. Results of calculations revealed that cytosine radicals formed by deprotonation of cytosine cation radicals can exothermically abstract hydrogen atoms from thiol groups, phenol, and α-positions of amino acid. Furthermore, comparison of acidity value of N–H sites of cytosine cation radical with the known proton affinities (PA) of organic and biological molecules implied that cytosine cation radical can exothermically transfer onto basic sites of amino acids and peptides.

POTENTIAL ENERGY SURFACES AND MICROWAVE SPECTRA FOR 20Ne–13C16O2, 22Ne–12C16O2 and 22Ne–13C16O2 COMPLEXES

Abstract: We report averaged potential energy surfaces for isotopic Ne–CO2 complexes (20Ne–13C16O2, 22Ne–12C16O2 and 22Ne–13C16O2). According to the latest ab initio potential of 20Ne–12C16O2 (Chen R, Jiao EQ, Zhu H, Xie DQ, J Chem Phys133:104302, 2010) including the Q3 normal mode for the υ3 antisymmetric stretching vibration of the CO2 molecule. We obtain the averaged potentials for 20Ne–13C16O2, 22Ne–12C16O2 and 22Ne–13C16O2 by the integration of the three-dimensional potential over the Q3 coordinate. The averaged potential surfaces are found to have a T-shaped global minimum and two equivalent linear local minima. The radial DVR/angular FBR method and the Lanczos algorithm are applied to calculate the rovibrational energy levels. Comparison with the available observed values showed an overall excellent agreement for all spectroscopic parameters and the microwave spectra.

Molecular modeling of the interactions between histone deacetylase 8 and inhibitors

Abstract: Inhibitors of histone deacetylases (HDACs) have become an attractive class of anticancer agent. To understand the interaction between HDAC8 and inhibitors, including "pan-" inhibitors that inhibit many HDACs isoforms and selective inhibitors with no linker domain, docking and molecular dynamics simulation were conducted. Docking results showed the presence of π-π interactions between "linkerless" inhibitors and the aromatic amino acid residues of HDAC8 in the active site. Binding between HDAC8 and inhibitors was also stabilized by hydrogen bond and hydrophobic interaction. In molecular dynamics simulations, the zinc ion was shown to coordinate one more atom of HDAC8-"linkerless" inhibitor complexes than HDAC8-"pan-" inhibitor complexes. Persistent hydrogen bonds also existed between Tyr306 of HDAC8 and some inhibitors. When inhibitors with large cap groups bound to the active pocket of HDAC8, Phe152 and Met274 shifted from their initial positions and the entrance of the active pocket became more open, resulting in the formation of sub-pocket. Hydrophobic interactions contributed most favorably to the binding free energy between HDAC8 and inhibitors. Lys33, Asp178, Asp267, Tyr306 and Leu308 of HDAC8 were favorable for binding with all inhibitors.

An ab initio molecular dynamics study on the solvation of formate ion and formic acid in water

Abstract: Formate ion and formic acid are linked in water by the equilibrium for the acidic dissociation of formic acid, which as the simplest carboxylic acid is an important model system. In this study, the microscopic details of the solvation around a formate ion and around a formic acid molecule in aqueous solution are explored by ab initio molecular dynamics simulations, at 300, 500, 700, and 900 K. The formate ion exerts a strong influence on the surrounding solvent molecules by hydrogen bonding, which restricts the access of other water molecules. With rising temperature, the hydrogen bonds are disrupted, and the space around formic acid becomes more accessible. Solvation of the formic acid is marked by its partial dissociation to produce a proton, and the hydrogen bond interaction around a formic acid is not as strong as that around a formate ion. The acidic dissociation becomes less favorable as temperature rises, which indicates a lesser catalytic role for the water molecules in the thermal dissociation of formic acid.

Exploring the molecular basis of h5n1 hemagglutinin binding with catechins in green tea: a flexible docking and molecular dynamics study

Abstract: 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.

Theoretical study on the second-order nonlinear optical properties of c,b-substituted carborane conjugated derivatives

Abstract: To systemically investigate structure–property relationship and design excellent nonlinear optical (NLO) material, the second-order NLO properties of a series of C,B-substituted carborane conjugated derivatives have been studied by density functional theory (DFT). The static first hyperpolarizabilities (βtot) were calculated at the M05-2X/6-31+G* level of theory. The results show that the βtot values gradually increase with the increasing of the conjugation length, especially the introduction of ferrocene. It is found that 1,3-benzo-o-carborane-ferrocene (2h) has the largest first hyperpolarizability (55.968 × 10-30 esu), which is 150 times larger than that of benzocarborane (1a). This means that the static first hyperpolarizabilities of the studied compounds can be substantially increased by structural modification. A basis for understanding the origin of these large NLO responses is proposed based on consideration of the frontier molecular orbitals (FMOs), orbital energy, transition energy of the studied compounds, and the two-state mode. The lower transition energy and larger oscillator strength play an important role in increasing the first hyperpolarizability value. This study may evoke possible ways to design preferable NLO materials.