Global potential energy surface, vibrational spectrum, and reaction dynamics of the first excited (Ã (2)A(')) state of HO(2)

The authors report extensive high-level ab initio studies of the first excited (A??(2)A(')) state of HO(2). A global potential energy surface (PES) was developed by spline-fitting 17?000 ab initio points at the internal contracted multireference configuration interaction (icMRCI) level with the AVQZ basis set. To ascertain the spectroscopic accuracy of the PES, the near-equilibrium region of the molecule was also investigated using three interpolating moving least-squares-based PESs employing dynamically weighted icMRCI methods in the complete basis set limit. Vibrational energy levels on all four surfaces agree well with each other and a new assignment of some vibrational features is proposed. In addition, the dynamics of both the forward and reverse directions of the H+O(2)(a??(1)Δ(g))?OH+O reaction (J=0) were studied using an exact wave packet method. The reactions are found to be dominated by sharp resonances.     

Intermolecular ground and excited state potential energy surfaces and charge-transfer spectrum of benzene: TCNE electron donor—acceptor complex

The six-dimensional intermolecular potential energy surface of the benzene:tetracyanoethylene (TCNE) electron donor—acceptor (EDA) complex has been explored, using a combination of ab initio and semiempirical quantum mechanical calculations, at 4732 discrete intermolecular geometries. Spectroscopic INDO calculations were also performed at a subset of the total sampled configurations. The charge-transfer absorption lineshape was then calculated according to a previously described semiclassical approach, using the improved ab initio potential to average the spectrum over the donor—acceptor distance coordinate, R, in place of the previously employed harmonic approximation. The calculated lineshape was found to be in good agreement with the experimental gas phase optical absorption spectrum.     

Conformational analysis and interpretation of ν(OH) band in the IR spectrum of o-vinylphenol: a DFT study

Two-dimensional cyclic potential energy surface for internal rotation of vinyl and hydroxyl substituents in o-vinylphenol molecule was constructed by the B3LYP/6-311G(d) method. It was shown that o-vinylphenol molecule exists in the gas phase as a mixture of seven rotamers denoted as A (A′), B (B′), C (C′) and D. The B3LYP/cc-pVTZ calculated percentage of the rotamers A and A′ in which OH…π intramolecular interaction occurs, is at most 24%. The height of barriers t interconversions between o-vinylphenol rotamers varies from 0.1 to 5.2 kcal mol⁻¹. According to B3LYP/cc-pVTZ calculations, the inclusion of solvent effect in the framework of the polarizable continuum model for a solution of o-vinylphenol in CCl₄ leads to a decrease in theoretical values of ν(OH) frequencies by about 4–9 cm⁻¹ and to an increase in the percentage of the rotamers without intramolecular hydrogen bond by about 4.3% compared to the corresponding gas-phase values. The simulated IR spectral contours of ν(OH) bands are in good agreement with experimental one Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 499–508, March, 2008.     

Ab initio/empirical potential energy functions and stretching vibrational frequencies of the X̃ 2Π and à 2Π states of the chloroacetylene cation

Anharmonic potential energy functions for the stretching vibrational motions of the two lowest doublet states of chloro-acetylene cation have been constructed using ab initio RHF SCF calculations and some experimental information. Stretching vibrational frequencies are calculated variationally for four different isotopomers. The ν₁ vibrations of H¹²C₂³⁵Cl⁺ are predicted to occur at 3176 (X̃ ²Π) and 3231 (à ²Π) and the ν₂ vibration of the à state at 2081 cm⁻¹.     

Stark spectrum simulation for X2Y4 molecules: application to the ν12 band of ethylene in a high-silica zeolite

The influence of an electric field of silicalite-1-zeolite on the FTIR vibrational absorption spectrum of ethylene has been simulated and compared to experimental spectra. The presence of silicalite-1 produces a global shift and a change of the structure of vibrational bands. To explain the global shift of the ν(12) band (CH(2) scissor mode) and therefore to estimate an effective average field produced by silicalite-1, Stark calculations were performed. These calculations were based on a tensorial formalism implemented in the D(2h)TDS-ST package [M. Sanzharov, M. Rotger, C. Wenger, M. Lo?te, V. Boudon, and A. Rouzée, J. Quant. Spectrosc. Radiat. Transf. 112, 41 (2011)]. The value of the field obtained using tensorial formalism (8-11 GV/m) is compared with values obtained using ab initio calculations. A theory of the molecular alignment in the electric field using tensorial formalism is also developed to model the interaction of ethylene in contact with a zeolite environment.     

Role of protein structure and the role of individual fingers in zinc finger protein–DNA recognition: a molecular dynamics simulation study and free energy calculations

Molecular dynamics and MM_GBSA energy calculations on various zinc finger proteins containing three and four fingers bound to their target DNA gave insights into the role of each finger in the DNA binding process as part of the protein structure. The wild type Zif 268 (PDB code: 1AAY) gave a ΔG value of ??76.1 (14) kcal/mol. Zinc fingers ZF1, ZF2 and ZF3 were mutated in one experiment and in another experiment one finger was cut and the rest of the protein was studied for binding. The ΔΔG values for the Zinc Finger protein with both ZF1 and ZF2 mutated was +?80 kcal/mol, while mutating only ZF1 the ΔΔG value was +?52 kcal/mol (relative to the wild type). Cutting ZF3 and studying the protein consisting only of ZF1 linked to ZF2 gave a ΔΔG value of +?68 kcal/mol. Upon cutting ZF1, the resulting ZF2 linked to ZF3 protein gave a ΔΔG value of +?41 kcal/mol. The above results shed light on the importance of each finger in the binding process, especially the role of ZF1 as the anchoring finger followed in importance by ZF2 and ZF3. The energy difference between the binding of the wild type protein Zif268 (1AAY) and that for individual finger binding to DNA according to the formula: ΔΔG_{linkers, otherstructuralfactors}?=?ΔG_zif268???(ΔG_F1+F2+F3) gave a value?=???44.5 kcal/mol. This stabilization can be attributed to the contribution of linkers and other structural factors in the intact protein in the DNA binding process. DNA binding energies of variant proteins of the wild type Zif268 which differ in their ZF1 amino acid sequence gave evidence of a good relationship between binding energy and recognition and specificity, this finding confirms the reported vital role of ZF1 in the ZF protein scanning and anchoring to the target DNA sequence. The role of hydrogen bonds in both specific and nonspecific amino acid-DNA contacts is discussed in relation to mutations. The binding energies of variant Zinc Finger proteins confirmed the role of ZF1 in the recognition, specificity and anchoring of the zinc finger protein to DNA.     

Is the enthalpy of fusion of tris(acetylacetonato)metal(III) complexes affected by their potential energy in the crystal state?

In this Article we present enthalpies of fusion and melting points obtained from new thermochemical measurements of tris(acetylacetonato)metal(III), M(acac)(3), complexes (M = Fe, Al, Cr, Mn, Co) using differential scanning calorimetry (DSC) and evaluate them in relation to their different values found in the literature. An enthalpy of fusion of 27.67 kJ mol(-)(1) was derived for Mn(acac)(3) from a symmetrical DSC thermogram captured for the first time. The enthalpy value was indirectly confirmed with the solubility measurements of Mn(acac)(3) in acetylacetone. A hypothesis has been stated that the enthalpy of fusion and the potential energy of M(acac)(3) in the crystal state may be related. To calculate molecular in-crystal potential energy, in this Article we proposed a molecular mechanics model for the M(acac)(3) class of compounds. Nine X-ray crystal structures of M(acac)(3) complexes (M = Fe, Al, V, Mn, Co, Cr, Sc) were included in the modeling. The conformational potential energy was minimized for a molecule surrounded by other molecules in the crystal lattice. The partial charges from two schemes, the electrostatic potential (ESP) fit and the natural population analysis (NPA), were used to construct two types of force fields to examine which force field type would yield a better fit with the experimental thermal properties. The final force fields were named FF-ESP and FF-NPA. Both force field sets reproduced well the experimental crystal data of nine M(acac)(3) complexes as well as of tris(3-methyl-2,4-pentanedionato-O,O')cobalt(III). Only in-crystal potential energies derived by FF-NPA yielded a significant correlation (correlation coefficient R = -0.71) with the measured enthalpies of fusion. The enthalpy of fusion for Co(acac)(3) could not be determined experimentally because of simultaneous decomposition and fusion, and it is predicted to be 33.2 kJ mol(-)(1) from the correlation regression line.     

Ab initio potential energy curves and transition dipole moments for the interaction of a ground state He with Na(3s–3p)

Potential energy curves of the states X ²Σ⁺, B (1)²Σ⁺ and A (1)²Π of the NaHe molecule have been calculated accurately in a large range of internuclear distances R from SA-CASSCF-MRCI calculations, using molecular orbitals expanded in cc-pV5Z basis sets. Transition dipole moments have also been calculated for the X–B, X–A and A–B transitions, in the same range of R. Their long-range behaviour have been considered.     

Exchange energy density and exchange potential via a hartree–fock plus mp2 study of the electron liquid in the ground-state conformer of glycine

Very recent criticisms of existing exchange-correlation functionals by Wanko et al. applied to systems of biological interest have led us to reopen the question of the ground-state conformer of glycine: the simplest amino acid. We immediately show that the global minimum of the Hartree–Fock (HF) ground-state leads to a planar structure of the five non-hydrogenic nuclei, in the non-ionized form NH₂–CH₂–COOH. This is shown to lie lower in energy than the zwitterion structure NHB₃ ⁺–CH₂–COO^?, as required by experiment. Refinement of the nuclear geometry using second-order Møller–Plesset perturbation theory (MP2) is also carried out, and bond lengths are found to accord satisfactorily with experimentally determined values. The ground-state electron density for the MP2 geometry is then redetermined by HF theory and equidensity contours are displayed. The HF first-order density matrix γ( r , r ′) is then used to obtain similar exchange-energy density (ε _x ( r )) contours for the lowest conformer of glycine. At first sight, their shape looks almost the same as for the density ρ( r ), which seems to vindicate the LDA proportional to ρ( r )^3/4. However, by way of an analytically soluble model for an atomic ion, it is shown that this has to be corrected to obtain an accurate HF exchange energy E_x as the volume integral of ε _x ( r ). Finally, recognizing that for larger amino acids, the use of HF plus MP2 perturbation corrections will become prohibitive, we have used the HF information for ε _x ( r ) and ρ( r ) to plot the truly non-local exchange potential proposed by Slater, from the density matrix γ( r , r ′). This latter calculation should be practicable for large amino acids, but there adopting Becke's one-parameter form of ε _x ( r ) correcting LDA exchange. Some future directions are suggested.     

Theoretical study on the singlet and triplet potential energy surfaces of NH (X3Σ−) + HCNO reaction

Both the singlet and triplet potential energy surfaces (PESs) of the NH (X³Σ^?) + HCNO reaction have been investigated at the BMC-CCSD level based on the UB3LYP/6-311++G(d, p) structures. The results show that the title reaction is more favorable through the singlet potential energy surface than the triplet one. For the singlet potential energy surface of the NH (X³Σ^?) + HCNO reaction, the most feasible association of NH (X³Σ^?) with HCNO is found to be a non-barrier nitrogen-to-carbon attack forming the adduct a (trans-HNCHNO), which can isomerize to the adduct b (cis-HNCHNO). The most feasible channel is that the 1, 3-H shift with N2–H2 and C–N1 bonds cleavage associated with the N1–H2 bond formation of adduct a leads to the product P ₁ (HCN + HNO). Moreover, P ₂ (HNC + HNO) should be the competitive product. The other products, including P ₃ (NH₂ + NCO) and P ₄ (N₂H₂ + CO), are minor products. The product P ₁ can be obtained through two competitive channels Path 1: R → a → P ₁ and Path 3: R → b → d → P ₁ , whereas the product P ₂ can be formed through Path 2: R → b → d → P ₂ . At high temperatures, the nitrogen-to-nitrogen approach may become feasible. For the triplet potential energy surface of the NH (X³Σ^?) + HCNO reaction, the Path 10: R → ³ a → ³ a ₁ → P ₁ should be the most feasible pathway due to the less reaction steps and lower barriers. These conclusions will have impacts on further experimental investigations.     

The pyrolysis process of wood biomass samples under isothermal experimental conditions—energy density considerations: application of the distributed apparent activation energy model with a mixture of distribution functions

This work deals with the isothermal pyrolysis of Pine and Beech wood samples and kinetic studies, using the thermo-analytical technique, at five different operating temperatures. Pyrolysis processes were investigated by using the distributed apparent activation energy model, which involves the complex mixture of different continuous distribution functions. It was found that decomposition processes of wood pseudo-components take place in different conversion areas during entire pyrolyses, whereby these areas, as well as the changes in apparent activation energy (E _a) values, are not the same for softwood and hardwood samples. Bulk density (Bden) and energy density (ED) considerations have shown that both biomass samples suffer from low Bden and ED values. It was concluded that pyrolysis can be used as a means of decreasing transportation costs of wood biomass materials, thus increasing energy density. The “pseudo” kinetic compensation effect was identified, which arises from kinetic model variation and wood species variation. In the current extensive study, it was concluded that primary pyrolysis refers to decomposition reactions of any of three major constituents of the considered wood samples. Also, it was established that primary reactions may proceed in parallel with simultaneous decomposition of lignin, hemicelluloses and cellulose in the different regions of wood samples, depending on the operating temperature. It was established that endothermic effects dominate, which are characterized with devolatilization and formation of volatile products. It has been suggested that the endothermic behavior that arises from pyrolyses of considered samples may indicate the endothermic depolymerization sequence of cellulose structures.     

Potential propelling and rotating functions of propeller-type complexes. II. Preparation and molecular dynamics simulation of tris(5-carboxy-2,2′-bipyridine)cobalt(III)

Isolation of four optically active isomers of the 5-substituted 2,2′-bipyridine complexes [Co(cbpy)₃]³⁺ (cbpy?=?5-carboxy-2,2′-bipyridine) was achieved using cation-exchange column chromatography (SP-Sephadex C-25) eluting with either sodium (?)-O,O′-dibenzoyltartrate or sodium ((+)-tartrato)antimonate(III). Structure optimization and molecular dynamics (MD) simulations of the system consisting of the propeller-type complex fac-[Co(cbpy-H)₃] (cbpy-H?=?2,2′-bipyridine-5-carboxylate anion) and 80 water molecules were performed using the AMBER?6 program. Results of the MD simulation revealed that distinct translating and rotating behaviors can be obtained in this complex in aqueous solution upon IR irradiation.     

Optical response of a nematic liquid crystal cell at the splay – bend transition: a model and dynamic simulation

We study the dynamical optical response of a nematic liquid crystal cell that undergoes the splay–bend transition after applying a voltage across the cell. We formulate a simplified model that takes into account both the flexoelectric coupling and the surface rotational viscosity. The dynamic equations of the model are solved numerically to calculate the temporal evolution of the director profile and of the transmittance. We evaluate the response time as a function of a number of parameters, such as dielectric and elastic anisotropies, asymmetry of the surface pretilt angles, anchoring energy, surface rotational viscosity and flexoelectricity.     

Influence of solvent polarity on the separation of leucine enantiomers by β-cyclodextrin: a molecular mechanics and dynamics simulation

The interaction between leucine and β-cyclodextrin with different solvents was studied by molecular mechanics and dynamics simulations. In order to analyse the influence of the solvent polarity on the inclusion complex formation and separation process of leucine enantiomers by β-cyclodextrin, the organic modifiers were characterised by the same value of dielectric constant in the electrostatic contribution to the interaction energy, and a different molecular configuration of amino acids (neutral or zwitterion). The complexes formed in polar solvents were more stable than those in non-polar solvents with the same dielectric constant, because the electrostatic contribution is negative for the former and positive for the latter. The optimized structures obtained for leucine enantiomers and β-cyclodextrin in vacuo are non-inclusion complexes. The solvent polarity contributes to increasing the probability of the presence in an inner position for the guest, whereas the results for non-polar configurations were smaller and distributed in larger areas. The regions where the enantiomers spend more time in the simulation correspond to locations with greater chiral discrimination. d-Leu was the first eluted enantiomer in every case, except for a polar solvent with $\epsilon =26$.     

Electronic effect of β-diketonato ligands on the redox potential of fac and mer tris(β-diketonato) iron(III) complexes: A density functional theory study and molecular electrostatic potential analysis

Experimental redox potentials of 16 derivatives of tris(β-diketonato)iron(III) complexes (where β-diketonato(R₁COCHCOR₂)^─, with substituents R₁ and R₂ in different combinations of H, C₄H₃S, C₄H₃O, CH₃, Ph, CF₃, or C (CH₃)₃), and 11 additional isomers, were studied theoretically in terms of the electronic properties, substituent effects, electron affinity, and molecular electrostatic potential (MESP) analysis, using density functional theory methods. The computational methods reproduced the experimental reduction potential to a very high level of accuracy, especially when the M062X functional was used (with mean absolute deviation [MAD] = 0.054 and 0.093 and correlation R² = 0.978 and 0.981 obtained by application of two slightly different free energy cycles, respectively). The most negative computed reduction potential corresponds to the most negative reported experimental reductions, which is indicative of the least favorable reduction potential, also in most cases the most stable molecules energetically. The calculated reduction potentials of the fac isomers of the molecules were generally higher (less negative) than that of the mer isomers when one of the ligand substituents R₁ or R₂ was CF₃ (M062X results), indicating better ease of reduction, although in many cases, the experimental reduction potential agreed better with the calculated reduction potential of the mer isomer instead. The calculated reduction potentials were also affected by the substituents in the order of CF₃ > H > C₄H₃S > C₄H₃O > Ph > CH₃ > C(CH₃)₃ (the most negative value). The stronger the electron withdrawing tendency of the substituent, the more favorable (less negative value) the reduction potential becomes. In relation to the CH₃-substituted molecule 1 as a reference, the molecules with electron withdrawing substituents resulted in an electron-deficient MESP iso-surface, in both the neutral state and reduced state. All the molecules in their reduced state were characterized with an electron-deficient MESP iso-surface compared with the reduced CH₃-substituted molecule 1, with the deficiency increasing in mer compared with fac, for both the neutral and reduced molecules. The relative MESP values of ΔV_Fe in the reduced state of the molecules were able to predict the corresponding experimental reduction potential to a significant level of accuracy (with MAD = 0.091).     

Helium mediated deposition: modeling the He-TiO2(110)-(1×1) interaction potential and application to the collision of a helium droplet from density functional calculations

This paper is the first of a two-part series dealing with quantum-mechanical (density-functional-based) studies of helium-mediated deposition of catalytic species on the rutile TiO(2)(110)-(1×1) surface. The interaction of helium with the TiO(2)(110)-(1×1) surface is first evaluated using the Perdew-Burke-Ernzerhof functional at a numerical grid dense enough to build an analytical three-dimensional potential energy surface. Three (two prototype) potential models for the He-surface interaction in helium scattering calculations are analyzed to build the analytical potential energy surface: (1) the hard-corrugated-wall potential model; (2) the corrugated-Morse potential model; and (3) the three-dimensional Morse potential model. Different model potentials are then used to study the dynamics upon collision of a (4)He(300) cluster with the TiO(2)(110) surface at zero temperature within the framework of a time-dependent density-functional approach for the quantum fluid [D. Mateo, D. Jin, M. Barranco, and M. Pi, J. Chem. Phys. 134, 044507 (2011)] and classical dynamics calculations. The laterally averaged density functional theory-based potential with an added long-range dispersion interaction term is further applied. At variance with classical dynamics calculations, showing helium droplet splashing out of the surface at impact, the time evolution of the macroscopic helium wave-function predicts that the helium droplet spreads on the rutile surface and leads to the formation of a thin film above the substrate. This work thus provides a basis for simulating helium mediated deposition of metallic clusters embedded within helium nanodroplets.     

Diels-Alder addition of some 6- and 5-member ring aromatic compounds on the Si(001)-2×l surface: dependence of the binding energy on the resonance energy of the aromatic compounds

An energy decomposition scheme is proposed for understanding of the relative low binding energy of the [4+2] cycloaddition of benzene on the Si(001)-2x1 surface. By means of density functional cluster model calculations, this scheme is demonstrated to be applicable to some other 6- and 5-member ring aromatic compounds, giving a trend that the binding energy of the [4+2] cycloaddition products of those aromatic compounds on the Si(001) surface depends strongly on their resonance energy.     

Synthesis, microwave spectrum, and dipole moment of allenylisocyanide (H2C═C═CHNC), a compound of potential astrochemical interest

An improved synthesis of a compound of potential astrochemical interest, allenylisocyanide (H(2)C═C═CHNC), is reported together with its microwave spectrum, which has been investigated in the 8-120 GHz spectral range to facilitate a potential identification in interstellar space. The spectra of the ground vibrational state and of five vibrationally excited states belonging to three different vibrational modes have been assigned for the parent species. A total of 658 transitions with a maximum value of J = 71 were assigned for the ground state and accurate values obtained for the rotational and quartic centrifugal distortion constants. The spectra of five heavy-atom ((13)C and (15)N) isotopologues were also assigned. The dipole moment was determined to be μ(a) = 11.93(16) × 10(-30) C m, μ(b) = 4.393(44) × 10(-30) C m, and μ(tot) = 12.71(16) × 10(-30) C m. The spectroscopic work has been augmented by theoretical calculations at the CCSD/cc-pVTZ and B3LYP/cc-pVTZ levels of theory. The theoretical calculations are generally in good agreement with the experimental results.