Energy Surface (energy + surface)

Distribution by Scientific Domains
Distribution within Chemistry

Kinds of Energy Surface

  • ab initio potential energy surface
  • initio potential energy surface
  • potential energy surface


  • Selected Abstracts


    ChemInform Abstract: New Molecular Species of Potential Interest to Atmospheric Chemistry: Isomers on the [H, S2, Br] Potential Energy Surface

    CHEMINFORM, Issue 17 2009
    Antonio Gustavo S. de Oliveira-Filho
    Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]


    ChemInform Abstract: An ab initio Potential Energy Surface and Vibrational Energy Levels of HXeBr.

    CHEMINFORM, Issue 38 2008
    Zheng Guo Huang
    Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]


    An ab initio Quantum Chemical and Kinetic Study of the NNH + O Reaction Potential Energy Surface: How Important Is this Route to NO in Combustion?

    CHEMINFORM, Issue 45 2003
    Naomi L. Haworth
    Abstract For Abstract see ChemInform Abstract in Full Text. [source]


    ChemInform Abstract: Microsolvation of Hydrogen Sulfide: Exploration of H2S×(H2O)n and SH - ×H3O+× (H2O)n-1 (n = 5,7) Cluster Structures on ab initio Potential Energy Surfaces by the Scaled Hypersphere Search Method.

    CHEMINFORM, Issue 27 2008
    Satoshi Maeda
    Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]


    Theoretical Study of the Potential Energy Surfaces of Nitrogen-Rich Ion N4H2F+.

    CHEMINFORM, Issue 52 2002
    Li Jie Wang
    No abstract is available for this article. [source]


    The Role of Axial Ligation in Nitrate Reductase: A Model Study by DFT Calculations on the Mechanism of Nitrate Reduction

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 34 2008
    Kuntal Pal
    Abstract The reactivity differences of the model anionic complexes [Mo(mnt)2(X)(PPh3)], [mnt2, = 1,2-dicyanoethylenedithiolate; X = SPh (1a), SEt (1b), Cl (1c), Br (1b)] towards oxygen atom transfer from nitrate, which is a key step performed by nitrate reductase, has been investigated by density functional theory calculations. Unlike complexes 1a and 1b, complexes 1c and 1d do not react with nitrate. Thermodynamically, all these complexes have a similar ability to generate the pentacoordinate active state [Mo(mnt)2(X)], by dissociation of PPh3, although the inaccessibility of the dxy orbital in 1c,d and the instability of the corresponding nitrate-bound enzyme substrate (ES) type complex contributes to their failure to reduce nitrate. The nature of the ES complex for 1a,b is described. The variation in the experimental data due to the change of axial ligation from SPh to SEt on the catalytic pathway has also been addressed. The gas-phase and solvent-corrected potential energy surface for the reaction of 1a,b with nitrate are established with fully optimized minima and transition states.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]


    Nitrogen Trifluoride as a Bifunctional Lewis Base: Implications for the Adsorption of NF3 on Solid Surfaces

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2004
    Paola Antoniotti
    Abstract The structure, stability, and thermochemistry of isomeric adducts between NF3 and the Lewis acids BH3,nFn (n = 0,3) have been investigated at the coupled-cluster and at the Gaussian-3 (G3) level of theory. At the CCD/cc-pVDZ level both the nitrogen- and the fluorine-coordinated structures of all BH3,nFn,(NF3) (n = 0,3) adducts were characterized as true minima on the potential energy surface, thus providing the first theoretical evidence for the behavior of NF3 as a bifunctional Lewis base when interacting with neutral Lewis acids. At the G3 level, and 298.15 K, including the contribution of the entropy term, the H3B,NF3 adduct is predicted to be more stable than H3B,F,NF2 by 4.3 kcal mol,1; this free energy difference is 3.7 kcal mol,1 at the CCSD(T)/cc-pVTZ//CCD/cc-pVDZ level of theory. Conversely, at the latter computational level, the fluorine-coordinated isomers of the BH2F,(NF3), BHF2,(NF3), and BF3,(NF3) adducts are practically degenerate with the nitrogen-coordinated ones. BH3,nFn,(NF3) (n = 0,3) complexes feature typical bond dissociation energies of ca. 1,2 kcal mol,1, and are predicted to be thermodynamically stable only at low temperatures. However, the appreciable influence of the basis set superposition error (BSSE) prevents a quantitative assessment of these small computed dissociation energies. Finally, we briefly discuss the implications of our calculations for the adsorption of NF3 on solid surfaces. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]


    Bent and Linear Forms of the (,-Oxo)bis[trichloroferrate(III)] Dianion: An Intermolecular Effect , Structural, Electronic and Magnetic Properties

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 23 2003
    Agustí Lledós
    Abstract We have analyzed the great diversity of Fe,O,Fe angles, 140,180°, found in the X-ray structures of the (,-oxo)bis[trichloroferrate(III)] dianion [Cl3FeOFeCl3]2, from both experimental and theoretical points of view. Theoretical calculations show that only the linear isomer is found as a minimum on the potential energy surface. Detailed analysis of the crystal packing indicates that the angular form is due to attractive intermolecular interactions. Analysis of a selected reduced set of the 45 crystal structures retrieved from the Cambridge Structural Database allowed us to classify the bending of the [Cl3FeOFeCl3]2, dianion in three categories, depending on the balance and strength of the intermolecular O···H,X contacts. A crystal diffraction study on the bis(benzyltrimethylammonium) salt has shown both bent (144.6°) and linear (180°) forms of the (,-oxo)bis[trichloroferrate(III)] dianion. The magnetic susceptibility of this compound has been fitted by assuming two equally weighted contributions (Jang and Jlin) of the two forms, considering Jang , Jlin estimated by theoretical calculations. The obtained Jang and Jlin of ,117 and ,133 cm,1 respectively, agree well with B3LYP results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]


    Use of Molecular Scaffolding for the Stabilization of an Intramolecular Dative PIII -PV System

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2003
    Petr Kilian
    Abstract The reaction of NapP2S4 (1; Nap = naphthalene-1,8-diyl) with chlorine gas gave [Nap(PCl2)(PCl4)] (2), displaying a rare ,4P-,6P bonding interaction. An X-ray structure analysis confirmed the PCl5 -like, P,P bond containing phosphonium-phosphoride structure of 2 in the crystal, which was also found in solution at low temperature. At ambient and higher temperatures, dynamic behaviour on the NMR time-scale was observed, which was assigned to interchange of the ionic phosphonium-phosphoride form 2 and the molecular bis(phosphorane) Nap(PCl3)2 form 3, rather than to the ionic phosphonium salt-phosphorane form [Nap(PCl3)(PCl2)][Cl] 4. Electronic structure calculations were performed at the B3LYP/6,31G(d,p) level of theory on structures 2 and 3; structure 3 was located as a local minimum on the potential energy surface, 15 kcal·mol,1 higher in energy than structure 2. The crystal structure and calculated P,P distances are 2.34 and 2.31 Ĺ for 2 and 3, respectively. An activation energy of 19.7 kcal·mol,1 was found for the transition state structure by coordinate driving calculations; the line-shape analysis of variable temperature 31P{1H} NMR spectra gave an activation energy of 14.4 kcal·mol,1. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source]


    Ab initio conformational study of the P6 potential surface: Evidence for a low-lying one-electron-bonded isomer

    HETEROATOM CHEMISTRY, Issue 2 2007
    Philippe C. Hiberty
    The low-lying isomers of the P6 species are investigated at various levels of calculations, ranging from MP2/6-31G(d) to CCSD(T) in triple-zeta basis set involving polarization functions up to f. In addition to the five possible normal-valent isomers, which obey the octet rules, several other conformations are found to be stationary points on the potential energy surface. Among the five normal-valent isomers, the benzvalene structure is found to be the most stable one, in agreement with former studies. The benzene-like D6h planar hexagon is the least stable one, lying 32.3 kcal/mol over benzvalene, and spontaneously distorts to a less symmetrical, nonplanar six-membered ring. Above the benzvalene structure, and lying, respectively, 5.8 and 15.8 kcal/mol higher, the two lowest lying isomers are the prismane and the chair-like forms. This latter conformation, which does not obey the octet rule, exhibits two one-electron PP hemibonds and can be considered as a generic model for a new category of heterobenzene analogs, among which is the recently discovered dimer of diphosphirenyl radical. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:129,134, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20324 [source]


    Kinetic isotope effects for the H2 + C2H , C2H2 + H reaction based on the ab initio calculations and a global potential energy surface

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2010
    Liping Ju
    In the present paper, kinetic isotope effects of the title reaction are studied with canonical variational transition state theory on the modified Wang Bowman (MWB) potential energy surface (PES) (Chem Phys Lett 2005, 409, 249) and the ab initio calculations at the quadratic configuration interaction (QCISD (T, full))/aug-cc-pVTZ//QCISD (full)/cc-pVTZ level. The calculated rate constants for the isotopic variants of this title reaction on the MWB PES have good agreement with those of the present ab initio calculations over the temperature range of 20,5000 K for the forward reactions and 800,5000 K for the reverse reactions, respectively. In particular, the forward rate constants for the title reaction and its isotopically substituted reactions have negative temperature dependences at about 40 K. Rate expressions are presented for all the studied reactions. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 289,298, 2010 [source]


    Dynamics and kinetics of the S + HO2 reaction: A theoretical study

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 9 2008
    M. Y. Ballester
    We report a quasi-classical trajectory study of the S + HO2 reaction using a previously reported global potential energy surface for the ground electronic state of HSO2. Zero-point energy leakage is approximately accounted for by using the vibrational energy quantum mechanical threshold method. Calculations are carried out both for specific ro-vibrational states of the reactants and thermalized ones, with rate constants being reported as a function of temperature. The results suggest that the title reaction is capture type, with OH and SO showing as the most favorable products. The internal energy distribution of such products and the reaction mechanism are also investigated. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 533,540, 2008 [source]


    Variational transition-state theory study of the atmospheric reaction OH + O3 , HO2 + O2

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 3 2007
    Li-Ping Ju
    We report variational transition-state theory calculations for the OH + O3, HO2 + O2 reaction based on the recently reported double many-body expansion potential energy surface for ground-state HO4 [Chem Phys Lett 2000, 331, 474]. The barrier height of 1.884 kcal mol,1 is comparable to the value of 1.77,2.0 kcal mol,1 suggested by experimental measurements, both much smaller than the value of 2.16,5.11 kcal mol,1 predicted by previous ab initio calculations. The calculated rate constant shows good agreement with available experimental results and a previous theoretical dynamics prediction, thus implying that the previous ab initio calculations will significantly underestimate the rate constant. Variational and tunneling effects are found to be negligible over the temperature range 100,2000 K. The O1O2 bond is shown to be spectator like during the reactive process, which confirms a previous theoretical dynamics prediction. © 2007 Wiley Periodicals, Inc. 39: 148,153, 2007 [source]


    A shock tube study of the reaction NH2 + CH4 , NH3 + CH3 and comparison with transition state theory

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 7 2003
    Soonho Song
    The rate coefficient for NH2 + CH4 , NH3 + CH3 (R1) has been measured in a shock tube in the temperature range 1591,2084 K using FM spectroscopy to monitor NH2 radicals. The measurements are combined with a calculation of the potential energy surface and canonical transition state theory with WKB tunneling to obtain an expression for k1 = 1.47 × 103T3.01e,5001/T(K) cm3 mol,1 s,1 that describes available data in the temperature range 300 ,2100 K. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 304,309, 2003 [source]


    Kinetics and mechanism for the CH2O + NO2 reaction: A computational study

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2003
    Z. F. Xu
    The reactants, products, and transition states of the CH2O + NO2 reaction on the ground electronic potential energy surface have been searched at both B3LYP/6,311+G(d,p) and MPW1PW91/6,311+G(3df,2p) levels of theory. The forward and reverse barriers are further improved by a modified Gaussian-2 method. The theoretical rate constants for the two most favorable reaction channels 1 and 2 producing CHO + cis -HONO and CHO + HNO2, respectively, have been calculated over the temperature range from 200 to 3000 K using the conventional and variational transition-state theory with quantum-mechanical tunneling corrections. The former product channel was found to be dominant below 1500 K, above which the latter becomes competitive. The predicted total rate constants for these two product channels can be presented by kt (T) = 8.35 × 10,11T6.68 exp(,4182/T) cm3/(mol s). The predicted values, which include the significant effect of small curvature tunneling corrections, are in quantitative agreement with the available experimental data throughout the temperature range studied (390,1650 K). © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 184,190, 2003 [source]


    Theoretical study of NMR chemical shift induced by H/D isotope effect

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2010
    Kimikazu Sugimori
    Abstract The isotope effect induced by deuterium substituted species is observed in molecular properties, such as geometry, kinetics, and electronic state, of the molecules through nuclear-electron interaction. Theoretical considerations and experimental alignments have been studied by ab initio molecular orbital, density functional theory, and other empirical strategies. The Born-Oppenheimer approximation with nuclear vibrational wavefunction can treat isotope effect because nuclear mass effect account for the average distance of vibrational motion. In this study, we introduce Morse anharmonic oscillator model to calculate average internuclear distance of diatomic molecules having X-H bonding and X-D bonding. Morse parameters are determined by fitting to potential energy surface of molecular orbital and/or density functional calculations, and then the average distance are obtained as the expectation value of the analytical Morse vibrational wavefunction. Nuclear magnetic resonance shielding constants of the H/D isotopomer are calculated again on the average distance by using GIAO with B3LYP and CCSD calculation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]


    Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed Hamiltonians

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010
    Florent Calvo
    Abstract Nested Markov chain Monte Carlo is a rigorous way to enhance sampling of a given energy landscape using an auxiliary, approximate potential energy surface. Its practical efficiency mainly depends on how cheap and how different are the auxiliary potential with respect to the reference system. In this article, a combined efficiency index is proposed and assessed for two important families of energy surfaces. As illustrated for water clusters, many-body polarizable potentials can be approximated by simplifying the polarization contribution and keeping only the two-body terms. In small systems, neglecting polarization entirely is also acceptable. When the reference potential energy is obtained from diagonalization of a quantum mechanical Hamiltonian, a first-order perturbation scheme can be used to estimate the energy difference occuring on a Monte Carlo move. Our results indicate that this perturbation approximation performs well provided that the number of steps between successive diagonalization is adjusted beforehand. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2342,2346, 2010 [source]


    Infrared spectra of water molecule encapsulated inside fullerene studied by instantaneous vibrational analysis,

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2009
    Kiyoshi Yagi
    Abstract Instantaneous vibrational analysis (IVA) is proposed for computing the infrared spectrum of dynamically fluctuating system, and applied to a water molecule encapsulated into fullerene (H2O@C60). A molecular dynamics simulation is first carried out to generate an ensemble of configurations averaging the rotational and translational motion of H2O inside fullerene. At each configuration, instantaneous vibrational frequencies of the water molecule are computed by the vibrational configuration interaction method, which are then employed to construct the line-shape of the spectrum. The vibrational spectrum in the OH stretching region is computed at a temperature of 10 and 100 K based on a direct potential energy surface incorporating the electronic structure theory. It is found that the vibrational frequency of the symmetric stretching mode is blue-shifted compared to that of isolated water, whereas that of the asymmetric stretching mode exhibits no shift in average. The relation between IVA and instantaneous normal mode analysis is presented, and their performances are compared. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]


    Bonding and correlation analysis of various Si2CO isomers on the potential energy surface

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009
    Zhong-Jun Zhou
    Abstract At various levels of theory, singlet and triplet potential energy surfaces (PESs) of Si2CO, which has been studied using matrix isolation infrared spectroscopy, are investigated in detail. A total of 30 isomers and 38 interconversion transition states are obtained at the B3LYP/6-311G(d) level. At the higher CCSD(T)/6-311+G(2d)//QCISD/6-311G(2d)+ZPVE level, the global minimum 11 (0.0 kcal/mol) corresponds to a three-membered ring singlet O-cCSiSi (1A,). On the singlet PES, the species 12 (0.2 kcal/mol) is a bent SiCSiO structure with a 1A, electronic state, followed by a three-membered ring isomer Si-cCSiO (1A,) 13 (23.1 kcal/mol) and a linear SiCOSi 14 (1,+) (38.6 kcal/mol). The isomers 11, 12, 13, and 14 possess not only high thermodynamic stabilities, but also high kinetic stabilities. On the triplet PES, two isomers 31 (3B2) (18.8 kcal/mol) and 37 (3A,) (23.3 kcal/mol) also have high thermodynamic and kinetic stabilities. The bonding natures of the relevant species are analyzed. The similarities and differences between C3O, C3S, SiC2O, and SiC2S are discussed. The present results are also expected to be useful for understanding the initial growing step of the CO-doped Si vaporization processes. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]


    Searching the global minimum of a peptide/bilayer potential energy surface by fast heating and cooling cycles of simulated annealing

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008
    C. A. Fuzo
    Abstract The total time reached by molecular dynamics simulation in the study of the interactions between hydrated bilayers and peptides is still very short. A scheme of fast heating and cooling cycles of simulated annealing (FHCCSA) is proposed to improve the efficiency of the search for the global minimum of the peptide/bilayer potential energy surface. In FHCCSA, the high temperatures facilitate the transitions between stable configurations; i.e., heating and cooling cycles make easier the escape of the system outside the local energy minimum. The FHCCSA efficiency is confirmed by comparing its results with conventional NpT simulations. The new scheme saves more than 90% of the total cpu time compared with ordinary NpT simulations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008
    Samuel Silva da Rocha Pita
    Abstract Since the middle 70s, the main molecular docking problem consists in limitations to treat adequately the degrees of freedom of protein (or a receptor) due to the energy landscape roughness and the high computational cost. Until recently, only few algorithms considering flexible simultaneously both ligand and receptor at low computational cost were developed. As a recent proposed Statistical Mechanics, generalized simulated annealing (GSA) has been employed at diverse works concerning global optimization problems. In this work, we used this method exploring the molecular docking problem taking into account the FGF-2 and heparin complex. Since the requirements of an efficient docking algorithm are accuracy and velocity, we tested the influence of GSA parameters qA (new configuration acceptance index), qV (energy surface visiting index), and qT (temperature decreasing control) on the performance of GSADOCK program. Our simulations showed that as temperature parameter qT increases, qA parameter follows this behavior in the interval ranging from 1.1 to 2.3. We found that the GSA parameters have the best performance for the qA values ranging from 1.1 to 1.3, qV values from 1.3 to 1.5, and qT values from 1.1 to 1.7. Most of good qV values were equal or next the good qT values. Finally, the implemented algorithm is trustworthy and can be employed as a tool of molecular modeling methods. The final version of the program will be free of charge and will be accessible at our home-page or could be requested to the authors for e-mail. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    Adiabatic decoupling of the reaction coordinate

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008
    J. C. Lorquet
    Abstract When the dynamics is constrained by adiabatic invariance, a reactive process can be described as a one-dimensional motion along the reaction coordinate in an effective potential. This simplification is often valid for central potentials and for the curved harmonic valley studied in the reaction path Hamiltonian model. For an ion,molecule reaction, the action integral ,P,, = (1/2,),P,d, is an adiabatic invariant. The Poisson bracket of ,P,,2 with Hamiltonians corresponding to a great variety of long-range electrostatic interactions is found to decrease with the separation coordinate r, faster than the corresponding potential. This indicates that the validity of the adiabatic approximation is not directly related to the shape of the potential energy surface. The leading role played by the translational momentum is accounted for by Jacobi's form of the least action principle. However, although the identification of adiabatic regions by this procedure is limited to a specific range of coordinate configurations, equivalent constraints must persist all along the reaction coordinate and must operate during the entire reaction, as a result of entropy conservation. The study of the translational kinetic energy released on the fragments is particularly appropriate to detect restrictions on energy exchange between the reaction coordinate and the bath of internal degrees of freedom. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    Mechanism for the gas-phase reaction between OH and 3-methylfuran: A theoretical study

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 7 2008
    Weichao Zhang
    Abstract The mechanism for the OH + 3-methylfuran reaction has been studied via ab initio calculations to investigate various reaction pathways on the doublet potential energy surface. Optimizations of the reactants, products, intermediates, and transition structures are conducted using the MP2 level of theory with the 6-311G(d,p) basis set. The single-point electronic energy of each optimized geometry is refined with G3MP2 and G3MP2B3 calculations. The theoretical study suggests that the OH + 3-methylfuran reaction is dominated by the formation of HC(O)CHC(CH3)CHOH (P7) and CH(OH)CHC(CH3)C(O)H (P9), formed from two low-lying adducts, IM1 and IM2. The direct hydrogen abstraction pathways and the SN2 reaction may play a minor or negligible role in the overall reaction of OH with 3-methylfuran. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energies

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2008
    Damanjit Kaur
    Abstract Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6-31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6-311++G*//B3LYP/6-31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    Theoretical study on the partial potential energy surface and formation mechanism of the reactive resonance state of HO + CH4 , H2O + CH3 system

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2008
    Xi Lu
    Abstract In the course of an extensive investigation aimed at understanding the detailed mechanism of a prototypical polyatomic reaction, several remarkable observations were uncovered. To interpret these findings, we surmise the existence of a reactive resonance in this polyatomic reaction. The concerned system is HO + CH4 , H2O + CH3, of which the partial potential energy surface is constructed by the coupling between vibrational models and reactive coordinates. Then we explain the formation mechanism of the reactive resonance state by the partial potential energy surface. Finally, we estimated the lifetime of the resonance state, and it is about 45fs. The study of the reactive resonance in a polyatomic reaction is more than just an extension from a typical atom + diatom reaction. As shown here, it holds great promise to disentangle the elusive intramolecular vibrational dynamics of the transient collision complex in the critical transition-state region. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]


    New valley ridge inflection point associated to the bifurcation of a valley on potential energy surfaces

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2007
    R. Palmeiro
    Abstract There are currently two definitions of valley ridge inflection point on an adiabatic potential energy surface (PES), one introduced by Basilevsky and the other by Valtazanos and Ruedenberg. Here, we investigate the validity of both definitions on bidimensional surfaces without symmetry constraints, with neither producing completely satisfactory results. Hence, we propose new conditions which must obey a valley bifurcation point (VBP) locally and demonstrate that such conditions are necessary when a valley splits into two, finishing at two energy minima. Finally, we localize such VBPs on the bidimensional surfaces and check the certainty of our previous deductions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]


    Conformational analysis for some nonclassical antagonists of histamine H3 receptor

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2007
    Ana Borota
    Abstract A conformational search in vacuum for a series of 1,3-substituted pyrrolidine derivatives has been performed using the AMBER, AM1, PM3, and MNDO methods. Conformational analysis of the pyrrolidine ligands suggests that these compounds could have many conformers that populate the low-energy minima on the potential energy surface (PES). The conformational space occupied by the ligands is large and, in vacuum, the rotation barriers of different flexible bonds have energies between 0.5 and thousands of kcal/mol. By optimization, most conformers have energy barriers of 0,5 kcal/mol; thus, they could interconvert easily to obtain better interactions in the receptor active site. Optimized conformers having energy barriers of >5 kcal/mol display bad geometries with very large bond lengths and deformed rings. Shapes and heights of rotation barriers obtained through COSMO,AM1 single-point calculations in water are similar to those obtained from single-point calculations in vacuum. However, in water the energy barriers are lower, allowing most conformers to convert in other low-energy conformers. The best conformers in vacuum and in water are different: the gas phase best conformer has a helical shape, while the best conformer in water has an extended shape. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]


    Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007
    Xiu Hui Lu
    Abstract Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Mřller,Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]


    Density functional and ab initio studies on structures and energies of the ground state of CrCO

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2007
    Joonghan Kim
    Abstract CrCO was studied using density functional theory (DFT) and ab initio methods. We obtained the two-dimensional potential energy surface (PES), geometry, and vibrational frequencies for CrCO in a septet state. Two minimum structures were found in the CCSD(T) calculation, including a local minimum that is a weak van der Waals (vdW) complex. All DFT methods yield only one minimum structure. We demonstrate that the bond dissociation energy (0.50 kcal/mol) and vibrational frequency (1981.1 cm,1) of CrCO calculated using CCSD(T) are in better agreement with experimental values (<1.5 kcal/mol and 1977 cm,1) than any of the reported theoretical studies. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source]


    Fitting potential energy surface of reactive systems via genetic algorithm

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006
    Wiliam Ferreira Da Cunha
    Abstract We present a new fitting of the Na+HF potential energy surface (PES) using a new optimization method based on genetic algorithm. Topology studies, such as isoenergetic contours and minimum energy path (MEP), show that the quality of this new PES is comparable to the best PES of literature. These facts suggest that this new approach can be used as a new tool to fit PES of reactive systems. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source]