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Sample records for bond dissociation energy

  1. The Bond Dissociation Energies of 1-Butene

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    The bond dissociation energies of 1-butene and several calibration systems are computed using the G2(MP2) approach. The agreement between the calibration systems and experiment is very good. The computed values for 1-butene are compared with calibration systems and the agreement between the computed results for 1-butene and the "rule of thumb" values from the smaller systems is remarkably good.

  2. Thermochemistry and bond dissociation energies of ketones.

    PubMed

    Hudzik, Jason M; Bozzelli, Joseph W

    2012-06-14

    Ketones are a major class of organic chemicals and solvents, which contribute to hydrocarbon sources in the atmosphere, and are important intermediates in the oxidation and combustion of hydrocarbons and biofuels. Their stability, thermochemical properties, and chemical kinetics are important to understanding their reaction paths and their role as intermediates in combustion processes and in atmospheric chemistry. In this study, enthalpies (ΔH°(f 298)), entropies (S°(T)), heat capacities (C(p)°(T)), and internal rotor potentials are reported for 2-butanone, 3-pentanone, 2-pentanone, 3-methyl-2-butanone, and 2-methyl-3-pentanone, and their radicals corresponding to loss of hydrogen atoms. A detailed evaluation of the carbon-hydrogen bond dissociation energies (C-H BDEs) is also performed for the parent ketones for the first time. Standard enthalpies of formation and bond energies are calculated at the B3LYP/6-31G(d,p), B3LYP/6-311G(2d,2p), CBS-QB3, and G3MP2B3 levels of theory using isodesmic reactions to minimize calculation errors. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) density functional level and are used to determine the entropies and heat capacities. The recommended ideal gas-phase ΔH°(f 298), from the average of the CBS-QB3 and G3MP2B3 levels of theory, as well as the calculated values for entropy and heat capacity are shown to compare well with the available experimental data for the parent ketones. Bond energies for primary, secondary, and tertiary radicals are determined; here, we find the C-H BDEs on carbons in the α position to the ketone group decrease significantly with increasing substitution on these α carbons. Group additivity and hydrogen-bond increment values for these ketone radicals are also determined.

  3. Theoretical study of the bond dissociation energies of methanol

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.

    1992-01-01

    A theoretical study of the bond dissociation energies for H2O and CH3OH is presented. The C-H and O-H bond energies are computed accurately with the modified coupled-pair functional method using a large basis set. For these bonds, an accuracy of +/- 2 kcal/mol is achieved, which is consistent with the C-H and C-C single bond energies of other molecules. The C-O bond is much more difficult to compute accurately because it requires higher levels of correlation treatment and more extensive one-particle basis sets.

  4. Periodic trends in bond dissociation energies. A theoretical study.

    PubMed

    Mó, Otilia; Yáñez, Manuel; Eckert-Maksić, Mirjana; Maksić, Zvonimir B; Alkorta, Ibón; Elguero, José

    2005-05-19

    Bond dissociation energies (BDEs) of all possible A-X single bonds involving the first- and second-row atoms, from Li to Cl, where the free valences are saturated by hydrogens, have been estimated through the use of the G3-theory and at the B3LYP/6-311+G(3df,2pd)//B3LYP/6-31G(2df,p) DFT level of theory. BDEs exhibit a periodical behavior. The A-X (A = Li, Be, B, Na, Mg, Al, and Si) BDEs show a steady increase along the first and the second row of the periodic table as a function of the atomic number Z(X). For A-X bonds involving electronegative atoms (A = C, N, O, F, P, S, and Cl) the bond energies achieve a maximum around Z(X) = 5. The same behavior is observed when BDEs are plotted against the electronegativity chi(X) of the atom X. Thus, for A-X bonds (A = Li, Be, B, Na, Mg, Al, Si), the BDEs for a fixed A increases, grosso modo, as the electronegativity differences between X and A increase, with some exceptions, which reflect the differences in the relaxation energies of the radicals produced upon the bond cleavage. A similar trend, albeit less pronounced, is found for single A-X bonds, where A = C, N, O, F, P, S, and Cl. However, there is an additional feature embodied in the enhancement of the strength of the A-boron bonds due to the ability of boron to act as a strong electron acceptor. The trends in bond lengths and charge densities at the bond critical points are in line with the aforementioned behavior.

  5. Accurate bond dissociation energies (D 0) for FHF- isotopologues

    NASA Astrophysics Data System (ADS)

    Stein, Christopher; Oswald, Rainer; Sebald, Peter; Botschwina, Peter; Stoll, Hermann; Peterson, Kirk A.

    2013-09-01

    Accurate bond dissociation energies (D 0) are determined for three isotopologues of the bifluoride ion (FHF-). While the zero-point vibrational contributions are taken from our previous work (P. Sebald, A. Bargholz, R. Oswald, C. Stein, P. Botschwina, J. Phys. Chem. A, DOI: 10.1021/jp3123677), the equilibrium dissociation energy (D e ) of the reaction ? was obtained by a composite method including frozen-core (fc) CCSD(T) calculations with basis sets up to cardinal number n = 7 followed by extrapolation to the complete basis set limit. Smaller terms beyond fc-CCSD(T) cancel each other almost completely. The D 0 values of FHF-, FDF-, and FTF- are predicted to be 15,176, 15,191, and 15,198 cm-1, respectively, with an uncertainty of ca. 15 cm-1.

  6. Calculation of bond dissociation energies of diatomic molecules using bond function basis sets with counterpoise corrections

    SciTech Connect

    Li, Z.; Pan, Y.K.; Tao, F.M.

    1996-01-15

    Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.

  7. Bond dissociation energy of the phenol O sbnd H bond from ab initio calculations

    NASA Astrophysics Data System (ADS)

    da Silva, Gabriel; Chen, Chiung-Chu; Bozzelli, Joseph W.

    2006-06-01

    The phenol O sbnd H bond dissociation energy (BDE) is currently disputed, despite its importance in combustion chemistry and in the reactions of antioxidants such as vitamin E. We have studied this BDE using the computational methods G3, G3B3 and CBS-APNO, with bond-isodesmic work reactions. These calculations yield a BDE of 89.0 ± 1.0 kcal mol -1, which supports other recent calculations [B.J. Costa Cabral, S. Canuto, Chem. Phys. Lett. 406 (2005) 300]. From our BDE we determine the enthalpy of formation of the phenoxy radical to be 13.9 ± 1.0 kcal mol -1. Comparison of the phenol C sbnd H BDE with the vinyl alcohol H sbnd CH dbnd CHOH BDE reveals the bond in phenol to be around 3 kcal mol -1 stronger than that in vinyl alcohol. Replacement of a H atom with the OH group on benzene or ethylene strengthens the C sbnd H bonds on adjacent carbons by 3 to 4 kcal mol -1.

  8. The calculation of bond dissociation energies of transition metal complexes using isostructural reactions

    NASA Astrophysics Data System (ADS)

    Dapprich, S.; Pidun, U.; Ehlers, A. W.; Frenking, G.

    1995-08-01

    The metal-ligand bond dissociation energies (CO) nM-L are theoretically predicted at the HF, MP2 and CCSD(T) levels of theory using effective core potentials for the metals for M = Cr, Mo, W, Ni, Pd, Pt and for L = CO, NO +, CN -, NC -, CS, SiO, N 2. The bond energies at the HF level are too low and the MP2 values are too high, while the CCSD(T) results are in good agreement with experimental data. The bond energies at MP2 show the same trend as the CCSD(T) values and may therefore be used for the prediction of relative bond dissociation energies. The absolute values for the bond energies calculated at MP2 are significantly improved when they are corrected using the energies of isostructural reactions M(CO) n + L → M(CO) n-1 L + CO.

  9. Bond dissociation energies of solvated silver(I)-amide complexes: competitive threshold collision-induced dissociations and calculations.

    PubMed

    Romanov, Vladimir; Siu, Chi-Kit; Verkerk, Udo H; Hopkinson, Alan C; Siu, K W Michael

    2010-07-08

    Using competitive threshold collision-induced dissociation (TCID) measurements, experimental bond dissociation energies have been evaluated for the water, methanol, and acetonitrile adducts of silver(I)-amide complexes. The influence of the solvent molecules on the binding energy of silver(I) to acetamide, N-methylacetamide, and N,N-dimethylacetamide was investigated. Experimental results show that solvents decrease the amide binding energy by 4-6 kcal mol(-1). Using density functional theory (DFT), binding energies were evaluated using nine functionals, after full geometry optimizations with the ECP28MWB basis set for silver and the 6-311++G(2df,2pd) basis set for the other atomic constituents of the ligands. In addition, calculations employing the DZVP basis set for Ag and DZVP2 for C, H, N, and O atoms at the B3LYP and MP2 levels of theory were used to investigate the influence of the basis set on the theoretical bond energies. A comparison of the experimental and theoretical silver(I)-ligand bond dissociation energies enables an assessment of the limitations in the basis sets and functionals in describing the energetics of the metal-solvent interaction and the metal-amide interaction. No single functional/basis set combination was found capable of predicting binding energies with a sufficiently high level of accuracy for the silver(I)-amide solvent complexes.

  10. The effect of bond functions on dissociation energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.

    1985-01-01

    The procedure employing bond functions recently suggested by Wright and Buenker has been applied to the N2 X 1 Sigma g + potential curve within the CAS SCF + MRSD CI treatment of electron correlation. The basis set used herein is identical to that employed by these authors in their SCF + CI calculations. The De and and the shape of the resulting potential curve, as judged by the computed vibrational levels, is not so accurate as would be expected from the results reported by Wright and Buenker (1984). The results indicate that using the CI superposition errors associated with bond functions to cancel basis set incompleteness depends on the treatment of the electron correlation.

  11. Interference energy in C-H and C-C bonds of saturated hydrocarbons: dependence on the type of chain and relationship to bond dissociation energy.

    PubMed

    Vieira, Francisco Senna; Fantuzzi, Felipe; Cardozo, Thiago Messias; Nascimento, Marco Antonio Chaer

    2013-05-16

    Interference energy for C-H and C-C bonds of a set of saturated hydrocarbons is calculated by the generalized product function energy partitioning (GPF-EP) method in order to investigate its sensitivity to the type of chain and also its contribution to the bond dissociation energy. All GPF groups corresponding to chemical bonds are calculated by use of GVB-PP wave functions to ensure the correct description of bond dissociation. The results show that the interference energies are practically the same for all the C-H bonds, presenting only small variations (0.5 kcal.mol(-1)) due to the structural changes in going from linear to branched and cyclic chains. A similar trend is verified for the C-C bonds, the sole exception being the cyclopropane molecule, for which only the C-C bond exhibits a more significant variation. On the other hand, although the interference energy is quantitatively the most important contribution to the bond dissociation energy (DE), one cannot predict DE only from the bond interference energy. Differences in the dissociation energies of C-C and C-H bonds due to structural changes in the saturated hydrocarbons can be mainly attributed to quasi-classical effects.

  12. Influence of charge and coordination number on bond dissociation energies, distances, and vibrational frequencies for the phosphorus-phosphorus bond.

    PubMed

    Chitnis, Saurabh S; Whalen, J Marc; Burford, Neil

    2014-09-03

    We report a comprehensive and systematic experimental and computational assessment of the P-P bond in prototypical molecules that represent a rare series of known compounds. The data presented complement the existing solid-state structural data and previous computational studies to provide a thorough thermodynamic and electronic understanding of the P-P bond. Comparison of homolytic and heterolytic bond dissociation for tricoordinate-tricoordinate, tricoordinate-tetracoordinate, and tetracoordinate-tetracoordinate P-P bonds in frameworks 1-6 provides fundamental insights into covalent bonding. For all types of P-P bond discussed, homolytic dissociation is favored over heterolytic dissociation, although the distinction is small for 2(1+) and 6(1+). The presence of a single cationic charge in a molecule substantially strengthens the P-P bond (relative to analogous neutral frameworks) such that it is comparable with the C-C bond in alkanes. Nevertheless, P-P distances are remarkably independent of molecular charge or coordination number, and trends in values of d(PC) and νsymm(PC) imply that a molecular cationic charge is distributed over the alkyl substituents. In the gas phase, the diphosphonium dication 3(2+) has similar energy to two [PMe3](+) radical cations, so that it is the lattice enthalpy of 3[OTf]2 in the solid-state that enables isolation, highlighting that values from gas-phase calculations are poor guides for synthetic planning for ionic compounds. There are no relationships or correlations between bond lengths, strengths, and vibrational frequencies.

  13. The computation of C-C and N-N bond dissociation energies for singly, doubly, and triply bonded systems

    NASA Technical Reports Server (NTRS)

    Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.; Taylor, Peter R.

    1989-01-01

    The bond dissociation energies (D sub e) of C2H2, C2H4, C2H6, N2, N2H2, and N2H4 are studied at various levels of correlation treatment. The convergence of D sub e with respect to the one particle basis is studied at the single reference modified coupled-pair functional (MCPF) level. At all levels of correlation treatment, the errors in the bond dissociation energies increase with the degree of multiple bond character. The multireference configuration interaction (MRCI) D sub e values, corrected for an estimate of higher excitations, are in excellent agreement with those determined using the size extensive averaged coupled pair functional (ACPF) method. It was found that the full valence complete active space self consistent field (CASSCF)/MRCI calculations are reproduced very well by MRCI calculations based on a CASSCF calculation that includes in the active space only those electrons involved in the C-C or N-N bonds. To achieve chemical accuracy (1 kcal/mole) for the D sub e values of the doubly bonded species C2H4 and N2H2 requires one particle basis sets including up through h angular momentum functions (l = 5) and a multireference treatment of electron correlation: still higher levels of calculation are required to achieve chemical accuracy for the triply bonded species C2H2 and N2.

  14. Theoretical study of the C-H bond dissociation energy of acetylene

    NASA Technical Reports Server (NTRS)

    Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1990-01-01

    The authors present a theoretical study of the convergence of the C-H bond dissociation energy (D sub o) of acetylene with respect to both the one- and n-particle spaces. Their best estimate for D sub o of 130.1 plus or minus 1.0 kcal/mole is slightly below previous theoretical estimates, but substantially above the value determined using Stark anticrossing spectroscopy that is asserted to be an upper bound.

  15. The computation of C-C and N-N bond dissociation energies for singly, doubly, and triply bonded systems

    NASA Technical Reports Server (NTRS)

    Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.; Taylor, Peter R.

    1991-01-01

    The bond dissociation energies (De) of C2H2, C2H4, C2H6, N2, N2H2, and N2H4 are studied at various levels of correlation treatment. The convergence of De with respect to the one-particle basis is studied at the single-reference modified coupled-pair-functional (MCPF)level. At all levels of correlation treatment, the errors in the bond dissociation energies increase with the degree of multiple bond character. The multireference configuration-interaction (MRCI) De values, corrected for an estimate of higher excitations, are in excellent agreement with those determined using the size-extensive averaged-coupled-pair-functional (ACPF) method. The full-valence complete-active-space self-consistent-field (CASSCF)/MRCI calculations are reproduced very well by MRCI calculations based on a CASSCF calculation that includes in the active space only those electrons involved in the C-C or N-N bonds.

  16. Theoretical study of the bond dissociation energies of propyne (C3H4)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1992-01-01

    The C-C and C-H bond dissociation energies (BDEs) of propyne have been computed using the modified coupled-pair functional method. Due to hyperconjugation, the C-C and methyl C-H single bonds are stronger and weaker, respectively than those in ethane. The acetylenic C-H and C triple bond C BDEs are larger and smaller, respectively, than in acetylene, also as a result of the hyperconjugation. Our best estimate of 92.5 +/- 2 kcal/mol for the methyl C-H BDE in propyne is slightly larger than the experimental value. For the acetylenic C-H BDE in propyne we predict 135.9 +/- 2 kcal/mol.

  17. Theoretical study of the C-H bond dissociation energy of C2H

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1990-01-01

    A theoretical study of the convergence of the C-H bond dissociation energy D(0) in C2H with respect to both the one- and n-particle spaces is presented. The calculated C-H bond energies of C2H2 and C2H4, which are in excellent agreement with experiment, are used for calibration. The best estimate for D(0) of 112.4 + or - 2.0 kcal/mol is slightly below the recent experimental value of 116.3 + or - 2.6 kcal/mol, but substantially above a previous theoretical estimate of 102 kcal/mol. The remaining discrepancy with experiment may reflect primarily the uncertainty in the experimental D(0) value of C2 required in the analysis.

  18. Prediction of the bond lengths, vibrational frequencies, and bond dissociation energy of octahedral seaborgium hexacarbonyl, Sg(CO){sub 6}

    SciTech Connect

    Nash, C.S.; Bursten, B.E.

    1999-11-24

    The recent syntheses of several new elements (including the recent reports of elements 116 and 118), coupled with the controversy surrounding the naming of elements 104--109, have stimulated a great interest in the chemistry of the transactinide elements. This contribution addresses hypothetical hexacarbonyl complex of seaborgium (Sg, element 106), which is predicted to be a 6d-block transition element with six valence electrons, analogous to Cr, Mo, and W. The authors have previously predicted that, if it were to exist, Sg(CO){sub 6} would exhibit metal-carbonyl bonding that is very similar to that in Cr(CO){sub 6}, Mo(CO){sub 6}, and W(CO){sub 6}, and quite unlike that of the unknown valence isoelectronic actinide complex U(CO){sub 6}. This finding is in accord with the scant experimental data available for Sg. The relativistic DV-X{alpha} method used in the earlier paper facilitated the analysis of the molecular orbitals of Sg(CO){sub 6}, but did not allow for the calculation of total-energy properties, such as bond lengths and vibrational frequencies. Here the authors will use the superior methodology they have applied to other transactinide molecules to compare the bond lengths, vibrational frequencies, and CO dissociation energy of hypothetical Sg(CO){sub 6} to those of Mo(CO){sub 6} and W(CO){sub 6}.

  19. C-H and N-H bond dissociation energies of small aromatic hydrocarbons

    SciTech Connect

    Barckholtz, C.; Barckholtz, T.A.; Hadad, C.M.

    1999-01-27

    A survey of computational methods was undertaken to calculate the homolytic bond dissociation energies (BDEs) of the C-H and N-H bonds in monocyclic aromatic molecules that are representative of the functionalities present in coal. These include six-membered rings (benzene, pyridine, pyridazine, pyrimidine, pyrazine) and five-membered rings (furan, thiophene, pyrrole, oxazole). By comparison of the calculated C-H BDEs with the available experimental values for these aromatic molecules, the B3LYP/6-31G(d) level of theory was selected to calculate the BDEs of polycyclic aromatic hydrocarbons (PAHs), including carbonaceous PAHs (naphthalene, anthracene, pyrene, coronene) and heteroatomic PAHs (benzofuran, benzothiophene, indole, benzoxazole, quinoline, isoquinoline, dibenzofuran, carbazole). The cleavage of a C-H or a N-H bond generates a {sigma} radical that is, in general, localized at the site from which the hydrogen atom was removed. However, delocalization of the unpaired electron results in {approximately} 7 kcal {center{underscore}dot} mol{sup {minus}1} stabilization of the radical with respect to the formation of phenyl when the C-H bond is adjacent to a nitrogen atom in the azabenzenes. Radicals from five-membered rings are {approximately} 6 kcal {center{underscore}dot} mol{sup {minus}1} less stable than those formed from six-membered rings due to both localization of the spin density and geometric factors. The location of the heteroatoms in the aromatic ring affects the C-H bond strengths more significantly than does the size of the aromatic network. Therefore, in general, the monocyclic aromatic molecules can be used to predict the C-H BDE of the large PAHs within 1 kcal {center{underscore}dot} mol{sup {minus}1}.

  20. Bond Dissociation Energies for Substituted Polycyclic Aromatic Hydrocarbons and Their Cations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)

    1998-01-01

    The B3LYP/4-31G approach is used to compute bond energies for a series of substituted benzene, naphthalene, and anthracene molecules and their cations. The benzene bond energies are compared with experiment. The trends in the bond energies are discussed. The ionization energies are also reported and compared with available experiments.

  1. PCM study of the solvent and substituent effects on bond dissociation energies of the C=NO bond

    NASA Astrophysics Data System (ADS)

    Li, Xiao-Hong; Tang, Zheng-Xin; Yang, Xiang-Dong

    Quantum chemical calculations are used to estimate the equilibrium C=NO bond dissociation energies (BDEs) for eight X=NO molecule (X = CCl3, C6F5, CH3, CH3CH2, iC3H7, tC4H9, CH2CHCH2, and C6H5CH2). These compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86) methods together with 6-31G** and 6-311G** basis sets and the complete basis set (CBS-QB3) method. The obtained results are compared with the available experimental results. It is demonstrated that B3P86/6-31G** and CBS-QB3 methods are accurate for computing the reliable BDEs for the X=NO molecule. Considering the inevitably computational cost of CBS-QB3 method and the reliability of the B3P86 calculations, B3P86 method with 6-31G** basis set may be more suitable to calculate the BDEs of the C=NO bond. The solvent effects on the BDEs of the C=NO bond are analyzed and it is shown that the C=NO BDEs in a vacuum computed by using B3PW91/6-311G** method are the closest to the computed values in acetontrile and the average solvent effect is 1.48 kcal/mol. Subsequently, the substituent effects of the BDEs of the C=NO bond are further analyzed and it is found that electron denoting group stabilizes the radical and as a result BDE decreases; whereas electron withdrawing group stabilizes the group state of the molecule and thus increases the BDE from the parent molecule.

  2. Prediction of Bond Dissociation Energies/Heats of Formation for Diatomic Transition Metal Compounds: CCSD(T) Works.

    PubMed

    Fang, Zongtang; Vasiliu, Monica; Peterson, Kirk A; Dixon, David A

    2017-03-14

    It was recently reported ( J. Chem. Theory Comput. 2015 , 11 , 2036 - 2052 ) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the first row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons. Revised experimental values for the hydrides are presented that are based on new heterolytic R-H bond dissociation energies, which are needed for analysis of the mass spectrometry experiments. The agreement between the calculated bond dissociation energies and the revised experimental values of the hydrides is good. Good agreement of the calculated bond dissociation energies/heats of formation is also found for most of the chlorides, oxides, and sulfides given the experimental error bars from experiment and those of the transition metal atoms in the gas phase. Thus, reliable results can be achieved by the CCSD(T) method at the CBS limit. The use of PW91 orbitals for the CCSD(T) calculations improves the predictions for some compounds with large T1 diagnostics at the HF-CCSD(T) level. The optimized bond distances and calculated vibrational frequencies for the diatomics also agree well with the available experimental values.

  3. Competitive threshold collision-induced dissociation: Gas-phase acidities and bond dissociation energies for a series of alcohols

    SciTech Connect

    DeTuri, V.F.; Ervin, K.M.

    1999-09-02

    Energy-resolved competitive collision-induced dissociation methods are used to measure the gas-phase acidities of a series of alcohols (methanol, ethanol, 2-propanol, and 2-methyl-2-propanol). The competitive dissociation reactions of fluoride-alcohol, [F{sup {minus}}{center{underscore}dot}HOR], alkoxide-water, [RO{sup {minus}}{center{underscore}dot}HOH], and alkoxide-methanol [RO{+-}{center{underscore}dot}HOCH{sub 3}] proton-bound complexes are studied using a guided ion beam tandem mass spectrometer. The reaction cross sections and product branching fractions to the two proton transfer channels are measured as a function of collision energy. The enthalpy difference between the two product channels is found by modeling the reaction cross sections near threshold using RRKM theory to account for the energy-dependent product branching ratio and kinetic shift. From the enthalpy difference, the alcohol gas-phase acidities are determined relative to the well-known values of HF and H{sub 2}O. The measured gas-phase acidities are {Delta}{sub acid}H{sub 298}(CH{sub 3}OH) = 1599 {+-} 3 kJ/mol, {Delta}{sub acid}H{sub 298}(CH{sub 3}CH{sub 2}OH) = 1586 {+-} 5 kJ/mol, {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 2}CHOH) = 1576 {+-} 4 kJ/mol, and {Delta}{sub acid}H{sub 298}((CH{sub 3}){sub 3}COH) = 1573 {+-} 3 kJ/mol.

  4. Bond Dissociation Energies of the Tungsten Fluorides and Their Singly-Charged Ions: A Density Functional Survey

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Arnold, James (Technical Monitor)

    1999-01-01

    The dissociation of WF6 and the related singly-charged cations and anions into the lower fluorides and fluorine atoms has been investigated theoretically using density functional theory (B3LYP) and relativistic effective core potentials, with estimates of spin-orbit effects included using a simple model. The inclusion of spin-orbit is essential for a correct description of the thermochemistry. The total atomization energy of the neutral and anionic WF6 is reproduced to within 25 kcal/mol, but comparison of individual bond dissociation energies with available experimental data shows discrepancies of up to 10 kcal/mol. The results are nevertheless useful to help resolve discrepancies in experimental data and provide estimates of missing data.

  5. Calculations of bond dissociation energies. New select applications of an old method.

    PubMed

    Boudreaux, Edward A

    2011-03-10

    Application of Sanderson's definition of electronegativity as stability ratios (SRs), which BE = [E(i) + E(DA)] (IC) + E(cov) had been applied in the past to a wide variety of organic and nontransitional metal inorganic compounds with very good success, has been revived, modified so as to be applied to any types of molecules, including those containing transition metals, lanthanides, and actinides. This paper is limited to a demonstration of the method which is applied to a few metal cyclopentadienyl compounds, plus specific emphasis on the U(III) metallocene (CpSiMe(3))(3)U-AlCp* recently prepared by Arnold and co-workers having no experimental bond energies available. It is shown that computed bond energies of pertinent metallocyclopentadieneyls are in excellent agreement with the available experimental data. Calculated bond energies for all essential bonds in the uranium metallocene cited above are provided together with a further analysis of the bonding and magnetic properties of this unique compound.

  6. Bond-Specific Dissociation Following Excitation Energy Transfer for Distance Constraint Determination in the Gas Phase

    PubMed Central

    2015-01-01

    Herein, we report chemistry that enables excitation energy transfer (EET) to be accurately measured via action spectroscopy on gaseous ions in an ion trap. It is demonstrated that EET between tryptophan or tyrosine and a disulfide bond leads to excited state, homolytic fragmentation of the disulfide bond. This phenomenon exhibits a tight distance dependence, which is consistent with Dexter exchange transfer. The extent of fragmentation of the disulfide bond can be used to determine the distance between the chromophore and disulfide bond. The chemistry is well suited for the examination of protein structure in the gas phase because native amino acids can serve as the donor/acceptor moieties. Furthermore, both tyrosine and tryptophan exhibit unique action spectra, meaning that the identity of the donating chromophore can be easily determined in addition to the distance between donor/acceptor. Application of the method to the Trpcage miniprotein reveals distance constraints that are consistent with a native-like fold for the +2 charge state in the gas phase. This structure is stabilized by several salt bridges, which have also been observed to be important previously in proteins that retain native-like structures in the gas phase. The ability of this method to measure specific distance constraints, potentially at numerous positions if combined with site-directed mutagenesis, significantly enhances our ability to examine protein structure in the gas phase. PMID:25174489

  7. Bond-specific dissociation following excitation energy transfer for distance constraint determination in the gas phase.

    PubMed

    Hendricks, Nathan G; Lareau, Nichole M; Stow, Sarah M; McLean, John A; Julian, Ryan R

    2014-09-24

    Herein, we report chemistry that enables excitation energy transfer (EET) to be accurately measured via action spectroscopy on gaseous ions in an ion trap. It is demonstrated that EET between tryptophan or tyrosine and a disulfide bond leads to excited state, homolytic fragmentation of the disulfide bond. This phenomenon exhibits a tight distance dependence, which is consistent with Dexter exchange transfer. The extent of fragmentation of the disulfide bond can be used to determine the distance between the chromophore and disulfide bond. The chemistry is well suited for the examination of protein structure in the gas phase because native amino acids can serve as the donor/acceptor moieties. Furthermore, both tyrosine and tryptophan exhibit unique action spectra, meaning that the identity of the donating chromophore can be easily determined in addition to the distance between donor/acceptor. Application of the method to the Trpcage miniprotein reveals distance constraints that are consistent with a native-like fold for the +2 charge state in the gas phase. This structure is stabilized by several salt bridges, which have also been observed to be important previously in proteins that retain native-like structures in the gas phase. The ability of this method to measure specific distance constraints, potentially at numerous positions if combined with site-directed mutagenesis, significantly enhances our ability to examine protein structure in the gas phase.

  8. On the Enthalpy of Formation of Hydroxyl Radical and Gas-Phase Bond Dissociation Energies of Water and Hydroxyl

    SciTech Connect

    Ruscic, Branko; Wagner, Albert F.; Harding, Lawerence B.; Asher, Robert L.; Feller, David F. ); Dixon, David A. ); Peterson, Kirk A.; Song, Yang; Qian, Ximei; Ng, C Y.; Liu, Jianbo; Wenwu, Chen

    2001-12-01

    Several photoionization experiments utilizing the positive ion cycle to derive the O-H bond energy converge to a consensus value of AE0(OH+/H2O)= 146117? 24 cm-1 (18.1162? 0.0030 eV). With the most accurate currently available ZEKE value. IE(OH)= 104989? 2 cm-1, corroborated by a number of photoelectron measurements,Error! Bookmark not defined.,Error! Bookmark not defined.,Error! Bookmark not defined.,Error! Bookmark not defined. this leads to D0(H?OH)= 41128? 24 cm-1= 117.59? 0.07 kcal/mol. This corresponds to DHf 0(OH)= 8.85? 0.07 kcal/mol, and implies D0(OH)= 35593? 24 cm-1= 101.76? 0.07 kcal/mol. The most sophisticated theoretical calculations performed so far on the HxO system, CCSD(T)/aug-cc-pVnZ, n=Q, 5, 6, and 7, extrapolated to the CBS limit and including corrections for core-valence effects, scalar relativistic effects, incomplete correlation recovery, and diagonal Born-Oppenheimer corrections reproduce the experimental results to within 0.0 - 0.2 k cal/mol. The new values of the two successive bond dissociation energies of water supersede the previously accepted values,Error! Bookmark not defined.,Error! Bookmark not defined. which were based on spectroscopic determinationsError! Bookmark not defined.,Error! Bookmark not defined. of D0(OH) using a very short Birge-Sponer extrapolation on OH/OD A1S+. An exhaustive analysis of the latter approach, combined with the application of the same procedure on a calculated potential energy curve for the state in question, demonstrates that the Birge-Sponer extrapolation underestimates the bond dissociation energy, in spite of the fact that only the last vibrational level was not observed experimentally. The new values affect a large number of other thermochemical quantities which directly or indirectly rely on or refer to D0(H-OH), D0(OH), or DHf?(OH).

  9. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    SciTech Connect

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-28

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  10. Size-extensivity-corrected multireference configuration interaction schemes to accurately predict bond dissociation energies of oxygenated hydrocarbons

    NASA Astrophysics Data System (ADS)

    Oyeyemi, Victor B.; Krisiloff, David B.; Keith, John A.; Libisch, Florian; Pavone, Michele; Carter, Emily A.

    2014-01-01

    Oxygenated hydrocarbons play important roles in combustion science as renewable fuels and additives, but many details about their combustion chemistry remain poorly understood. Although many methods exist for computing accurate electronic energies of molecules at equilibrium geometries, a consistent description of entire combustion reaction potential energy surfaces (PESs) requires multireference correlated wavefunction theories. Here we use bond dissociation energies (BDEs) as a foundational metric to benchmark methods based on multireference configuration interaction (MRCI) for several classes of oxygenated compounds (alcohols, aldehydes, carboxylic acids, and methyl esters). We compare results from multireference singles and doubles configuration interaction to those utilizing a posteriori and a priori size-extensivity corrections, benchmarked against experiment and coupled cluster theory. We demonstrate that size-extensivity corrections are necessary for chemically accurate BDE predictions even in relatively small molecules and furnish examples of unphysical BDE predictions resulting from using too-small orbital active spaces. We also outline the specific challenges in using MRCI methods for carbonyl-containing compounds. The resulting complete basis set extrapolated, size-extensivity-corrected MRCI scheme produces BDEs generally accurate to within 1 kcal/mol, laying the foundation for this scheme's use on larger molecules and for more complex regions of combustion PESs.

  11. Molecular models of site-isolated cobalt, rhodium, and iridium catalysts supported on zeolites: Ligand bond dissociation energies

    DOE PAGES

    Chen, Mingyang; Serna, Pedro; Lu, Jing; ...

    2015-09-28

    The chemistry of zeolite-supported site-isolated cobalt, rhodium, and iridium complexes that are essentially molecular was investigated with density functional theory (DFT) and the results compared with experimentally determined spectra characterizing rhodium and iridium species formed by the reactions of Rh(C2H4)2(acac) and Ir(C2H4)2(acac) (acac = acetylacetonate) with acidic zeolites such as dealuminated HY zeolite. The experimental results characterize ligand exchange reactions and catalytic reactions of adsorbed ligands, including olefin hydrogenation and dimerization. Two molecular models were used to characterize various binding sites of the metal complexes in the zeolites, and the agreement between experimental and calculated infrared frequencies and metal-ligand distancesmore » determined by extended X-ray absorption fine structure spectroscopy was generally very good. The calculated structures and energies indicate a metal-support-oxygen (M(I)-O) coordination number of two for most of the supported complexes and a value of three when the ligands include the radicals C2H5 or H. The results characterizing various isomers of the supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. Ligand bond dissociation energies (LDEs) are reported to explain the observed reactivity trends. The experimental observations of a stronger M-CO bond than M-(C2H4) bond for both Ir and Rh match the calculated LDEs, which show that the single-ligand LDEs of the mono and dual-ligand complexes for CO are similar to 12 and similar to 15 kcal/mol higher in energy (when the metal is Rh) and similar to 17 and similar to 20 kcal/mol higher (when the metal is Ir) than the single-ligand LDEs of the mono and dual ligand complexes for C2H4, respectively. The results provide a foundation for the prediction of the catalytic properties of numerous supported metal complexes, as summarized in detail here.« less

  12. Molecular models of site-isolated cobalt, rhodium, and iridium catalysts supported on zeolites: Ligand bond dissociation energies

    SciTech Connect

    Chen, Mingyang; Serna, Pedro; Lu, Jing; Gates, Bruce C.; Dixon, David A.

    2015-09-28

    The chemistry of zeolite-supported site-isolated cobalt, rhodium, and iridium complexes that are essentially molecular was investigated with density functional theory (DFT) and the results compared with experimentally determined spectra characterizing rhodium and iridium species formed by the reactions of Rh(C2H4)2(acac) and Ir(C2H4)2(acac) (acac = acetylacetonate) with acidic zeolites such as dealuminated HY zeolite. The experimental results characterize ligand exchange reactions and catalytic reactions of adsorbed ligands, including olefin hydrogenation and dimerization. Two molecular models were used to characterize various binding sites of the metal complexes in the zeolites, and the agreement between experimental and calculated infrared frequencies and metal-ligand distances determined by extended X-ray absorption fine structure spectroscopy was generally very good. The calculated structures and energies indicate a metal-support-oxygen (M(I)-O) coordination number of two for most of the supported complexes and a value of three when the ligands include the radicals C2H5 or H. The results characterizing various isomers of the supported metal complexes incorporating hydrocarbon ligands indicate that some carbene and carbyne ligands could form. Ligand bond dissociation energies (LDEs) are reported to explain the observed reactivity trends. The experimental observations of a stronger M-CO bond than M-(C2H4) bond for both Ir and Rh match the calculated LDEs, which show that the single-ligand LDEs of the mono and dual-ligand complexes for CO are similar to 12 and similar to 15 kcal/mol higher in energy (when the metal is Rh) and similar to 17 and similar to 20 kcal/mol higher (when the metal is Ir) than the single-ligand LDEs of the mono and dual ligand complexes for C2H4, respectively. The results provide a foundation for the prediction

  13. A promising tool to achieve chemical accuracy for density functional theory calculations on Y-NO homolysis bond dissociation energies.

    PubMed

    Li, Hong Zhi; Hu, Li Hong; Tao, Wei; Gao, Ting; Li, Hui; Lu, Ying Hua; Su, Zhong Min

    2012-01-01

    A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol(-1)) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol(-1) to 0.15 and 0.18 kcal·mol(-1), respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol(-1). This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules.

  14. The Dissociation Energies of He2, HeH, and ArH; A Bond Function Study

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Arnold, James (Technical Monitor)

    1998-01-01

    The bond energies and bond lengths are determined for He2, HeH, and ArH at the CCSD(T) level using both atom-centered basis sets and those that include bond functions. The addition of bond functions dramatically improves the rate of convergence of the results with respect to the size of the atom-centered basis set; with bond functions, triple zeta atom-centered basis set, outperform quintuple zeta basis sets without bond functions. The addition of bond functions also reduces the number of diffuse functions that must be added to the atom-centered sets. Employing bond functions appear to offer a very cost effective method of computing the interaction between weakly bound systems, especially for He.

  15. Bond dissociation energies of diatomic transition metal selenides: TiSe, ZrSe, HfSe, VSe, NbSe, and TaSe

    NASA Astrophysics Data System (ADS)

    Sorensen, Jason J.; Persinger, Thomas D.; Sevy, Andrew; Franchina, Jordan A.; Johnson, Eric L.; Morse, Michael D.

    2016-12-01

    Predissociation thresholds have been observed in the resonant two-photon ionization spectra of TiSe, ZrSe, HfSe, VSe, NbSe, and TaSe. It is argued that the sharp onset of predissociation corresponds to the bond dissociation energy in each of these molecules due to their high density of states as the ground separated atom limit is approached. The bond dissociation energies obtained are D0(TiSe) = 3.998(6) eV, D0(ZrSe) = 4.902(3) eV, D0(HfSe) = 5.154(4) eV, D0(VSe) = 3.884(3) eV, D0(NbSe) = 4.834(3) eV, and D0(TaSe) = 4.705(3) eV. Using these dissociation energies, the enthalpies of formation were found to be Δf,0 KHo(TiSe(g)) = 320.6 ± 16.8 kJ mol-1, Δf,0 KHo(ZrSe(g)) = 371.1 ± 8.5 kJ mol-1, Δf,0 KHo(HfSe(g)) = 356.1 ± 6.5 kJ mol-1, Δf,0 KHo(VSe(g)) = 372.9 ± 8.1 kJ mol-1, Δf,0 KHo(NbSe(g)) = 498.9 ± 8.1 kJ mol-1, and Δf,0 KHo(TaSe(g) ) = 562.9 ± 1.5 kJ mol-1. Comparisons are made to previous work, when available. Also reported are calculated ground state electronic configurations and terms, dipole moments, vibrational frequencies, bond lengths, and bond dissociation energies for each molecule. A strong correlation of the measured bond dissociation energy with the radial expectation value, ⟨r⟩nd, for the metal atom is found.

  16. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  17. The antimony-group 11 chemical bond: Dissociation energies of the diatomic molecules CuSb, AgSb, and AuSb

    SciTech Connect

    Carta, V.; Ciccioli, A. E-mail: andrea.ciccioli@uniroma1.it; Gigli, G. E-mail: andrea.ciccioli@uniroma1.it

    2014-02-14

    The intermetallic molecules CuSb, AgSb, and AuSb were identified in the effusive molecular beam produced at high temperature under equilibrium conditions in a double-cell-like Knudsen source. Several gaseous equilibria involving these species were studied by mass spectrometry as a function of temperature in the overall range 1349–1822 K, and the strength of the chemical bond formed between antimony and the group 11 metals was for the first time measured deriving the following thermochemical dissociation energies (D{sub 0}{sup ∘}, kJ/mol): 186.7 ± 5.1 (CuSb), 156.3 ± 4.9 (AgSb), 241.3 ± 5.8 (AuSb). The three species were also investigated computationally at the coupled cluster level with single, double, and noniterative quasiperturbative triple excitations (CCSD(T)). The spectroscopic parameters were calculated from the potential energy curves and the dissociation energies were evaluated at the Complete Basis Set limit, resulting in an overall good agreement with experimental values. An approximate evaluation of the spin-orbit effect was also performed. CCSD(T) calculations were further extended to the corresponding group 11 arsenide species which are here studied for the first time and the following dissociation energies (D{sub 0}{sup ∘}, kJ/mol): 190 ± 10 (CuAs), 151 ± 10 (AgAs), 240 ± 15 (AuAs) are proposed. Taking advantage of the new experimental and computational information here presented, the bond energy trends along group 11 and 4th and 5th periods of the periodic table were analyzed and the bond energies of the diatomic species CuBi and AuBi, yet experimentally unobserved, were predicted on an empirical basis.

  18. Trends in Homolytic Bond Dissociation Energies of Five- and Six-Coordinate Hydrides of Group 9 Transition Metals: Co, Rh, Ir.

    PubMed

    Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Elbert, Stephen T; Franz, James A

    2017-03-09

    The homolytic bond dissociation energies of a series of five- and six-coordinate mono- and dihydride complexes of the type HM(diphosphine)2 and [H2M(diphosphine)2](+) (where M = Co, Rh, and Ir) are calculated and compared with experimental values. This work probes the relationship between the homolytic bond dissociation energies (HMBDEs) of these complexes in these two different coordination environments and formal oxidation states. The results of these calculations and previous experimental observations suggest that for M = Rh the HMBDE of the five-coordinate HM(diphosphine)2 species are 0-2 kcal/mol larger than the HMBDE of the corresponding six-coordinate [H2M(diphosphine)2](+) species. For M = Ir the bond energies of the five- and six-coordinate complexes are nearly the same and for M = Co the six-coordinate species are 1-5 kcal/mol less than the corresponding five-coordinate species. Simplified models of large and complicated ligands seem to capture the essential trends and give very good estimates of these thermodynamic properties compared with experimentally available data that are difficult to obtain.

  19. Sequential bond energies and barrier heights for the water loss and charge separation dissociation pathways of Cd2+(H2O)n, n = 3-11

    NASA Astrophysics Data System (ADS)

    Cooper, Theresa E.; Armentrout, P. B.

    2011-03-01

    The bond dissociation energies for losing one water from Cd2+(H2O)n complexes, n = 3-11, are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer coupled with a thermal electrospray ionization source. Kinetic energy dependent cross sections are obtained for n = 4-11 complexes and analyzed to yield 0 K threshold measurements for loss of one, two, and three water ligands after accounting for multiple collisions, kinetic shifts, and energy distributions. The threshold measurements are converted from 0 to 298 K values to give the hydration enthalpies and free energies for sequentially losing one water from each complex. Theoretical geometry optimizations and single point energy calculations are performed on reactant and product complexes using several levels of theory and basis sets to obtain thermochemistry for comparison to experiment. The charge separation process, Cd2+(H2O)n → CdOH+(H2O)m + H+(H2O)n-m-1, is also observed for n = 4 and 5 and the competition between this process and water loss is analyzed. Rate-limiting transition states for the charge separation process at n = 3-6 are calculated and compared to experimental threshold measurements resulting in the conclusion that the critical size for this dissociation pathway of hydrated cadmium is ncrit = 4.

  20. The evaluation of bond dissociation energies for NO2 scission in nitro compounds using density functional and complete basis set methods

    NASA Astrophysics Data System (ADS)

    Shao, Ju-Xiang; Cheng, Xin-Lu; Yang, Xiang-Dong; He, Bi

    2006-02-01

    By using the density functional theory (B3LYP) and four highly accurate complete basis set (CBS-Q, CBS-QB3, CBS-Lq and CBS-4M) ab initio methods, the X(C, N, O)-NO2 bond dissociation energies (BDEs) for CH3NO2, C2H3NO2, C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 (CH3)2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy (BDE); however, all four CBS models are generally able to give reliable predication of the X(C, N, O)-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered. Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.

  1. Excitation energies with linear response density matrix functional theory along the dissociation coordinate of an electron-pair bond in N-electron systems

    NASA Astrophysics Data System (ADS)

    van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

    2014-01-01

    Time dependent density matrix functional theory in its adiabatic linear response formulation delivers exact excitation energies ωα and oscillator strengths fα for two-electron systems if extended to the so-called phase including natural orbital (PINO) theory. The Löwdin-Shull expression for the energy of two-electron systems in terms of the natural orbitals and their phases affords in this case an exact phase-including natural orbital functional (PILS), which is non-primitive (contains other than just J and K integrals). In this paper, the extension of the PILS functional to N-electron systems is investigated. With the example of an elementary primitive NO functional (BBC1) it is shown that current density matrix functional theory ground state functionals, which were designed to produce decent approximations to the total energy, fail to deliver a qualitatively correct structure of the (inverse) response function, due to essential deficiencies in the reconstruction of the two-body reduced density matrix (2RDM). We now deduce essential features of an N-electron functional from a wavefunction Ansatz: The extension of the two-electron Löwdin-Shull wavefunction to the N-electron case informs about the phase information. In this paper, applications of this extended Löwdin-Shull (ELS) functional are considered for the simplest case, ELS(1): one (dissociating) two-electron bond in the field of occupied (including core) orbitals. ELS(1) produces high quality ωα(R) curves along the bond dissociation coordinate R for the molecules LiH, Li2, and BH with the two outer valence electrons correlated. All of these results indicate that response properties are much more sensitive to deficiencies in the reconstruction of the 2RDM than the ground state energy, since derivatives of the functional with respect to both the NOs and the occupation numbers need to be accurate.

  2. S-OO bond dissociation energies and enthalpies of formation of the thiomethyl peroxyl radicals CH{sub 3}S(O){sub n}OO (n=0,1,2)

    SciTech Connect

    Salta, Zoi; Kosmas, Agnie Mylona; Lesar, Antonija

    2014-10-06

    Optimized geometries, S-OO bond dissociation energies and enthalpies of formation for a series of thiomethyl peroxyl radicals are investigated using high level ab initio and density functional theory methods. The results show that the S-OO bond dissociation energy is largest in the methylsulfonyl peroxyl radical, CH{sub 3}S(O){sub 2}OO, which contains two sulfonic type oxygen atoms followed by the methylthiyl peroxyl radical, CH{sub 3}SOO. The methylsulfinyl peroxyl radical, CH{sub 3}S(O)OO, which contains only one sulfonic type oxygen shows the least stability with regard to dissociation to CH{sub 3}S(O)+O{sub 2}. This stabilization trend is nicely reflected in the variations of the S-OO bond distance which is found to be shortest in CH{sub 3}S(O){sub 2}OO and longest in CH{sub 3}S(O)OO.

  3. Metal cation dependence of interactions with amino acids: bond dissociation energies of Rb(+) and Cs(+) to the acidic amino acids and their amide derivatives.

    PubMed

    Armentrout, P B; Yang, Bo; Rodgers, M T

    2014-04-24

    Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu

  4. Effect of substituents on the strength of N-X (X = H, F, and Cl) bond dissociation energies: a high-level quantum chemical study.

    PubMed

    O'Reilly, Robert J; Karton, Amir; Radom, Leo

    2011-06-02

    The effect of substituents on the strength of N-X (X = H, F, and Cl) bonds has been investigated using the high-level W2w thermochemical protocol. The substituents have been selected to be representative of the key functional groups that are likely to be of biological, synthetic, or industrial importance for these systems. We interpreted the effects through the calculation of relative N-X bond dissociation energies (BDE) or radical stabilization energies (RSE(NX)). The BDE and RSE(NX) values depend on stabilizing/destabilizing effects in both the reactant molecule and the product radical of the dissociation reactions. To assist us in the analysis of the substituent effects, a number of additional thermochemical quantities have been introduced, including molecule stabilization energies (MSE(NX)). We find that the RSE(NH) values are (a) increased by electron-donating alkyl substituents or the vinyl substituent, (b) increased in imines, and (c) decreased by electron-withdrawing substituents such as CF(3) and carbonyl moieties or through protonation. A different picture emerges when considering the RSE(NF) and RSE(NCl) values because of the electronegativities of the halogen atoms. The RSE(NX)s differ from the RSE(NH) values by an amount related to the stabilization of the N-halogenated molecules and given by MSE(NX). We find that substituents that stabilize/destabilize the radicals also tend to stabilize/destabilize the N-halogenated molecules. As a result, N-F- and N-Cl-containing molecules that include alkyl substituents or correspond to imines are generally associated with RSE(NF) and RSE(NCl) values that are less positive or more negative than the corresponding RSE(NH). In contrast, N-F- and N-Cl-containing molecules that include electron-withdrawing substituents or are protonated are generally associated with RSE(NF) and RSE(NCl) values that are more positive or less negative than the corresponding RSE(NH).

  5. Three methods to measure RH bond energies

    NASA Astrophysics Data System (ADS)

    Berkowitz, Joseph; Ellison, G. Barney; Gutman, David

    1993-03-01

    In this paper, the authors compare and contrast three powerful methods for experimentally measuring bond energies in polyatomic molecules. The methods are: radical kinetics; gas phase acidity cycles; and photoionization mass spectroscopy. The knowledge of the values of bond energies are a basic piece of information to a chemist. Chemical reactions involve the making and breaking of chemical bonds. It has been shown that comparable bonds in polyatomic molecules, compared to the same bonds in radicals, can be significantly different. These bond energies can be measured in terms of bond dissociation energies.

  6. Three methods to measure RH bond energies

    SciTech Connect

    Berkowitz, J.; Ellison, G.B.; Gutman, D.

    1993-03-21

    In this paper the authors compare and contrast three powerful methods for experimentally measuring bond energies in polyatomic molecules. The methods are: radical kinetics; gas phase acidity cycles; and photoionization mass spectroscopy. The knowledge of the values of bond energies are a basic piece of information to a chemist. Chemical reactions involve the making and breaking of chemical bonds. It has been shown that comparable bonds in polyatomic molecules, compared to the same bonds in radicals, can be significantly different. These bond energies can be measured in terms of bond dissociation energies.

  7. Thermochemical properties and bond dissociation energies of C3-C5 cycloalkyl hydroperoxides and peroxy radicals: cycloalkyl radical + (3)O2 reaction thermochemistry.

    PubMed

    Auzmendi-Murua, Itsaso; Bozzelli, Joseph W

    2012-07-19

    Cyclic aliphatic hydrocarbons are major components in modern fuels; they can be present in the reactants, and they can be formed during the gas-phase oxidation processes. In combustion and thermal oxidation processes, these cyclics will form radicals that react with (3)O(2) to form peroxy radicals. In this study, density functional theory and higher level ab initio calculations are used to calculate thermochemical properties and bond dissociation energies of 3-5-membered cycloalkanes, corresponding hydroperoxides, hydroperoxycycloalkyl radicals, and cycloalkyl radicals that occur in these reaction systems. Geometries, vibration frequencies, and thermochemical properties, ΔH(f 298)°, are calculated with the B3LYP/6-31 g(d,p), B3LYP/6-31 g(2d,2p), composite CBS-QB3, and G3MP2B3 methods. Standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Group additivity contributions are developed, and application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities, S°(T) and C(p)°(T) (5 K ≤ T ≤ 5000), are determined using geometric parameters and frequencies from the B3LYP/6-31 g(d,p) calculations.

  8. Thermochemistry of C7H16 to C10H22 alkane isomers: primary, secondary, and tertiary C-H bond dissociation energies and effects of branching.

    PubMed

    Hudzik, Jason M; Bozzelli, Joseph W; Simmie, John M

    2014-10-09

    Standard enthalpies of formation (ΔH°f 298) of methyl, ethyl, primary and secondary propyl, and n-butyl radicals are evaluated and used in work reactions to determine internal consistency. They are then used to calculate the enthalpy of formation for the tert-butyl radical. Other thermochemical properties including standard entropies (S°(T)), heat capacities (Cp(T)), and carbon-hydrogen bond dissociation energies (C-H BDEs) are reported for n-pentane, n-heptane, 2-methylhexane, 2,3-dimethylpentane, and several branched higher carbon number alkanes and their radicals. ΔH°f 298 and C-H BDEs are calculated using isodesmic work reactions at the B3LYP (6-31G(d,p) and 6-311G(2d,2p) basis sets), CBS-QB3, CBS-APNO, and G3MP2B3 levels of theory. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) level for contributions to entropy and heat capacities. Enthalpy calculations for these hydrocarbon radical species are shown to have consistency with the CBS-QB3 and CBS-APNO methods using all work reactions. Our recommended ideal gas phase ΔH°f 298 values are from the average of all CBS-QB3, CBS-APNO, and for G3MP2B3, only where the reference and target radical are identical types, and are compared with literature values. Calculated values show agreement between the composite calculation methods and the different work reactions. Secondary and tertiary C-H bonds in the more highly branched alkanes are shown to have bond energies that are several kcal mol(-1) lower than the BDEs in corresponding smaller molecules often used as reference species. Entropies and heat capacities are calculated and compared to literature values (when available) when all internal rotors are considered.

  9. Thermochemical Properties and Bond Dissociation Energies for Fluorinated Methanol, CH3-xFxOH, and Fluorinated Methyl Hydroperoxides, CH3-xFxOOH: Group Additivity.

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-09-08

    Oxygenated fluorocarbons are routinely found in sampling of environmental soils and waters as a result of the widespread use of fluoro and chlorofluoro carbons as heat transfer fluids, inert materials, polymers, fire retardants and solvents; the influence of these chemicals on the environment is a growing concern. The thermochemical properties of these species are needed for understanding their stability and reactions in the environment and in thermal process. Structures and thermochemical properties on the mono- to trifluoromethanol, CH3-xFxOH, and fluoromethyl hydroperoxide, CH3-xFxOOH (1 ≤ x ≤ 3), are determined by CBS-QB3, CBS-APNO, and G4 calculations. Entropy, S°298, and heat capacities, Cp(T)'s (300 ≤ T/K ≤ 1500) from vibration, translation, and external rotation contributions are calculated on the basis of the vibration frequencies and structures obtained from the B3LYP/6-31+G(d,p) density functional method. Potential barriers for the internal rotations are also calculated from this method and used to calculate hindered rotor contributions to S°298 and Cp(T)'s using direct integration over energy levels of the internal rotational potentials. Standard enthalpies of formation, ΔfH°298 (units in kcal mol(-1)) are CH2FOOH (-83.7), CHF2OOH (-138.1), CF3OOH (-193.6), CH2FOO(•) (-44.9), CHF2OO(•) (-99.6), CF3OO(•) (-153.8), CH2FOH (-101.9), CHF2OH (-161.6), CF3OH (-218.1), CH2FO(•) (-49.1), CHF2O(•) (-97.8), CF3O(•) (-150.5), CH2F(•) (-7.6), CHF2(•) (-58.8), and CF3(•) (-112.6). Bond dissociation energies for the R-OOH, RO-OH, ROO-H, R-OO(•), RO-O(•), R-OH, RO-H, R-O(•), and R-H bonds are determined and compared with methyl hydroperoxide to observe the trends from added fluoro substitutions. Enthalpy of formation for the fluoro-hydrocarbon oxygen groups C/F/H2/O, C/F2/H/O, C/F3/O, are derived from the above fluorinated methanol and fluorinated hydroperoxide species for use in Benson's Group Additivity. It was determined that

  10. Fundamentals of tandem mass spectrometry: a dynamics study of simple C-C bond cleavage in collision-activated dissociation of polyatomic ions at low energy.

    PubMed

    Shukla, A K; Qian, K; Anderson, S; Futrell, J H

    1990-02-01

    The loss of methyl radical in collision-activated dissociation (CAD) of acetone and propane molecular ions has been studied at low energy using a tandem hybrid mass spectrometer. Although the two processes are very similar chemically and energetically, very different dynamical features are observed. Acetyl ions from acetone ion are predominantly backward-scattered, with intensity maxima lying inside and outside the elastic scattering circle, confirming our previous observation that electronically excited states are important in low-energy acetone CAD. Ethyl ions from propane ion show a forward-scattered peak maximum at a nonzero scattering angle, which is consistent with generally accepted models for vibrational excitation and redistribution of energy before dissociation. Both processes demonstrate that CAD at low energy proceeds via small-impact-parameter collisions with momentum transfer. Comparison of the present results with higher energy CAD dynamics studies and earlier work leads to some tentative general conclusions about energy transfer in these processes.

  11. On the dissociation energy of Mg2

    NASA Astrophysics Data System (ADS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Pettersson, Lars G. M.; McLean, A. D.; Liu, Bowen

    1990-05-01

    The bonding in the X 1Sigma(+)g state of Mg2 is investigated using near-complete valence one-particle Slater and Gaussian basis sets containing up to h functions. It is shown that the four-electron complete CI limit can be approached using a sequence of either second-order CI (SOCI) or interacting correlated fragment (ICF) calculations. At the valence level, the best estimate of the dissociation energy D(e) was 464/cm. This is a lower limit and is probably within 5/cm of the complete basis value.

  12. Dissociation energies and charge distribution of the Co-NO bond for nitrosyl-alpha,beta,gamma,delta-tetraphenylporphinatocobalt(II) and nitrosyl-alpha,beta,gamma,delta-tetraphenylporphinatocobalt(III) in benzonitrile solution.

    PubMed

    Zhu, Xiao-Qing; Li, Qian; Hao, Wei-Fang; Cheng, Jin-Pei

    2002-08-21

    The first two series of Co-NO bond dissociation enthalpies in benzonitrile solution were determined for 12 cobalt(II) nitrosyl porphyrins and for 12 cobalt(III) nitrosyl porphyrins by titration calorimetry with suitable thermodynamic cycles. The results display that the energy scales of the heterolytic Co(III)-NO bond dissociation, the homolytic Co(III)-NO bond dissociation, and the homolytic Co(II)-NO bond dissociation are 14.7-23.2, 15.1-17.5, and 20.8-24.6 kcal/mol in benzonitrile solution, respectively, which not only indicates that the thermodynamic stability of cobalt(II) nitrosyl porphyrins is larger than that of the corresponding cobalt(III) nitrosyl porphyrins for homolysis in benzonitrile solution but also suggests that both cobalt(III) nitrosyl porphyrins and cobalt(II) nitrosyl porphyrins are excellent NO donors, and in addition, cobalt(III) nitrosyl porphyrins are also excellent NO(+) contributors. Hammett-type linear free energy analyses suggest that the nitrosyl group carries negative charges of 0.49 +/- 0.06 and 0.27 +/- 0.04 in T(G)PPCo(II)NO and in T(G)PPCo(III)NO, respectively, which indicates that nitric oxide is an electron-withdrawing group both in T(G)PPCo(II)NO and in T(G)PPCo(III)NO, behaving in a manner similar to Lewis acids rather than to Lewis bases. The energetic and structural information disclosed in the present work is believed to furnish hints to the understanding of cobalt nitrosyl porphyrins' biological functions in vivo.

  13. Assessment of Orbital-Optimized MP2.5 for Thermochemistry and Kinetics: Dramatic Failures of Standard Perturbation Theory Approaches for Aromatic Bond Dissociation Energies and Barrier Heights of Radical Reactions.

    PubMed

    Soydaş, Emine; Bozkaya, Uğur

    2015-04-14

    An assessment of orbital-optimized MP2.5 (OMP2.5) [ Bozkaya, U.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 204105 ] for thermochemistry and kinetics is presented. The OMP2.5 method is applied to closed- and open-shell reaction energies, barrier heights, and aromatic bond dissociation energies. The performance of OMP2.5 is compared with that of the MP2, OMP2, MP2.5, MP3, OMP3, CCSD, and CCSD(T) methods. For most of the test sets, the OMP2.5 method performs better than MP2.5 and CCSD, and provides accurate results. For barrier heights of radical reactions and aromatic bond dissociation energies OMP2.5-MP2.5, OMP2-MP2, and OMP3-MP3 differences become obvious. Especially, for aromatic bond dissociation energies, standard perturbation theory (MP) approaches dramatically fail, providing mean absolute errors (MAEs) of 22.5 (MP2), 17.7 (MP2.5), and 12.8 (MP3) kcal mol(-1), while the MAE values of the orbital-optimized counterparts are 2.7, 2.4, and 2.4 kcal mol(-1), respectively. Hence, there are 5-8-folds reductions in errors when optimized orbitals are employed. Our results demonstrate that standard MP approaches dramatically fail when the reference wave function suffers from the spin-contamination problem. On the other hand, the OMP2.5 method can reduce spin-contamination in the unrestricted Hartree-Fock (UHF) initial guess orbitals. For overall evaluation, we conclude that the OMP2.5 method is very helpful not only for challenging open-shell systems and transition-states but also for closed-shell molecules. Hence, one may prefer OMP2.5 over MP2.5 and CCSD as an O(N(6)) method, where N is the number of basis functions, for thermochemistry and kinetics. The cost of the OMP2.5 method is comparable with that of CCSD for energy computations. However, for analytic gradient computations, the OMP2.5 method is only half as expensive as CCSD.

  14. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

    NASA Astrophysics Data System (ADS)

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  15. Dissociation of energy-selected 1,1-dimethylhydrazine ions.

    PubMed

    Gengeliczki, Zsolt; Borkar, Sampada N; Sztáray, Bálint

    2010-05-27

    The unimolecular dissociation of 1,1-dimethylhydrazine ions was studied by threshold photoelectron photoion coincidence spectroscopy (TPEPICO). Time-of-flight distributions and breakdown curves were recorded in the photon energy range of 9.5-10.4 eV. The 0 K appearance energies of the fragment ions were extracted by modeling the experimental data with rigid activated complex (RAC-) RRKM theory. It was found that the data could be well-reproduced with a single TS for each dissociation channel if two different H-loss channels were assumed, one corresponding to a C-H and the other to a N-H bond dissociation. Once the appearance energies were established, heats of formation of the fragment ions could be derived. The heat of formation of the neutral molecule was computed by applying composite ab initio methods (G3, CBS-APNO, W1U) on a series of isodesmic reactions between methyl hydrazines and methyl amines.

  16. Dissociation energies of PH and PH+.

    NASA Astrophysics Data System (ADS)

    Reddy, R. R.; Nazeer Ahammed, Y.; Srinivasa Rao, A.; Rao, T. V. R.

    1995-12-01

    Dissociation energies for the ground electronic states of diatomic PH and PH+ are determined by fitting empirical potential functions to the respective RKRV curves using correlation coefficients. The estimated ground state dissociation energies of PH and PH+ are 3.10 and 3.20 eV respectively by the curve fitting procedure using the Lippincott potential function. The computed values are in good agreement with experimental values.

  17. Reliability theory for receptor-ligand bond dissociation

    NASA Astrophysics Data System (ADS)

    Tees, David F. J.; Woodward, John T.; Hammer, David A.

    2001-05-01

    Cell adhesion in the presence of hydrodynamic forces is a critical factor in inflammation, cancer metastasis, and blood clotting. A number of assays have recently been developed to apply forces to small numbers of the receptor-ligand bonds responsible for adhesion. Examples include assays using hydrodynamic shear in flow chambers or elastic probe deflection assays such as the atomic force microscope or the biomembrane force probe. One wishes to use the data on the time distribution of dissociation from these assays to derive information on the force dependence of reaction rates, an important determinant of cell adhesive behavior. The dissociation process can be described using the theory developed for reliability engineering of electronic components and networks. We use this framework along with the Bell model for the reverse reaction rate (kr=kr0exp[r0 f/kT], where f is the applied force and kr0 and r0 are Bell model parameters) to write closed form expressions for the probability distribution of break-up with multiple independent or interacting bonds. These expressions show that the average lifetime of n bonds scales with the nth harmonic number multiplied by the lifetime of a single bond. Results from calculation and simulations are used to describe the effect of experimental procedures in forced unbinding assays on the estimation of parameters for the force dependence of reverse reaction rates.

  18. Predicting Bond Dissociation Energies of Transition-Metal Compounds by Multiconfiguration Pair-Density Functional Theory and Second-Order Perturbation Theory Based on Correlated Participating Orbitals and Separated Pairs.

    PubMed

    Bao, Junwei Lucas; Odoh, Samuel O; Gagliardi, Laura; Truhlar, Donald G

    2017-02-14

    We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.

  19. Accurate Dissociation of Chemical Bonds Using DFT-in-DFT Embedding Theory with External Orbital Orthogonality.

    PubMed

    Tamukong, Patrick K; Khait, Yuriy G; Hoffmann, Mark R

    2017-01-12

    Our recent density functional theory (DFT)-in-DFT embedding protocol, which enforces intersubsystem (or external orbital) orthogonality, is used for the first time to investigate covalent bond dissociation and is shown to do so accurately. Full potential energy curves for the dissociation of a H-O bond in H2O and the C-C bond in H3C-CH3 have been constructed using the new embedding method, as have the challenging ionic bonds in LiH and LiF, and were found to match the reference Kohn-Sham (KS)-DFT curves to at least one part in 10(6). The added constraint of external orbital orthogonality allows for the formulation of an embedding protocol that does not rely on approximate kinetic energy functionals for the evaluation of the so-called nonadditive kinetic potential, does not introduce compensatory potentials, and does not require a total system calculation at any stage. The present work extends the demonstrated applicability of the external orthogonality variant of embedding theory by more than a factor of 2 to the interaction strength range of strong single bonds. In particular, it is demonstrated that homolytic cleavage of both covalent and ionic bonds into radicals can be accomplished.

  20. Active Thermochemical Tables: Sequential Bond Dissociation Enthalpies of Methane, Ethane, and Methanol and the Related Thermochemistry.

    PubMed

    Ruscic, Branko

    2015-07-16

    Active Thermochemical Tables (ATcT) thermochemistry for the sequential bond dissociations of methane, ethane, and methanol systems were obtained by analyzing and solving a very large thermochemical network (TN). Values for all possible C-H, C-C, C-O, and O-H bond dissociation enthalpies at 298.15 K (BDE298) and bond dissociation energies at 0 K (D0) are presented. The corresponding ATcT standard gas-phase enthalpies of formation of the resulting CHn, n = 4-0 species (methane, methyl, methylene, methylidyne, and carbon atom), C2Hn, n = 6-0 species (ethane, ethyl, ethylene, ethylidene, vinyl, ethylidyne, acetylene, vinylidene, ethynyl, and ethynylene), and COHn, n = 4-0 species (methanol, hydroxymethyl, methoxy, formaldehyde, hydroxymethylene, formyl, isoformyl, and carbon monoxide) are also presented. The ATcT thermochemistry of carbon dioxide, water, hydroxyl, and carbon, oxygen, and hydrogen atoms is also included, together with the sequential BDEs of CO2 and H2O. The provenances of the ATcT enthalpies of formation, which are quite distributed and involve a large number of relevant determinations, are analyzed by variance decomposition and discussed in terms of principal contributions. The underlying reasons for periodic appearances of remarkably low and/or unusually high BDEs, alternating along the dissociation sequences, are analyzed and quantitatively rationalized. The present ATcT results are the most accurate thermochemical values currently available for these species.

  1. The Dissociation Energies of CH4 and C2H2 Revisited

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The bond dissociation energies of CH4 and C2H2 and their fragments are investigated using basis set extrapolations and high levels of correlation. The computed bond dissociation energies (D(sub e)) are accurate to within 0.2 kcal/mol. The agreement with the experimental (D(sub 0)) values is excellent if we assume that the zero-point energy of C2H is 9.18 kcal/mol. The effect of core (1s) correlation on the bond dissociation energies of C-H bonds is shown to vary from 0.2 to 0.7 kcal/mol and that for C-C bonds varies from 0.4 to 2.2 kcal/mol.

  2. High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of cobalt carbide (CoC) and its cation (CoC+)

    NASA Astrophysics Data System (ADS)

    Lau, Kai-Chung; Pan, Yi; Lam, Chow-Shing; Huang, Huang; Chang, Yih-Chung; Luo, Zhihong; Shi, Xiaoyu; Ng, C. Y.

    2013-03-01

    The ionization energy (IE) of CoC and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for CoC and CoC+ are predicted by the wavefunction based coupled-cluster theory with single, double, triple and quadruple excitations (CCSDTQ) and complete basis set (CBS) approach. The CCSDTQ/CBS calculations presented here involve the approximation to the CBS limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy, high-order correlation, core-valence (CV) electronic, spin-orbit coupling, and scalar relativistic effect corrections. The present calculations provide the correct symmetry, 1Σ+, for the ground state of CoC+. The CCSDTQ/CBS IE(CoC) = 7.740 eV is found in good agreement with the experimental IE value of 7.73467 ± 0.00007 eV, determined in a two-color laser photoion and pulsed field ionization-photoelectron study. This work together with the previous experimental and theoretical investigations support the conclusion that the CCSDTQ/CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC, CoC, and NiC. Among the single-reference based coupled-cluster methods and multi-reference configuration interaction (MRCI) approach, the CCSDTQ and MRCI methods give the best predictions to the harmonic frequencies ωe (ωe+) = 956 (992) and 976 (1004) cm-1 and the bond lengths re (re+) = 1.560 (1.528) and 1.550 (1.522) Å, respectively, for CoC (CoC+) in comparison with the experimental values. The CCSDTQ/CBS calculations give the prediction of D0(Co+-C) - D0(Co-C) = 0.175 eV, which is also consistent with the experimental determination of 0.14630 ± 0.00014 eV. The theoretical results show that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of CoC/CoC+. For the experimental D0 and ΔHof0

  3. The C-H Dissociation Energy of C2H6

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    The C-H bond energy in C2H6 is computed to be 99.76 +/- 0.35 kcal/mol, which is in excellent agreement with the most recent experimental values. The calculation of the C-H bond energy by direct dissociation and by an isodesmic reaction is discussed.

  4. Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Hutchins, Patrick M.; Murphy, Robert C.

    2011-05-01

    Oxidative modification of polyunsaturated fatty acids, which occurs through enzymatic and nonenzymatic processes, is typically initiated by the attachment of molecular oxygen to an unsaturated fatty acyl chain forming a lipid hydroperoxide (LOOH). Enzymatic pathways are critical for cellular homeostasis but aberrant lipid peroxidation has been implicated in important pathologies. Analysis of primary oxidation products such as hydroperoxides has proven to be challenging for a variety of reasons. While negative ion electrospray ionization has been used for the specific detection of some LOOH species, hydroperoxide dehydration in the ion source has been a significant drawback. Here we describe positive ion electrospray ionization of ammoniated 13-hydroperoxy-9Z, 11E-octadecadienoyl cholesterol and 9-hydroperoxy-10E, 12Z-octadecadienoyl cholesterol, [M + NH4]+, following normal phase high-pressure liquid-chromatography. Dehydration in the ion source was not prevalent and the ammoniated molecular ion was the major species observed. Collisionally induced dissociation of the two positional isomers yielded unique product ion spectra resulting from carbon-carbon cleavages along their acyl chains. Further investigation of this behavior revealed that complex collision induced dissociations were initiated by scission of the hydroperoxide bond that drove subsequent acyl chain cleavages. Interestingly, some of the product ions retained the ammonium nitrogen through the formation of covalent carbon-nitrogen or oxygen-nitrogen bonds. These studies were carried out using hydroperoxy-octadecadienoate cholesteryl esters as model compounds, however the observed mechanisms of [LOOH + NH4]+ ionization and dissociation are likely applicable to the analysis of other lipid hydroperoxides and may serve as the basis for selective LOOH detection as well as aid in the identification of unknown lipid hydroperoxides.

  5. Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX

    NASA Astrophysics Data System (ADS)

    Liu, Lin-Lin; Liu, Pei-Jin; Hu, Song-Qi; He, Guo-Qiang

    2017-01-01

    NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10‑10 s‑1) when the temperature was less than 1000 K.

  6. Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX

    PubMed Central

    Liu, Lin-lin; Liu, Pei-jin; Hu, Song-qi; He, Guo-qiang

    2017-01-01

    NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10−10 s−1) when the temperature was less than 1000 K. PMID:28094774

  7. Birge-Sponer Estimation of the C-H Bond Dissociation Energy in Chloroform Using Infrared, Near-Infrared, and Visible Absorption Spectroscopy: An Experiment in Physical Chemistry

    ERIC Educational Resources Information Center

    Myrick, M. L.; Greer, A. E.; Nieuwland, A. A.; Priore, R. J.; Scaffidi, J.; Andreatta, Danielle; Colavita, Paula

    2008-01-01

    The fundamental and overtone vibrational absorption spectroscopy of the C-H unit in CHCl[subscript 3] is measured for transitions from the v = 0 energy level to v = 1 through v = 5 energy levels. The energies of the transitions exhibit a linearly-decreasing spacing between adjacent vibrational levels as the vibrational quantum number increases.…

  8. High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of nickel carbide (NiC) and its cation (NiC+).

    PubMed

    Lau, Kai-Chung; Chang, Yih Chung; Shi, Xiaoyu; Ng, C Y

    2010-09-21

    The ionization energy (IE) of NiC and the 0 K bond dissociation energies (D(0)) and heats of formation at 0 K (ΔH(o)(f0)) and 298 K (ΔH(o)(f298)) for NiC and NiC(+) are predicted by the wavefunction based CCSDTQ(Full)/CBS approach and the multireference configuration interaction (MRCI) method with Davidson correction (MRCI+Q). The CCSDTQ(Full)/CBS calculations presented here involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation, core-valence electronic (CV), spin-orbit coupling (SO), and scalar relativistic effect (SR) corrections. The present calculations provide the correct symmetry predictions for the ground states of NiC and NiC(+) to be (1)∑(+) and (2)∑(+), respectively. The CCSDTQ(Full)/CBS IE(NiC)=8.356 eV is found to compare favorably with the experimental IE value of 8.372 05±0.000 06 eV. The predicted IE(NiC) value at the MRCI+Q/cc-pwCV5Z level, including the ZPVE, SO, and SR effects is 8.00 eV, which is 0.37 eV lower than the experimental value. This work together with the previous experimental and theoretical investigations supports the conclusion that the CCSDTQ(Full)/CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC and NiC. Furthermore, the CCSDTQ(Full)/CBS calculations give the prediction of D(0)(Ni-C)-D(0)(Ni(+)-C)=0.688 eV, which is also consistent with the experimental determination of 0.732 21±0.000 06 eV, whereas the MRCI+Q calculations (with relativistic and CV effects) predict a significantly lower value of 0.39 eV for D(0)(Ni-C)-D(0)(Ni(+)-C). The analysis of the correction terms shows that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of NiC/NiC(+). For the experimental D(0) and ΔH(o)(f0) values of

  9. Combustion Pathways of the Alkylated Heteroaromatics: Bond Dissociation Enthalpies and Alkyl Group Fragmentations

    NASA Astrophysics Data System (ADS)

    Hayes, Carrigan J.; Hadad, Christopher M.

    2009-04-01

    The bond dissociation enthalpies (BDEs) of the alkyl groups of the alkyl-substituted heterocycles have been studied and compiled using DFT methodology, with the intent of modeling the larger heterocyclic functionalities found in coal. DFT results were calibrated against CBS-QB3 calculations, and qualitative trends were reproduced between these methods. Loss of hydrogen at the benzylic position provided the most favorable route to radical formation, for both the azabenzenes and five-membered heterocycles. The ethyl derivatives had lower BDE values than the methyl derivatives due to increased stabilization of the corresponding radicals. Calculated spin densities correlated well with bond dissociation enthalpies for these compounds, while geometric effects were minimal with respect to the heterocycles themselves. Temperature effects on the bond dissociation enthalpies were minor, ranging by about 5 kcal/mol from 298 to 2000 K; the free energies of reaction dropped significantly over the same range due to entropic effects. Monocyclic heteroaromatic rings were seen to replicate the chemistry of multicyclic heteroaromatic systems.

  10. Theoretical dissociation energies for ionic molecules

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.

    1986-01-01

    Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.

  11. The dissociative chemisorption of water on Ni(111): Mode- and bond-selective chemistry on metal surfaces

    SciTech Connect

    Farjamnia, Azar; Jackson, Bret

    2015-06-21

    A fully quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of H{sub 2}O, HOD, and D{sub 2}O on Ni(111). For this late barrier system, excitation of both the bending and stretching modes significantly enhances dissociative sticking. The vibrational efficacies vary somewhat from mode-to-mode but are all relatively close to one, in contrast to methane dissociation, where the behavior is less statistical. Similar to methane dissociation, the motion of lattice atoms near the dissociating molecule can significantly modify the height of the barrier to dissociation, leading to a strong variation in dissociative sticking with substrate temperature. Given a rescaling of the barrier height, our results are in reasonable agreement with measurements of the dissociative sticking of D{sub 2}O on Ni(111), for both laser-excited molecules with one or two quanta of excitation in the antisymmetric stretch and in the absence of laser excitation. Even without laser excitation, the beam contains vibrationally excited molecules populated at the experimental source temperature, and these make significant contributions to the sticking probability. At high collision energies, above the adiabatic barrier heights, our results correlate with these barrier heights and mode softening effects. At lower energies, dissociative sticking occurs primarily via vibrationally nonadiabatic pathways. We find a preference for O–H over O–D bond cleavage for ground state HOD molecules at all but the highest collision energies, and excitation of the O–H stretch gives close to 100% O–H selectivity at lower energies. Excitation of the O–D stretch gives a lower O–D cleavage selectivity, as the interaction with the surface leads to energy transfer from the O–D stretch into the O–H bond, when mode softening makes these vibrations nearly degenerate.

  12. The dissociation energy of N2

    NASA Technical Reports Server (NTRS)

    Almlof, Jan; Deleeuw, Bradley J.; Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Siegbahn, Per

    1989-01-01

    The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.

  13. The Breathing Orbital Valence Bond Method in Diffusion Monte Carlo: C-H Bond Dissociation ofAcetylene

    SciTech Connect

    Domin, D.; Braida, Benoit; Lester Jr., William A.

    2008-05-30

    This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 {+-} 0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 {+-} 0.7 kcal/mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 {+-} 0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 {+-} 0.5 kcal/mol).

  14. A Redetermination of the Dissociation Energy of MgO(+)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry

    1994-01-01

    In 1986, we reported a dissociation energy (D(sub 0) of 2.31 eV for the X(sup 2)Pi ground state of MgO(+). This value was determined by computing the dissociation energy to the Mg(2+) + O(-) limit and adjusting the value to the Mg(+) + O limit using the experimental Ionization Potential (IP) of Mg(+) and the Electron Affinity (EA) of O. The success of this method relies on the assumption that there is little covalent contribution to the bonding. The very small (0.04 eV) correlation contribution to the binding energy was taken as corroboration for the validity of this approach. Our earlier theoretical value was estimated to be accurate to at least 0.2 eV. It is in excellent agreement with the subsequent value of 2.30 +/- 0.13 eV determined by Freiser and co-workers from photodissociation experiments. It is also consistent with the upper (less than 3.1 eV) and lower (greater than 1.1 eV) bounds determined by Rowe obtained by studying the reactions of Mg(+) with 03 and NO2. However, it is inconsistent with an upper bound of 1.7 eV reported by Kappes and Staley based on their failure to observe MgO(+) in the reaction of Mg(+) with N2O. The picture became somewhat clouded, however, by the recent guided-ion beam mass spectrometric studies of Dalleska and Armentrout. Their initial analysis of the reaction data for Mg(+) + O2 lead to a bond dissociation energy of 2.92 +/- 0.25 eV, which is considerably larger than the value of 2.47 +/- 0.06 eV deduced from their studies of the Mg(+)+NO2 reaction.

  15. Hydrogen bonding. Part 26. Thermodynamics of dissociation and infrared spectracrystal structure correlations for betaine monohydrate and trimethylamine oxide dihydrate

    NASA Astrophysics Data System (ADS)

    Toccalino, Patricia L.; Harmon, Kenneth M.; Harmon, Jennifer

    1988-10-01

    Thermodynamic parameters for the dissociation of betaine monohydrate and trimethylamine oxide dihydrate have been determined by equilibrium vapor pressure measurements. Betaine monohydrate appears in two slightly different crystalline forms, one obtained by crystallization from water and the other by addition of water vapor to solid anhydrous betaine. Hydrogen bond energies in these hydrates are at least 8-9 kcal mol -1 per OH⋯O bond. Hydrogen bond energies in trimethylamine oxide dihydrate average at least 14 kcal mol -1 per OH⋯O bond; however, as there are two distinct types of hydrogen bonds in this hydrate, some bonds are stronger and some weaker than 14 kcal mol -1. These studies show conclusively that trimethylamine oxide monohydrate does not exist. The infrared spectrum of trimethylamine oxide dihydrate is correlated with the crystal structure.

  16. The nature of electron correlation in a dissociating bond

    NASA Astrophysics Data System (ADS)

    Hollett, Joshua W.; McKemmish, Laura K.; Gill, Peter M. W.

    2011-06-01

    We have constructed the unrestricted Hartree-Fock (UHF), restricted Hartree-Fock (RHF), and full configuration interaction (FCI) position and momentum intracules and holes for HṡṡṡH at bond lengths R from 1 to 10 bohrs. We trace the recently discovered inversion of the UHF position hole at intermediate R to over-localization of the spin-orbitals, and support this by a correlation energy component analysis. The RHF and UHF momentum holes are found to be more complicated; however their features are explained through decomposition of electron correlation effects. The UHF momentum hole is also found to invert and exhibits interesting behavior at large R. The RHF (but not UHF) and FCI momentum intracules exhibit Young-type interference patterns related to recent double photoionization experiments. Our analyses yield the most comprehensive picture to date of the behavior of the electrons during homolytic bond fission.

  17. Dissociation energies of some high temperature molecules containing aluminum

    NASA Technical Reports Server (NTRS)

    Stearns, C. A.; Kohl, F. J.

    1972-01-01

    The Knudsen cell mass spectrometric method has been used to investigate the gaseous molecules Al2, AlSi,AlSiO, AlC2, Al2C2, and AlAuC2. Special attention was given to the experimental considerations and techniques needed to identify and to measure ion intensities for very low abundance molecular species. Second- and third-law procedures were used to obtain reaction enthalpies for pressure calibration independent and isomolecular exchange reactions. Dissociation energies for the molecules were derived from the measured ion intensities, free-energy functions obtained from estimated molecular constants, and auxiliary thermodynamic data. The bonding and stability of these aluminum containing molecules are compared with other similar species.

  18. Computational study of bond dissociation enthalpies for lignin model compounds. Substituent effects in phenethyl phenyl ethers.

    PubMed

    Beste, Ariana; Buchanan, A C

    2009-04-03

    Lignin is an abundant natural resource that is a potential source of valuable chemicals. Improved understanding of the pyrolysis of lignin occurs through the study of model compounds for which phenethyl phenyl ether (PhCH(2)CH(2)OPh, PPE) is the simplest example representing the dominant beta-O-4 ether linkage. The initial step in the thermal decomposition of PPE is the homolytic cleavage of the oxygen-carbon bond. The rate of this key step will depend on the bond dissociation enthalpy, which in turn will depend on the nature and location of relevant substituents. We used modern density functional methods to calculate the oxygen-carbon bond dissociation enthalpies for PPE and several oxygen-substituted derivatives. Since carbon-carbon bond cleavage in PPE could be a competitive initial reaction under high-temperature pyrolysis conditions, we also calculated substituent effects on these bond dissociation enthalpies. We found that the oxygen-carbon bond dissociation enthalpy is substantially lowered by oxygen substituents situated at the phenyl ring adjacent to the ether oxygen. On the other hand, the carbon-carbon bond dissociation enthalpy shows little variation with different substitution patterns on either phenyl ring.

  19. The bond length and bond energy of gaseous CrW.

    PubMed

    Matthew, Daniel J; Oh, Sang Hoon; Sevy, Andrew; Morse, Michael D

    2016-06-07

    Supersonically cooled CrW was studied using resonant two-photon ionization spectroscopy. The vibronically resolved spectrum was recorded over the region 21 100 to 23 400 cm(-1), showing a very large number of bands. Seventeen of these bands, across three different isotopologues, were rotationally resolved and analyzed. All were found to arise from the ground (1)Σ(+) state of the molecule and to terminate on states with Ω' = 0. The average r0 bond length across the three isotopic forms was determined to be 1.8814(4) Å. A predissociation threshold was observed in this dense manifold of vibronic states at 23 127(10) cm(-1), indicating a bond dissociation energy of D0(CrW) = 2.867(1) eV. Using the multiple bonding radius determined for atomic Cr in previous work, the multiple bonding radius for tungsten was calculated to be 1.037 Å. Comparisons are made between CrW and the previously investigated group 6 diatomic metals, Cr2, CrMo, and Mo2, and to previous computational studies of this molecule. It is also found that the accurately known bond dissociation energies of group 5/6 metal diatomics Cr2, V2, CrW, NbCr, VNb, Mo2, and Nb2 display a qualitative linear dependence on the sum of the d-orbital radial expectation values, r; this relationship allows the bond dissociation energies of other molecules of this type to be estimated.

  20. Relationship of parental bonding to child abuse and dissociation in eating disorders in Japan.

    PubMed

    Berger, D; Ono, Y; Saito, S; Tezuka, I; Takahashi, Y; Uno, M; Ishikawa, Y; Kuboki, T; Asai, M; Suematsu, H

    1995-04-01

    Parental bonding patterns were studied in 52 female Japanese eating disorder outpatients with and without histories of sexual or physical abuse and with dissociation. Instruments included the Parental Bonding Instrument (PBI), the Dissociative Experiences Scale (DES) and the Dissociative Disorders Interview Schedule (DDIS). Those with physical abuse history, but not sexual abuse history, had significantly different parental bonding scores and higher DES scores compared with subjects without physical abuse. DES scores and PBI scores were not correlated. Although the PBI was useful in discriminating between those with and those without abuse histories, it did not detect differences in degree of dissociation. Lack of association of sexual abuse to PBI and DES scores may have been due to mild abuse.

  1. Dissociation energy for O2 release from gas-phase iron oxide clusters measured by temperature-programmed desorption experiments

    NASA Astrophysics Data System (ADS)

    Koyama, Kohei; Kudoh, Satoshi; Miyajima, Ken; Mafuné, Fumitaka

    2015-04-01

    Thermal dissociation of gas phase iron oxide cluster ions, FenOm+ (n = 2-6), was observed by mass spectrometry. The dissociation processes were investigated by temperature-programmed desorption (TPD) measurements for different sized clusters. Oxygen molecules were found to be released from the cluster ions. The threshold energy required for dissociation, determined by analyzing TPD, was compared with the energies obtained by experiments of collision-induced dissociation and by calculations of density functional theory. The agreement of the energies indicates that the oxygen atoms bonded to the terminal site of clusters are more readily released into the gas phase than those in the bridge site.

  2. Selectivity of peptide bond dissociation on excitation of a core electron: Effects of a phenyl group

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Cheng; Chen, Jien-Lian; Hu, Wei-Ping; Lin, Yi-Shiue; Lin, Huei-Ru; Lee, Tsai-Yun; Lee, Yuan T.; Ni, Chi-Kung; Liu, Chen-Lin

    2016-09-01

    The selective dissociation of a peptide bond upon excitation of a core electron in acetanilide and N-benzylacetamide was investigated. The total-ion-yield near-edge X-ray absorption fine structure spectra were recorded and compared with the predictions from time-dependent density functional theory. The branching ratios for the dissociation of a peptide bond are observed as 16-34% which is quite significant. This study explores the core-excitation, the X-ray photodissociation pathways, and the theoretical explanation of the NEXAFS spectra of organic molecules containing both a peptide bond and a phenyl group.

  3. Dissociation energy of the ground state of NaH

    NASA Astrophysics Data System (ADS)

    Huang, Hsien-Yu; Lu, Tsai-Lien; Whang, Thou-Jen; Chang, Yung-Yung; Tsai, Chin-Chun

    2010-07-01

    The dissociation energy of the ground state of NaH was determined by analyzing the observed near dissociation rovibrational levels. These levels were reached by stimulated emission pumping and fluorescence depletion spectroscopy. A total of 114 rovibrational levels in the ranges 9≤v″≤21 and 1≤J″≤14 were assigned to the X Σ1+ state of NaH. The highest vibrational level observed was only about 40 cm-1 from the dissociation limit in the ground state. One quasibound state, above the dissociation limit and confined by the centrifugal barrier, was observed. Determining the vibrational quantum number at dissociation vD from the highest four vibrational levels yielded the dissociation energy De=15 815±5 cm-1. Based on new observations and available data, a set of Dunham coefficients and the rotationless Rydberg-Klein-Rees curve were constructed. The effective potential curve and the quasibound states were discussed.

  4. Dissociation potential for breaking a CH bond in methane

    NASA Astrophysics Data System (ADS)

    Brown, Franklin B.; Truhlar, Donald G.

    1985-02-01

    The potential energy along the dissociation coordinate for CH 4 → CH 3 + H is calculated by the multi-reference configuration interaction method, including all single and double excitations, with a triple-split-plus-diffuse-and-extended-polarization basis set. The three-parameter Lippincott and Varshni potential curves provide better approximations to the dissociation potential than does the Morse model.

  5. Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

    The contacts between the N-terminal domain of heat shock protein 90 (N-Hsp90) and ADP involve both direct and water-mediated hydrogen bonds in X-ray crystallographic structure. We perform all-atom molecular dynamics (MD) simulations of N-Hsp90 and ADP to investigate the changes of the hydrogen bond lengths during ADP dissociation. We show the difference between the hydrogen bonds in the crystal structure and MD simulations. Moreover, the N6 group of ADP does not contact with the Cγ group of Asp93, and the hydrogen bonds between Asn51 side chain and ADP are stable in the early step of ADP dissociation.

  6. Zero-Point Energy Constraint for Unimolecular Dissociation Reactions. Giving Trajectories Multiple Chances To Dissociate Correctly.

    PubMed

    Paul, Amit K; Hase, William L

    2016-01-28

    A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

  7. Coupling of disulfide bond and distal histidine dissociation in human ferrous cytoglobin regulates ligand binding.

    PubMed

    Beckerson, Penny; Reeder, Brandon J; Wilson, Michael T

    2015-02-13

    Earlier kinetics studies on cytoglobin did not assign functional properties to specific structural forms. Here, we used defined monomeric and dimeric forms and cysteine mutants to show that an intramolecular disulfide bond (C38-C83) alters the dissociation rate constant of the intrinsic histidine (H81) (∼1000 fold), thus controlling binding of extrinsic ligands. Through time-resolved spectra we have unequivocally assigned CO binding to hexa- and penta-coordinate forms and have made direct measurement of histidine rebinding following photolysis. We present a model that describes how the cysteine redox state of the monomer controls histidine dissociation rate constants and hence extrinsic ligand binding.

  8. Entropic-elasticity-controlled dissociation and energetic-elasticity-controlled rupture induce catch-to-slip bonds in cell-adhesion molecules.

    PubMed

    Wei, YuJie

    2008-03-01

    We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

  9. Metal carbon bond energies for adsorbed hydrocarbons from calorimetric data

    NASA Astrophysics Data System (ADS)

    Gross, Heike; Campbell, Charles T.; King, David A.

    2004-11-01

    Single crystal adsorption calorimetry (SCAC) is a powerful new method for measuring adsorption and reaction energies. Particularly for hydrocarbons, where little or no information is available from either experiment or theory on well-defined surfaces, this method can provide crucially needed information. Assignment of the measured calorimetric heats to the appropriate surface reaction yields directly reaction heats and heats of formation of surface species. An important extension using these results is to derive values for metal-carbon bond energies in adsorbed hydrocarbon species. In this paper we review the definition of the bond dissociation energy for a surface species and discuss methodologies and limitations for calculating accurate values of this quantity from measured calorimetric data. As a step in establishing benchmark data for adsorbed hydrocarbons, we calculate a Pt-C σ bond strength, < D(Pt-C)>, of about 245 kJ/mol from data for ethylidyne on Pt{1 1 1}. Two independent methods, the quasiempirical valence bond (QVB) method and an average bond energy (ABE) method, were used to obtain this value, and the two values derived from these two approaches agree quite well. We also discuss the implications and applicability of this value of D(Pt-C) for other adsorbed hydrocarbons and on other Pt surfaces, and estimates of how this bond energy should differ when the C atom's ligands are different.

  10. Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

    SciTech Connect

    Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng; Truhlar, Donald G.

    2015-05-12

    Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules against the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used

  11. Force-induced selective dissociation of noncovalent antibody-antigen bonds.

    PubMed

    Yao, Li; Xu, Shoujun

    2012-08-23

    Specific noncovalent binding between antibody and antigen molecules is the basis for molecular recognition in biochemical processes. Quantitative investigation of the binding forces could lead to molecular specific analysis and potentially mechanical manipulation of these processes. Using our force-induced remnant magnetization spectroscopy, we revealed a well-defined binding force for the bonds between mouse immunoglobulin G and magnetically labeled α-mouse immunoglobulin G. The force was calibrated to be 120 ± 15 pN. In comparison, the binding force was only 17 ± 3 pN for physisorption and much higher than 120 pN for biotin-streptavidin bonds. A unique rebinding method was used to confirm the dissociation of the antibody-antigen bonds. A well-defined and molecule-specific binding force opens a new avenue for distinguishing different noncovalent bonds in biochemical processes.

  12. Energy and Entropy Effects in Dissociation of Peptide Radical Anions

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Lam, Corey; Chu, Ivan K.

    2012-04-15

    Time- and collision energy-resolved surface-induced dissociation (SID) of peptide radical anions was studied for the first time using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for SID experiments. Peptide radical cations and anions were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. The effect of the charge, radical, and the presence of a basic residue on the energetics and dynamics of dissociation of peptide ions was examined using RVYIHPF (1) and HVYIHPF (2) as model systems. Comparison of the survival curves for of [M+H]{sup +}, [M-H]{sup -}, M{sup +{sm_bullet}}, and [M-2H]{sup -{sm_bullet}} ions of these precursors demonstrated that even-electron ions are more stable towards fragmentation than their odd-electron counterparts. RRKM modeling of the experimental data demonstrated that the lower stability of the positive radicals is mainly attributed to lower dissociation thresholds while entropy effects are responsible the relative instability of the negative radicals. Substitution of arginine with less basic histidine residue has a strong destabilizing effect on the [M+H]{sup +} ions and a measurable stabilizing effect on the odd-electron ions. Lower threshold energies for dissociation of both positive and negative radicals of 1 are attributed to the presence of lower-energy dissociation pathways that are most likely promoted by the presence of the basic residue.

  13. Bonding energetics in clusters formed by cesium salts: a study by collision-induced dissociation and density functional theory.

    PubMed

    Maria, Pierre-Charles; Massi, Lionel; Box, Natzaret Sindreu; Gal, Jean-François; Burk, Peeter; Tammiku-Taul, Jaana; Kutsar, Martin

    2006-01-01

    In relation to the interaction between (137)Cs and soil organic matter, electrospray mass spectrometry experiments and density functional theory (DFT) calculations were carried out on the dissociation of positively charged adducts formed by cesium nitrate and cesium organic salts attached to a cesium cation [Cs(CsNO(3))(CsA)](+) (A = benzoate, salicylate, hydrogen phthalate, hydrogen maleate, hydrogen fumarate, hydrogen oxalate, and hydrogen malonate ion). These mixed clusters were generated by electrospray from methanol solutions containing cesium nitrate and an organic acid. Collision-induced dissociation of [Cs(CsNO(3))(CsA)](+) in a quadrupole ion trap gave [Cs(CsNO(3))](+) and [Cs(CsA)](+) as major product ions. Loss of HNO(3) was observed, and also CO(2) loss in the case of A = hydrogen malonate. Branching ratios for the dissociation into [Cs(CsNO(3))](+) and [Cs(CsA)](+) were treated by the Cooks' kinetic method to obtain a quantitative order of bonding energetics (enthalpies and Gibbs free energies) between Cs(+) and the molecular salt (ion pair) CsA, and were correlated with the corresponding values calculated using DFT. The kinetic method leads to relative scales of Cs(+) affinities and basicities that are consistent with the DFT-calculated values. This study brings new data on the strong interaction between the cesium cation and molecular salts CsA.

  14. Bond breaks of nucleotides by dissociative electron transfer of nonequilibrium prehydrated electrons: a new molecular mechanism for reductive DNA damage.

    PubMed

    Wang, Chun-Rong; Nguyen, Jenny; Lu, Qing-Bin

    2009-08-19

    DNA damage is a central mechanism in the pathogenesis and treatment of human diseases, notably cancer. Little is known about reductive DNA damage in causing genetic mutations during oncogenesis and killing cancer cells during radiotherapy. The prehydrated electron (e(-)(pre)) has the highest yield among all the radicals generated in cells during ionizing radiation and has subpicosecond lifetimes (10(-13) s) and energies below 0 eV, but its role in DNA damage is unknown. In this work, our real-time measurements by femtosecond time-resolved laser spectroscopy have revealed that while adenine and cytosine can effectively trap an e(-)(pre) to form stable anions, thymidine and especially guanine are highly susceptible to dissociative electron transfer of e(-)(pre), leading to bond dissociation in DNA. Our finding demonstrates a dissociative electron transfer pathway for reductive DNA damage that might be related to various diseases such as cancer and stroke. Moreover, this finding challenges the conventional notion that damage to the genome is mainly induced by the oxidizing OH* radical and might eventually lead to improved radiotherapy of cancer and radioprotection of humans.

  15. Low-energy dissociative recombination in small polyatomic molecules.

    PubMed

    Jungen, Ch; Pratt, S T

    2010-12-07

    Indirect dissociative recombination of low-energy electrons and molecular ions often occurs through capture into vibrationally excited Rydberg states. Properties of vibrational autoionization, the inverse of this capture mechanism, are used to develop some general ideas about the indirect recombination process, and these ideas are illustrated by examples from the literature. In particular, the Δv = -1 propensity rule for vibrational autoionization, i.e., that vibrational autoionization occurs by the minimum energetically allowed change in vibrational quantum numbers, leads to the prediction of thresholds in the dissociative recombination cross sections and rates at the corresponding vibrational thresholds. Capture into rotationally excited Rydberg states is also discussed in terms of recent low-temperature studies of the dissociative recombination of H(3)(+).

  16. On the dissociation energy of the BN molecule

    NASA Astrophysics Data System (ADS)

    Reddy, R. R.; Reddy, A. S. R.; Rao, T. V. R.

    1985-09-01

    For the electronic ground state, X 3II, of the BN molecule, the true potential energy curve is constructed by the method of Rydberg-Klein-Rees as modified by Vanderslice et al. By curve fitting of the modified form of Lippincott's three-parameter empirical potential function, the dissociation energy is estimated to be 3.36±0.16 eV.

  17. Thermochemical properties and bond dissociation enthalpies of 3- to 5-member ring cyclic ether hydroperoxides, alcohols, and peroxy radicals: cyclic ether radical + (3)O(2) reaction thermochemistry.

    PubMed

    Auzmendi-Murua, Itsaso; Bozzelli, Joseph W

    2014-05-01

    The formation of cyclic ethers is a major product in the oxidation of hydrocarbons, and the oxidation of biomass derived alcohols. Cyclic ethers are formed in the initial reactions of alkyl radicals with dioxygen in combustion and precombustion processes that occur at moderate temperatures. They represent a significant part of the oxygenated pollutants found in the exhaust gases of engines. Cyclic ethers can also be formed from atmospheric reactions of olefins. Additionally, cyclic ethers have been linked to the formation of the secondary organic aerosol (SOA) in the atmosphere. In combustion and thermal oxidation processes these cyclic ethers will form radicals that react with (3)O2 to form peroxy radicals. Density functional theory and higher level ab initio calculations are used to calculate thermochemical properties and bond dissociation enthalpies of 3 to 5 member ring cyclic ethers (oxirane, yC2O, oxetane, yC3O, and oxolane, yC4O), corresponding hydroperoxides, alcohols, hydroperoxy alkyl, and alkyl radicals which are formed in these oxidation reaction systems. Trends in carbon-hydrogen bond dissociation energies for the ring and hydroperoxide group relative to ring size and to distance from the ether group are determined. Bond dissociation energies are calculated for use in understanding effects of the ether oxygen in the cyclic ethers, their stability, and kinetic properties. Geometries, vibration frequencies, and enthalpies of formation, ΔH°f,298, are calculated at the B3LYP/6-31G(d,p), B3LYP/6-31G(2d,2p), the composite CBS-QB3, and G3MP2B3 methods. Entropy and heat capacities, S°(T) and Cp°(T) (5 K ≤ T ≤ 5000), are determined using geometric parameters and frequencies from the B3LYP/6-31G(d,p) calculations. The strong effects of ring strain on the bond dissociation energies in these peroxy systems are also of fundamental interest. Oxetane and oxolane exhibit a significant stabilization, 10 kcal mol(-1), lower ΔfH°298 when an oxygen group is on

  18. Theoretical determination of the alkali-metal superoxide bond energies

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Sodupe, Mariona; Langhoff, Stephen R.

    1992-01-01

    The bond dissociation energies for the alkali-metal superoxides have been computed using extensive Gaussian basis sets and treating electron correlation at the modified coupled-pair functional level. Our computed D0 values are 61.4, 37.2, 40.6, and 38.4 kcal/mol for LiO2, NaO2, KO2, and RbO2, respectively. These values, which are expected to be lower bounds and accurate to 2 kcal/mol, agree well with some of the older flame data, but rule out several recent experimental measurements.

  19. Hydrogen Dissociation in Generalized Hartree-Fock Theory: Breaking the diatomic bond

    NASA Astrophysics Data System (ADS)

    Jerke, Jonathan; Masood, Samina; Tymczak, Cj

    Generalized Hartree Fock theory predicts molecular Hydrogen dissociation without correlation. A variational Gaussian-Sinc linear superposition is the basis of 50 calculations with 3-4 significant digits of quality. The spin singlet covalent bond spontaneously breaks into a pair of uncorrelated doublets at atomic separation of 1.22 Angstroms. Quantum spin numbers and energetic comparison with Configuration Interaction theory--correlation--point to a first order phase transition in the molecular Hydrogen bond without correlation. Welch Foundation (Grant J-1675), the ARO (Grant W911Nf-13-1-0162), the Texas Southern University High Performance Computing Center (http:/hpcc.tsu.edu/; Grant PHY-1126251) and NSF-CREST CRCN project (Grant HRD-1137732).

  20. Potential function and dissociation energy of alkali halide

    NASA Astrophysics Data System (ADS)

    Srivastava, Abhay P.; Pandey, Anjani K.; Pandey, Brijesh K.

    2016-05-01

    Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L5 potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.

  1. Unrestricted prescriptions for open-shell singlet diradicals: using economical ab initio and density functional theory to calculate singlet-triplet gaps and bond dissociation curves.

    PubMed

    Ess, Daniel H; Cook, Thomas C

    2012-05-24

    Here we present and test several computational prescriptions for calculating singlet-triplet (ST) gap energies and bond dissociation curves for open-shell singlet diradicals using economical unrestricted single reference type calculations. For ST gap energies from Slipchenko and Krylov's atom and molecule test set (C, O, Si, NH, NF, OH(+), O(2), CH(2), and NH(2)(+)) spin unrestricted Hartree-Fock and MP2 energies result in errors greater than 15 kcal/mol. However, spin-projected (SP) Hartree-Fock theory in combination with spin-component-scaled (SCS) or scaled-opposite-spin (SOS) second-order perturbation theory gives ST gap energies with a mean unsigned error (MUE) of less than 2 kcal/mol. Density functionals generally give poor results for unrestricted energies and only the ωB97X-D, the M06, and the M06-2X functionals provide reasonable accuracy after spin-projection with MUE values of 4.7, 4.3, and 3.0 kcal/mol, respectively, with the 6-311++G(2d,2p) basis set. We also present a new one parameter hybrid density functional, diradical-1 (DR-1), based on Adamo and Barone's modified PW exchange functional with the PW91 correlation functional. This DR-1 method gives a mean error (ME) of 0.0 kcal/mol and a MUE value of 1.3 kcal/mol for ST gap energies. As another test of unrestricted methods the bond dissociation curves for methane (CH(4)) and hydrofluoric acid (H-F) were calculated with the M06-2X, DR-1, and ωB97X-D density functionals. All three of these functionals give reasonable results for the methane C-H bond but result in errors greater than 50 kcal/mol for the H-F bond dissociation. Spin-projection is found to significantly degrade bond dissociation curves past ~2.2 Å. Although unrestricted Hartree-Fock theory provides a very poor description of H-F bond dissociation, unrestricted SCS-MP2 and SOS-MP2 methods give accurate results.

  2. Dissociation of internal energy-selected methyl bromide ion revealed from threshold photoelectron-photoion coincidence velocity imaging.

    PubMed

    Tang, Xiaofeng; Zhou, Xiaoguo; Sun, Zhongfa; Liu, Shilin; Liu, Fuyi; Sheng, Liusi; Yan, Bing

    2014-01-28

    Dissociative photoionization of methyl bromide (CH3Br) in an excitation energy range of 10.45-16.90 eV has been investigated by using threshold photoelectron-photoion coincidence (TPEPICO) velocity imaging. The coincident time-of-flight mass spectra indicate that the ground state X(2)E of CH3Br(+) is stable, and both A(2)A1 and B(2)E ionic excited states are fully dissociative to produce the unique fragment ion of CH3 (+). From TPEPICO 3D time-sliced velocity images of CH3 (+) dissociated from specific state-selected CH3Br(+) ion, kinetic energy release distribution (KERD) and angular distribution of CH3 (+) fragment ion are directly obtained. Both spin-orbit states of Br((2)P) atom can be clearly observed in fast dissociation of CH3Br(+)(A(2)A1) ion along C-Br rupture, while a KERD of Maxwell-Boltzmann profile is obtained in dissociation of CH3Br(+)(B(2)E) ion. With the aid of the re-calculated potential energy curves of CH3Br(+) including spin-orbit coupling, dissociation mechanisms of CH3Br(+) ion in A(2)A1 and B(2)E states along C-Br rupture are revealed. For CH3Br(+)(A(2)A1) ion, the CH3 (+) + Br((2)P1/2) channel is occurred via an adiabatic dissociation by vibration, while the Br((2)P3/2) formation is through vibronic coupling to the high vibrational level of X(2)E state followed by rapid dissociation. C-Br bond breaking of CH3Br(+)(B(2)E) ion can occur via slow internal conversion to the excited vibrational level of the lower electronic states and then dissociation.

  3. Estimation of dissociation energy of NiC molecule

    NASA Astrophysics Data System (ADS)

    Sambasiva Rao, P.; Reddy, R. R.; Potukuchi, D. M.

    2006-03-01

    The experimental potential-energy curve for the electronic ground state of an astrophysically important NiC molecule is constructed by applying the Rydberg Klein Rees method as modified by Vanderslice et al. The ground state dissociation energy is estimated by a curve-fitting technique using the modified Lippincott potential function, and this estimated value of D0=3.454eV is in good agreement with the value of D0⩾3.34eV reported by Brugh and Morse.

  4. Effects of Carbonyl Bond and Metal Cluster Dissociation and Evaporation Rates on Predictions of Nanotube Production in HiPco

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2002-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNT) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the co-formation of CO2. It is shown that the production of CO2 is significantly greater for FeCO due to its lower bond energy as compared with that ofNiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  5. Gas-phase dissociation of ionic liquid aggregates studied by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation.

    PubMed

    Fernandes, Ana M; Coutinho, João A P; Marrucho, Isabel M

    2009-01-01

    Positive singly charged ionic liquid aggregates [(C(n)mim)(m+1)(BF(4))(m)](+) (mim = 3-methylimidazolium; n = 2, 4, 8 and 10) and [(C(4)mim)(m+1)(A)(m)](+) (A = Cl(-), BF(4) (-), PF(6) (-), CF(3)SO(3) (-) and (CF(3)SO(2))(2)N(-)) were investigated by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation. The electrospray ionisation mass spectra (ESI-MS) showed the formation of an aggregate with extra stability for m = 4 for all the ionic liquids with the exception of [C(4)mim][CF(3)SO(3)]. ESI-MS-MS and breakdown curves of aggregate ions showed that their dissociation occurred by loss of neutral species ([C(n)mim][A])(a) with a >or= 1. Variable-energy collision induced dissociation of each aggregate from m = 1 to m = 8 for all the ionic liquids studied enabled the determination of E(cm, 1/2) values, whose variation with m showed that the monomers were always kinetically much more stable than the larger aggregates, independently of the nature of cation and anion. The centre-of-mass energy values correlate well with literature data on ionic volumes and interaction and hydrogen bond energies.

  6. Selective cleavage of protonated penetratin and its substitutes under low-energy collision-induced dissociation condition.

    PubMed

    Peng, Juan; Zu, Lily; Fang, Weihai; Huang, Lingyun; Wang, Yaru; He, Dacheng

    2010-06-01

    An understanding of the dissociation of penetratin is important for improving its metabolic stability and cargo-delivery efficiency. In this study, we describe the selective cleavage of the K15-K16 amide bond of penetratin under the low-energy collision-induced dissociation condition in mass spectrometry. A variety of penetratin substitutes have been studied in which key basic amino acids have been substituted within the sequence. The calculated structure indicates that an alpha-helix structure prevents the fragmentation of the central peptide domain and the side chain of lysine is involved in the proton translocation process.

  7. Bond-Energy and Surface-Energy Calculations in Metals

    ERIC Educational Resources Information Center

    Eberhart, James G.; Horner, Steve

    2010-01-01

    A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…

  8. S H bond dissociation enthalpies: The importance of a complete basis set approach

    NASA Astrophysics Data System (ADS)

    Cabral do Couto, P.; Costa Cabral, Benedito J.; Martinho Simões, José A.

    2006-04-01

    The S-H homolytic bond dissociation enthalpies (BDEs) for several compounds of reference were estimated by different theoretical methods including CCSD(T), CBS-QB3, and the multi-coefficient extrapolated density functional theory multi-level approaches, MCG3-MPWB and MCG3-TS. Emphasis was placed on the importance of extrapolating theoretical BDEs to complete basis set. A very good agreement between S-H BDEs from CCSD(T) calculations and experiment is observed when a simple dual extrapolation scheme to complete basis set proposed by Truhlar is adopted. For thiophenol, our CCSD(T) estimate for the S-H BDE (347.2 kJ mol -1) supports a recent experimental value obtained from time-resolved photoacoustic calorimetry (349 ± 5 kJ mol -1).

  9. Ozone-induced dissociation: elucidation of double bond position within mass-selected lipid ions.

    PubMed

    Thomas, Michael C; Mitchell, Todd W; Harman, David G; Deeley, Jane M; Nealon, Jessica R; Blanksby, Stephen J

    2008-01-01

    Ions formed from lipids during electrospray ionization of crude lipid extracts have been mass-selected within a quadrupole linear ion trap mass spectrometer and allowed to react with ozone vapor. Gas-phase ion-molecule reactions between unsaturated lipid ions and ozone are found to yield two primary product ions for each carbon-carbon double bond within the molecule. The mass-to-charge ratios of these chemically induced fragments are diagnostic of the position of unsaturation within the precursor ion. This novel analytical technique, dubbed ozone-induced dissociation (OzID), can be applied both in series and in parallel with conventional collision-induced dissociation (CID) to provide near-complete structural assignment of unknown lipids within complex mixtures without prior fractionation or derivatization. In this study, OzID is applied to a suite of complex lipid extracts from sources including human lens, bovine kidney, and commercial olive oil, thus demonstrating the technique to be applicable to a broad range of lipid classes including both neutral and acidic glycerophospholipids, sphingomyelins, and triacylglycerols. Gas-phase ozonolysis reactions are also observed with different types of precursor ions including [M+H]+, [M+Li]+, [M+Na]+, and [M-H]-: in each case yielding fragmentation data that allow double bond position to be unambiguously assigned. Within the human lens lipid extract, three sphingomyelin regioisomers, namely SM(d18:0/15Z-24:1), SM(d18:0/17Z-24:1), and SM(d18:0/19Z-24:1), and a novel phosphatidylethanolamine alkyl ether, GPEtn(11Z-18:1e/9Z-18:1), are identified using a combination of CID and OzID. These discoveries demonstrate that lipid identification based on CID alone belies the natural structural diversity in lipid biochemistry and illustrate the potential of OzID as a complementary approach within automated, high-throughput lipid analysis protocols.

  10. Collision Induced Dissociation and Energy Transfer in Molecular Hydroge

    NASA Astrophysics Data System (ADS)

    Mandy, Margot E.

    2006-06-01

    Molecular hydrogen is a significant constituent in giant molecular clouds in the interstellar medium. Shocks in these clouds are associated with star formation. The cooling of the shocks is governed by competition of collisional energy transfer and dissociation with radiative cooling by quadrupole emission. Thus a detailed understanding of collisional behaviour of molecular hydrogen is needed. Work in this group has examined energy transfer and dissociation in molecular energy transfer as the result of collisions with H, D, He, and H2. Using quasiclassical trajectories and chemically accurate ab initio potentials state-to-state rate coefficients have been determined. The uncertainties of the cross sections are propagated rigourously to give uncertainties of the rate coefficients and the rate coefficients are parameterized as a function of temperature. Comparisons with quantum calculations are discussed and the proposed website is described.This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada. The calculations were carried out using the high performance computing facility jointly supported by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, and Silicon Graphics at the University of Northern British Columbia.

  11. Adhesive bonding using variable frequency microwave energy

    DOEpatents

    Lauf, Robert J.; McMillan, April D.; Paulauskas, Felix L.; Fathi, Zakaryae; Wei, Jianghua

    1998-01-01

    Methods of facilitating the adhesive bonding of various components with variable frequency microwave energy are disclosed. The time required to cure a polymeric adhesive is decreased by placing components to be bonded via the adhesive in a microwave heating apparatus having a multimode cavity and irradiated with microwaves of varying frequencies. Methods of uniformly heating various articles having conductive fibers disposed therein are provided. Microwave energy may be selectively oriented to enter an edge portion of an article having conductive fibers therein. An edge portion of an article having conductive fibers therein may be selectively shielded from microwave energy.

  12. Adhesive bonding using variable frequency microwave energy

    DOEpatents

    Lauf, R.J.; McMillan, A.D.; Paulauskas, F.L.; Fathi, Z.; Wei, J.

    1998-08-25

    Methods of facilitating the adhesive bonding of various components with variable frequency microwave energy are disclosed. The time required to cure a polymeric adhesive is decreased by placing components to be bonded via the adhesive in a microwave heating apparatus having a multimode cavity and irradiated with microwaves of varying frequencies. Methods of uniformly heating various articles having conductive fibers disposed therein are provided. Microwave energy may be selectively oriented to enter an edge portion of an article having conductive fibers therein. An edge portion of an article having conductive fibers therein may be selectively shielded from microwave energy. 26 figs.

  13. Adhesive bonding using variable frequency microwave energy

    DOEpatents

    Lauf, R.J.; McMillan, A.D.; Paulauskas, F.L.; Fathi, Z.; Wei, J.

    1998-09-08

    Methods of facilitating the adhesive bonding of various components with variable frequency microwave energy are disclosed. The time required to cure a polymeric adhesive is decreased by placing components to be bonded via the adhesive in a microwave heating apparatus having a multimode cavity and irradiated with microwaves of varying frequencies. Methods of uniformly heating various articles having conductive fibers disposed therein are provided. Microwave energy may be selectively oriented to enter an edge portion of an article having conductive fibers therein. An edge portion of an article having conductive fibers therein may be selectively shielded from microwave energy. 26 figs.

  14. Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

    2017-01-01

    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

  15. The Kinetics of Dissociations of Aluminum - Oxygen Bonds in Aqueous Complexes - An NMR Study

    SciTech Connect

    Dr. William Casey

    2003-09-03

    OAK B262 The Kinetics of Dissociations of Aluminum--Oxygen Bonds in Aqueous Complexes--An NMR Study. In this project we determined rates and mechanisms of Al(III)-O bond rupture at mineral surfaces and in dissolved aluminum complexes. We then compared the experimental results to simulations in an attempt to predict rate coefficients. Most of the low-temperature reactions that are geochemically important involve a bonded atom or molecule that is replaced with another. We probe these reactions at the most fundamental level in order to establish a model to predict rates for the wide range of reactions that cannot be experimentally studied. The chemistry of small aluminum cluster (Figure) provides a window into the hydrolytic processes that control rates of mineral formation and the transformation of adsorbates into extended structures. The molecule shown below as an example exposes several types of oxygens to the bulk solution including seven structurally distinct sets of bridging hydroxyls. This molecule is a rich model for the aqueous interface of aluminum (hydr)oxide minerals, since it approaches colloidal dimensions in size, yet is a dissolved complex with +18 charge. We have conducted both {sup 17}O- {sup 27}Al- and {sup 19}F-NMR experiments to identify the reactive sites and to determine the rates of isotopic exchange between these sites and the bulk solution. The research was enormously successful and led to a series of papers that are being used as touchstones for assessing the accuracy of computer models of bond ruptures in water.

  16. Rovibrational energy transfer and dissociation in O2-O collisions.

    PubMed

    Andrienko, Daniil A; Boyd, Iain D

    2016-03-14

    A set of state-specific transition rates for each rovibrational level is generated for the O2(X(3)Σ(g)(-))-O(3)P system using the quasi-classical trajectory method at temperatures observed in hypersonic flows. A system of master equations describes the relaxation of the rovibrational ensemble to thermal equilibrium under ideal heat bath conditions at a constant translational temperature. Vibrational and rotational relaxation times, obtained from the average internal energies, exhibit a pattern inherent in a chemically reactive collisional pair. An intrinsic feature of the O3 molecular system with a large attractive potential is a weak temperature dependence of the rovibrational transition rates. For this reason, the quasi-steady vibrational and rotational temperatures experience a maximum at increasing translational temperature. The energy rate coefficients, that characterize the average loss of internal energy due to dissociation, quickly diminish at high temperatures, compared to other molecular systems.

  17. Rovibrational energy transfer and dissociation in O2-O collisions

    NASA Astrophysics Data System (ADS)

    Andrienko, Daniil A.; Boyd, Iain D.

    2016-03-01

    A set of state-specific transition rates for each rovibrational level is generated for the O 2 ( X 3 Σg - ) - O (" separators=" 3 P ) system using the quasi-classical trajectory method at temperatures observed in hypersonic flows. A system of master equations describes the relaxation of the rovibrational ensemble to thermal equilibrium under ideal heat bath conditions at a constant translational temperature. Vibrational and rotational relaxation times, obtained from the average internal energies, exhibit a pattern inherent in a chemically reactive collisional pair. An intrinsic feature of the O3 molecular system with a large attractive potential is a weak temperature dependence of the rovibrational transition rates. For this reason, the quasi-steady vibrational and rotational temperatures experience a maximum at increasing translational temperature. The energy rate coefficients, that characterize the average loss of internal energy due to dissociation, quickly diminish at high temperatures, compared to other molecular systems.

  18. Low-energy behavior of exothermic dissociative electron attachment

    NASA Astrophysics Data System (ADS)

    Fabrikant, Ilya I.; Hotop, Hartmut

    2001-02-01

    We discuss two models for electron attachment to molecules: the Vogt-Wannier model for capture into a polarization well and the resonance model for dissociative attachment. The Vogt-Wannier model is generalized for the case of a target with a permanent dipole moment, and results are presented for dissociative attachment to CH3I. It is shown that the resonance theory should incorporate in this case a weakly bound dipole-supported state of CH3I-, whereas the generalized Vogt-Wannier theory gives a reasonable estimate for the cross section in the meV and sub-meV region. The Vogt-Wannier model is also applied to the process of attachment to SF6, CCl4, and C60. In the first case the s-wave capture model provides a satisfactory description of the experimental data for energies below the first vibrational excitation threshold, whereas for CCl4 it underestimates the attachment cross section by a factor of 2 in the sub-meV region. For C60 we suggest that electron attachment is dominated by s-wave capture in the region below 2 meV and by p-wave capture in the energy range above 4 meV. Our model reproduces data for Rydberg electron and free-electron attachment observed in beam experiments. It is, however, at variance with the strong rise of the attachment rate coefficients with electron temperature observed in flowing afterglow-Langmuir probe measurements.

  19. Defining the disulfide bonds of insulin-like growth factor-binding protein-5 by tandem mass spectrometry with electron transfer dissociation and collision-induced dissociation.

    PubMed

    Nili, Mahta; Mukherjee, Aditi; Shinde, Ujwal; David, Larry; Rotwein, Peter

    2012-01-06

    The six high-affinity insulin-like growth factor-binding proteins (IGFBPs) comprise a conserved family of secreted molecules that modulate IGF actions by regulating their half-life and access to signaling receptors, and also exert biological effects that are independent of IGF binding. IGFBPs are composed of cysteine-rich amino- (N-) and carboxyl- (C-) terminal domains, along with a cysteine-poor central linker segment. IGFBP-5 is the most conserved IGFBP, and contains 18 cysteines, but only 2 of 9 putative disulfide bonds have been mapped to date. Using a mass spectrometry (MS)-based strategy combining sequential electron transfer dissociation (ETD) and collision-induced dissociation (CID) steps, in which ETD fragmentation preferentially induces cleavage of disulfide bonds, and CID provides exact disulfide linkage assignments between liberated peptides, we now have definitively mapped 5 disulfide bonds in IGFBP-5. In addition, in conjunction with ab initio molecular modeling we are able to assign the other 4 disulfide linkages to within a GCGCCXXC motif that is conserved in five IGFBPs. Because of the nature of ETD fragmentation MS experiments were performed without chemical reduction of IGFBP-5. Our results not only establish a disulfide bond map of IGFBP-5 but also define a general approach that takes advantage of the specificity of ETD and the scalability of tandem MS, and the predictive power of ab initio molecular modeling to characterize unknown disulfide linkages in proteins.

  20. Low-energy dissociative electron attachment to CF2

    NASA Astrophysics Data System (ADS)

    Chourou, S. T.; Larson, Ã.; Orel, A. E.

    2015-08-01

    We present the results of a theoretical study of dissociative electron attachment (DEA) of low-energy electrons to CF2. We carried out electron scattering calculations using the complex Kohn variational method at the static-exchange and relaxed self-consistent field (SCF) level at the equilibrium geometry and compare our differential cross sections to other results. We then repeated these calculations as a function of the three internal degrees of freedom to obtain the resonance energy surfaces and autoionization widths. We use this data as input to form the Hamiltonian relevant to the nuclear dynamics. The multidimensional wave equation is solved using the multiconfiguration time-dependent Hartree (MCTDH) approach within the local approximation.

  1. Application of MALDI TOF/TOF mass spectrometry and collision-induced dissociation for the identification of disulfide-bonded peptides.

    PubMed

    Janecki, Dariusz J; Nemeth, Jennifer F

    2011-07-01

    This paper describes a method for the fast identification and composition of disulfide-bonded peptides. A unique fragmentation signature of inter-disulfide-bonded peptides is detected using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry and high-energy collision-induced dissociation (CID). This fragmentation pattern identifies peptides with an interconnected disulfide bond and provides information regarding the composition of the peptides involved in the pairing. The distinctive signature produced using CID is a triplet of ions resulting from the cleavage of the disulfide bond to produce dehydroalanine, cysteine or thiocysteine product ions. This method is not applicable to intra-peptide disulfide bonds, as the cleavage mechanism is not the same and a triplet pattern is not observed. This method has been successfully applied to identifying disulfide-bonded peptides in a number of control digestions, as well as study samples where disulfide bond networks were postulated and/or unknown.

  2. Collisional Dissociation of CO: ab initio Potential Energy Surfaces and Quasiclassical Trajectory Rate Coefficients

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Jaffe, Richard L.; Chaban, Galina M.

    2016-01-01

    We have generated accurate global potential energy surfaces for CO+Ar and CO+O that correlate with atom-diatom pairs in their ground electronic states based on extensive ab initio electronic structure calculations and used these potentials in quasi-classical trajectory nuclear dynamics calculations to predict the thermal dissociation rate coefficients over 5000- 35000 K. Our results are not compatible with the 20-45 year old experimental results. For CO + Ar we obtain fairly good agreement with the experimental rate coefficients of Appleton et al. (1970) and Mick and Roth (1993), but our computed rate coefficients exhibit a stronger temperature dependence. For CO + O our dissociation rate coefficient is in close agreement with the value from the Park model, which is an empirical adjustment of older experimental results. However, we find the rate coefficient for CO + O is only 1.5 to 3.3 times larger than CO + Ar over the temperature range of the shock tube experiments (8000-15,000 K). The previously accepted value for this rate coefficient ratio is 15, independent of temperature. We also computed the rate coefficient for the CO + O ex- change reaction which forms C + O2. We find this reaction is much faster than previously believed and is the dominant process in the removal of CO at temperatures up to 16,000 K. As a result, the dissociation of CO is accomplished in two steps (react to form C+O2 and then O2 dissociates) that are endothermic by 6.1 and 5.1 eV, instead of one step that requires 11.2 eV to break the CO bond.

  3. The physical origin of large covalent-ionic resonance energies in some two-electron bonds.

    PubMed

    Hiberty, Philippe C; Ramozzi, Romain; Song, Lingchun; Wu, Wei; Shaik, Sason

    2007-01-01

    This study uses valence bond (VB) theory to analyze in detail the previously established finding that alongside the two classical bond families of covalent and ionic bonds, which describe the electron-pair bond, there exists a distinct class of charge-shift bonds (CS-bonds) in which the fluctuation of the electron pair density plays a dominant role. Such bonds are characterized by weak binding, or even a repulsive, covalent component, and by a large covalent-ionic resonance energy RE(cs) that is responsible for the major part, or even for the totality, of the bonding energy. In the present work, the nature of CS-bonding and its fundamental mechanisms are analyzed in detail by means of a VB study of some typical homonuclear bonds (H-H, H3C-CH3, H2N-NH2, HO-OH, F-F, and Cl-Cl), ranging from classical-covalent to fully charge-shift bonds. It is shown that CS-bonding is characterized by a covalent dissociation curve with a shallow minimum situated at long interatomic distances, or even a fully repulsive covalent curve. As the atoms that are involved in the bond are taken from left to right or from bottom to top of the periodic table, the weakening effect of the adjacent bonds or lone pairs increases, while at the same time the reduced resonance integral, that couples the covalent and ionic forms, increases. As a consequence, the weakening of the covalent interaction is gradually compensated by a strengthening of CS-bonding. The large RE(cs) quantity of CS-bonds is shown to be an outcome of the mechanism necessary to establish equilibrium and optimum bonding during bond formation. It is shown that the shrinkage of the orbitals in the covalent structure lowers the potential energy, V, but excessively raises the kinetic energy, T, thereby tipping the virial ratio off-balance. Subsequent addition of the ionic structures lowers T while having a lesser effect on V, thus restoring the requisite virial ratio (T/-V = 1/2). Generalizing to typically classical covalent bonds

  4. Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of alpha-helical peptides?

    PubMed

    Pouthier, Vincent; Tsybin, Yury O

    2008-09-07

    Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alpha-helices with the recent experimental results on ECD of alpha-helical peptides through consideration of amide-I relaxation-induced hydrogen bond distortion. Based on a single spine of H-bonded peptide units, we assume that charge neutralization upon electron capture by a charged alpha-helix excites a nearby amide-I mode, which relaxes over a few picoseconds due to Fermi resonances with intramolecular normal modes. The amide-I population plays the role of an external force, which drives the displacements of each peptide unit. It induces a large immobile contraction of the H bonds surrounding the excited site whose lifetime is about the amide-I lifetime. In addition, it creates two lattice deformations describing H bond stretchings, which propagate from the excited region toward both termini of the alpha-helix, get reflected at the termini and yield H bond contractions which move back to the excited region. Consequently, we show that H bonds experience rather large contractions whose amplitude depends on general features such as the position of the amide-I mode, the peptide length and the H bond force constants. When an H bond contraction is sufficiently large, it may promote a hydrogen atom transfer between two neighboring peptide units leading to the formation of a radical at charge site remote carbonyl carbon which is known to be a precursor to the rupture of the corresponding N[Single Bond]C(alpha) bond. The introduced here way of excitation energy generation and transfer may significantly advance ECD understanding and complement existing ECD mechanisms.

  5. The thermodynamics and kinetics of phosphoester bond formation, use, and dissociation in biology, with the example of polyphosphate in platelet activation, trasience, and mineralization.

    NASA Astrophysics Data System (ADS)

    Omelon, S. J.

    2014-12-01

    Mitochondria condense orthophosphates (Pi), forming phosphoester bonds for ATP production that is important to life. This represents an exchange of energy from dissociated carbohydrate bonds to phosophoester bonds. These bonds are available to phosphorylate organic compounds or hydrolyze to Pi, driving many biochemical processes. The benthic bacteria T. namibiensis 1 and Beggiatoa 2 condense Pi into phosphate polymers in oxygenated environments. These polyphosphates (polyPs) are stored until the environment becomes anoxic, when these bacteria retrieve the energy from polyP dissociation into Pi3. Dissociated Pi is released outside of the bacteria, where it precipitates as apatite.The Gibbs free energy of polyP phosphoester bond hydrolysis is negative, however, the kinetics are slow4. Diatoms contain a polyP pool that is stable until after death, after which the polyPs hydrolyze and form apatite5. The roles of polyP in eukaryotic organism biochemistry continue to be discovered. PolyPs have a range of biochemical roles, such as bioavailable P-storage, stress adaptation, and blood clotting6. PolyP-containing granules are released from anuclear platelets to activate factor V7 and factor XII in the blood clotting process due to their polyanionic charge8. Platelets have a lifespan of approximately 8 days, after which they undergo apoptosis9. Data will be presented that demonstrate the bioactive, thermodynamically unstable polyP pool within older platelets in vitro can spontaneously hydrolyze and form phosphate minerals. This process is likely avoided by platelet digestion in the spleen and liver, possibly recycling platelet polyPs with their phosphoester bond energy for other biochemical roles. 1 Schulz HN et al. Science (2005) 307: 416-4182 Brüchert V et al. Geochim Cosmochim Acta (2003) 67: 4505-45183 Goldhammer T et al. Nat Geosci (2010) 3: 557-5614 de Jager H-J et al. J Phys Chem A (1988) 102: 2838-28415 Diaz, J et al. Science (2008) 320: 652-6556 Mason KD et al

  6. Energy-Dependent Electron Activated Dissociation of Metal-Adducted Permethylated Oligosaccharides

    PubMed Central

    Yu, Xiang; Huang, Yiqun; Lin, Cheng; Costello, Catherine E.

    2013-01-01

    The effects of varying the electron energy and cationizing agents on electron activated dissociation (ExD) of metal-adducted oligosaccharides were explored, using permethylated maltoheptaose as the model system. Across the examined range of electron energy, the metal-adducted oligosaccharide exhibited several fragmentation processes, including electron capture dissociation (ECD) at low energies, hot-ECD at intermediate energies, and electronic excitation dissociation (EED) at high energies. The dissociation threshold depended on the metal charge carrier(s), whereas the types and sequence spans of product ions were influenced by the metal-oligosaccharide binding pattern. Theoretical modeling contributed insight into the metal-dependent behavior of carbohydrates during low-energy ECD. When ExD was applied to a permethylated high mannose N-linked glycan, EED provided more structural information than either collision-induced dissociation (CID) or low-energy ECD, thus demonstrating its potential for oligosaccharide linkage analysis. PMID:22881449

  7. Bond Energies in Models of the Schrock Metathesis Catalyst

    SciTech Connect

    Vasiliu, Monica; Li, Shenggang; Arduengo, Anthony J.; Dixon, David A.

    2011-06-23

    Heats of formation, adiabatic and diabatic bond dissociation energies (BDEs) of the model Schrock-type metal complexes M(NH)(CRR)(OH)₂ (M = Cr, Mo, W; CRR = CH₂, CHF, CF₂) and MO₂(OH)₂ compounds, and Brønsted acidities and fluoride affinities for the M(NH)(CH₂)(OH) ₂ transition metal complexes are predicted using high level CCSD(T) calculations. The metallacycle intermediates formed by reaction of C₂H4 with M(NH)-(CH₂)(OH)2 and MO₂(OH)₂ are investigated at the same level of theory. Additional corrections were added to the complete basis set limit to obtain near chemical accuracy ((1 kcal/mol). A comparison between adiabatic and diabatic BDEs is made and provides an explanation of trends in the BDEs. Electronegative groups bonded on the carbenic carbon lead to less stable Schrock-type complexes as the adiabatic BDEs ofMdCF₂ andMdCHF bonds are much lower than theMdCH₂ bonds. The Cr compounds have smaller BDEs than theWorMo complexes and should be less stable. Different M(NH)(OH)₂(C₃H₆) and MO(OH)₂(OC₂H4) metallacycle intermediates are investigated, and the lowest-energy metallacycles have a square pyramidal geometry. The results show that consideration of the singlet_triplet splitting in the carbene in the initial catalyst as well as in the metal product formed by the retro [2+2] cycloaddition is a critical component in the design of an effective olefin metathesis catalyst in terms of the parent catalyst and the groups being transferred.

  8. RKRV potential energy curves and dissociation energies of NH and PH

    NASA Astrophysics Data System (ADS)

    Reddy, R. R.; Viswanath, R.

    1989-05-01

    The turning points of the potential energy curves for the ground states of NH and PH molecules were calculated using the approach of Rydberg-Klein-Rees modified by Vanderslice et al. (1960), together with the energy values obtained from the Lippincott potential function. These values were compared with those obtained by Jarmain (1960). The values of the dissociation energies of the NH and PH were estimated to be about 3.45 and 3.16, respectively.

  9. Combined use of ion mobility and collision-induced dissociation to investigate the opening of disulfide bridges by electron-transfer dissociation in peptides bearing two disulfide bonds.

    PubMed

    Massonnet, Philippe; Upert, Gregory; Smargiasso, Nicolas; Gilles, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2015-01-01

    Disulfide bonds are post-translational modifications (PTMs) often found in peptides and proteins. They increase their stability toward enzymatic degradations and provide the structure and (consequently) the activity of such folded proteins. The characterization of disulfide patterns, i.e., the cysteine connectivity, is crucial to achieve a global picture of the active conformation of the protein of interest. Electron-transfer dissociation (ETD) constitutes a valuable tool to cleave the disulfide bonds in the gas phase, avoiding chemical reduction/alkylation in solution. To characterize the cysteine pairing, the present work proposes (i) to reduce by ETD one of the two disulfide bridges of model peptides, resulting in the opening of the cyclic structures, (ii) to separate the generated species by ion mobility, and (iii) to characterize the species using collision-induced dissociation (CID). Results of this strategy applied to several peptides show different behaviors depending on the connectivity. The loss of SH· radical species, observed for all the peptides, confirms the cleavage of the disulfides during the ETD process.

  10. Hydration Energies of Zinc(II): Threshold Collision-Induced Dissociation Experiments and Theoretical Studies

    NASA Astrophysics Data System (ADS)

    Cooper, Theresa E.; Carl, D. R.; Armentrout, P. B.

    2009-11-01

    The first experimentally determined sequential bond dissociation energies of Zn2+(H2O)n complexes, where n = 6-10, are measured using threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer coupled with an electrospray ionization source. Kinetic energy dependent cross sections are obtained and analyzed to yield 0 K threshold measurements for the loss of one and two water ligands after accounting for multiple collisions, kinetic shifts, and energy distributions. The threshold measurements are then converted from 0 to 298 K values to give the hydration energies for sequentially losing one water from each parent complex. Theoretical geometry optimizations and single-point energy calculations are performed using several levels of theory for comparison to experiment. Although different levels of theory disagree on the ground-state conformation of most complexes examined here leading to potential ambiguities in the final thermochemical values, calculations at the MP2(full) level provide the best agreement with experiment. On this basis, the present experiments are most consistent with the inner solvent shell of Zn2+ being five waters, except for Zn2+(H2O)6 where all waters bind directly to the metal ion. The charge separation process, Zn2+(H2O)n → ZnOH+(H2O)m + H+(H2O)n-m-1, which is in competition with the loss of water from the parent complex, is also observed for n = 6-8. These processes are analyzed in detail in the following paper.

  11. Potential energy curves and dissociation energy of group IIA diatomic fluorides

    NASA Astrophysics Data System (ADS)

    Varma, M. P.; Ishwar, N. B.; Jha, B. L.

    1982-04-01

    Reliable (RKRV) potential energy curves have been constructed for different experimentally observed electronic states of BeF, MgF, CaF, SrF and BaF molecules from the latest spectroscopic data using the method of Rao and Venkateswarlu. Using a three-parameters Lippincott potential function the precise values of ground state dissociation energies of these molecules have been obtained. Values so obtained are found to be in close agreement with the experimental results.

  12. Identification of disulfide bonds in wheat gluten proteins by means of mass spectrometry/electron transfer dissociation.

    PubMed

    Lutz, Elena; Wieser, Herbert; Koehler, Peter

    2012-04-11

    Disulfide bonds within gluten proteins play a key role in the breadmaking performance of wheat flour. In the present study, disulfide bonds of wheat gluten proteins were identified by using a new liquid chromatography-mass spectrometry (LC-MS) technique with alternating electron transfer dissociation (ETD)/collision-induced dissociation (CID). Wheat flour was partially hydrolyzed with thermolysin (pH 6.5, 37 °C, 16 h), and the digest was subjected to LC-MS with alternating ETD/CID fragmentation. Whereas CID provided peptide fragments with intact disulfide bonds, cleavage of disulfide bonds was preferred over peptide backbone fragmentations in ETD. The simultaneous observation of disulfide-linked and disulfide-cleaved peptide ions in the mass spectra not only provided distinct interpretation with high confidence but also simplified the conventional approach for determination of disulfide bonds, which often requires two separate experiments with and without chemical reduction. By application of the new method 14 cystine peptides were identified. Eight peptides confirmed previously established disulfide bonds within gluten proteins, and the other six cystine peptides were identified for the first time. One of the newly identified cystine peptides represented a "head-to-tail" cross-link between high molecular weight glutenin subunits. This type of cross-link, which has been postulated as an integral part of glutenin models published previously, has now been proven experimentally for the first time. From the six remaining cystine peptides interchain disulfide bonds between α-gliadins, γ-gliadins, and low molecular weight glutenin subunits were established.

  13. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

    PubMed

    Li, Dechang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

    2011-04-29

    To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.

  14. Potential energy surface for C2H4I2+ dissociation including spin-orbit effects

    SciTech Connect

    Siebert, Matthew R.; Aquino, Adelia J.; De Jong, Wibe A.; Granucci, Giovanni; Hase, William L.

    2012-10-24

    Previous experiments [Baer, et al. J. Phys. Chem. A 116, 2833 (2012)] have studied the dissociation of 1,2-diiodoethane radical cation (C2H4I2+•) and found a one-dimensional distribution of translational energy; an odd finding considering most product relative translational energy distributions are two-dimensional. The goal of this study is to obtain an accurate understanding of the potential energy surface (PES) topology for the unimolecular decomposition reaction C2H4I2+• - C2H4I+ + I•. This is done through comparison of many single-reference electronic structure methods, coupled-cluster single point (energy) calculations, and multi-reference calculations used to quantify spin-orbit (SO) coupling effects. We find that the structure of the C2H4I2+• reactant has a substantial effect on the role of SO coupling on the reaction energy. Both the BHandH and MP2 theories with an ECP/6-31++G** basis set, and without SO coupling corrections, provide accurate models for the reaction energetics. MP2 theory gives an unsymmetric structure with different C-I bond lengths, resulting in a SO energy for C2H4I2+• similar to that for the product I-atom and a negligible SO correction to the reaction energy. In contrast, DFT gives a symmetric structure for C2H4I2+•, similar to that of the neutral C2H4I2 parent, resulting in a substantial SO correction and increasing the reaction energy by 6.0-6.5 kcal/mol. Also, we find that for this system single point energy calculations are inaccurate, since a small change in geometry can lead to a large change in energy.

  15. Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer.

    PubMed

    Řezáč, Jan; Hobza, Pavel

    2014-08-12

    Hydrogen fluoride dimer is a perfect model system for studying hydrogen bonding. Its size makes it possible to apply the most advanced theoretical methods available, yet it is a full-featured complex of molecules with nontrivial electronic structure and dynamic properties. Moreover, the dissociation energy of the HF dimer has been measured experimentally with an unparalleled accuracy of ±1 cm(-1)(Bohac et al. J. Chem. Phys. 1992, 9, 6681). In this work, we attempt to reproduce it by purely ab initio means, using advanced quantum-mechanical computational methods free of any empiricism. The purpose of this study is to demonstrate the capabilities of today's computational chemistry and to point out its limitations by identifying the contributions that introduce the largest uncertainty into the result. The dissociation energy is calculated using a composite scheme including large basis set CCSD(T) calculations, contributions of higher excitations up to CCSDTQ, relativistic and diagonal Born-Oppenheimer corrections and anharmonic vibrational calculations. The error of the calculated dissociation energy is 0.07 kcal/mol (25 cm(-1), 2.5%) when compared to the experiment. The major part of this error can be attributed to the inaccuracy of the calculations of the zero-point vibrational energy.

  16. Measuring internal energy deposition in collisional activation using hydrated ion nanocalorimetry to obtain peptide dissociation energies and entropies.

    PubMed

    Demireva, Maria; Williams, Evan R

    2010-07-01

    The internal energy deposited in both on- and off-resonance collisional activation in Fourier transform ion cyclotron resonance mass spectrometry is measured with ion nanocalorimetry and is used to obtain information about the dissociation energy and entropy of a protonated peptide. Activation of Na(+)(H(2)O)(30) results in sequential loss of water molecules, and the internal energy of the activated ion can be obtained from the abundances of the product ions. Information about internal energy deposition in on-resonance collisional activation of protonated peptides is inferred from dissociation data obtained under identical conditions for hydrated ions that have similar m/z and degrees-of-freedom. From experimental internal energy deposition curves and Rice-Ramsperger-Kassel-Marcus (RRKM) theory, dissociation data as a function of collision energy for protonated leucine enkephalin, which has a comparable m/z and degrees-of-freedom as Na(+)(H(2)O)(30), are modeled. The threshold dissociation energies and entropies are correlated for data acquired at a single time point, resulting in a relatively wide range of threshold dissociation energies (1.1 to 1.7 eV) that can fit these data. However, this range of values could be significantly reduced by fitting data acquired at different dissociation times. By measuring the internal energy of an activated ion, the number of fitting parameters necessary to obtain information about the dissociation parameters by modeling these data is reduced and could result in improved accuracy for such methods.

  17. Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

    PubMed

    Gu, Quanli; Knee, J L

    2012-09-14

    The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

  18. Dissociative Scattering of Hyperthermal Energy CF3+ Ions from Modified Surfaces

    SciTech Connect

    Rezayat, Talayeh; Shukla, Anil K.

    2007-02-28

    We have studied surface-induced dissociation (SID) of a small polyatomic ion, CF3+, at several collision energies between 29 eV and 159 eV in collision with fluorinated alkyl thiol on gold 111 crystal.

  19. Electron-nuclear energy sharing in above-threshold multiphoton dissociative ionization of H2.

    PubMed

    Wu, J; Kunitski, M; Pitzer, M; Trinter, F; Schmidt, L Ph H; Jahnke, T; Magrakvelidze, M; Madsen, C B; Madsen, L B; Thumm, U; Dörner, R

    2013-07-12

    We report experimental observation of the energy sharing between electron and nuclei in above-threshold multiphoton dissociative ionization of H2 by strong laser fields. The absorbed photon energy is shared between the ejected electron and nuclei in a correlated fashion, resulting in multiple diagonal lines in their joint energy spectrum governed by the energy conservation of all fragment particles.

  20. How low can you go? Minimum energy pathways for O2 dissociation on Pt(111).

    PubMed

    McEwen, J-S; Bray, J M; Wu, C; Schneider, W F

    2012-12-28

    Many DFT studies of O(2) dissociation on Pt(111) give conflicting information on preferred paths and final states. Here we report large p(4 × 4) unit cell minimum energy pathway evaluations and compare O(2) adsorption and dissociated states on Pt(111). Calculations reveal how the pathways for O(2) dissociation starting from top-fcc-bridge, top-hcp-bridge, and top-bridge-top sites are interconnected. They also provide a direct reaction pathway for the dissociation of an O(2) molecule from a top-fcc-bridge into an hcp and an fcc site, which is consistent with low temperature scanning tunneling microscope experiments. Such a pathway is shown to be considerably perturbed by the presence of co-adsorbed oxygen atoms. We quantify the coverage dependence through the construction of a Brønsted-Evans-Polanyi relationship relating the O(2) dissociation activation energies to the binding energies of the dissociated O atoms. We also show that all pathways starting from a top-fcc-bridge site give the smallest barriers for O(2) dissociation.

  1. Accurate studies of dissociation energies and vibrational energies on alkali metals

    NASA Astrophysics Data System (ADS)

    Liu, Xiu-Ying; Sun, Wei-Guo; Fan, Qun-Chao

    2008-06-01

    This paper studies full vibrational spectra {Ev} and molecular dissociation energies De by using conventional least-squares (LS) fitting and an algebraic method (AM) proposed recently for 10 diatomic electronic states of 7Li2, Na2, NaK and NaLi molecules based on some known experimental vibrational energies in a subset [Evexpt] respectively. Studies show that: (1) although both the full AM spectrum {EvAM} and the LS spectrum {EvLS} can reproduce the known experimental energies in [Evexpt], the {EvAM} is superior to the {EvLS} in that the high-lying AM vibrational energies which may not be available experimentally have better or much better accuracy than those LS counterparts in {EvLS}, and so is the AM dissociation energy DeAM; (2) the main source of the errors in the data obtained by using the LS fitting is that the fitting which is just a pure mathematical process does not use any physical criteria that must be satisfied by the full vibrational spectrum, while the AM method does. This study suggests that when fitting or solving a physical equation using a set of source data, it is important not only to apply a proper mathematical tool, but also to use correct physical criteria which measure the physical properties of the data, kick out those data having bigger errors, and impose conditional convergence on the numerical process.

  2. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico.

    PubMed

    Kononova, Olga; Kholodov, Yaroslav; Theisen, Kelly E; Marx, Kenneth A; Dima, Ruxandra I; Ataullakhanov, Fazly I; Grishchuk, Ekaterina L; Barsegov, Valeri

    2014-12-10

    Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force-deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the reversible dissociation of lateral bonds followed by irreversible dissociation of the longitudinal bonds. We have determined the free energies of dissociation of the lateral (6.9 ± 0.4 kcal/mol) and longitudinal (14.9 ± 1.5 kcal/mol) tubulin-tubulin bonds. These values in conjunction with the large flexural rigidity of tubulin protofilaments obtained (18,000-26,000 pN·nm(2)) support the idea that the disassembling microtubule is capable of generating a large mechanical force to move chromosomes during cell division. Our computational modeling offers a comprehensive quantitative platform to link molecular tubulin characteristics with the physiological behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration of biomechanical properties of other cytoskeletal and multiprotein assemblies.

  3. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    SciTech Connect

    Valentini, Paolo Schwartzentruber, Thomas E. Bender, Jason D. Nompelis, Ioannis Candler, Graham V.

    2015-08-15

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

  4. Antioxidant activity of phenolic and related compounds: a density functional theory study on the O-H bond dissociation enthalpy.

    PubMed

    Giacomelli, Cristiano; Miranda, Fabio da Silva; Gonçalves, Norberto Sanches; Spinelli, Almir

    2004-01-01

    We report here on calculations at the hybrid DFT/HF (B3-LYP/6-31G(d, p)) level of the O-H bond dissociation enthalpy (O-H BDE) of phenylpropenoic acids (caffeic, ferulic, p-coumaric and cinnamic) and phenolic acids and related compounds (gallic, methylgallate, vanillic and gentisic) in order to gain insight into the understanding of structure-antioxidant activity relationships. The results were correlated and discussed mainly on the basis of experimental data in a companion work (Galato D, Giacomelli C, Ckless K, Susin MF, Vale RMR, Spinelli A. Antioxidant capacity of phenolic and related compounds: correlation among electrochemical, visible spectroscopy methods and structure-antioxidant activity. Redox Report 2001; 6: 243-250). The O-H BDE values showed remarkable dependence on the hydroxyl position in the benzene ring and the existence of additional interaction due to hydrogen bonding. For parent molecules, the experimental antioxidant activity (AA) order was properly obeyed only when intramolecular hydrogen bonding was present in the radicalized structures of o-dihydroxyl moieties. In structurally related compounds, excellent correlation with experimental data was in general observed (0.64 < rho < 0.99). However, it is shown that excellent correlation can also be obtained for this series of compounds considering p-radicalized structures which were not stabilized by intramolecular hydrogen bonding, but this had no physical meaning. These findings suggested that the antioxidant activity evaluation of phenolic and related compounds must take into consideration the characteristics of each particular compound.

  5. Comparative study of the dissociation energies of Ni2 and Ni2(+)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

    1992-01-01

    Computations at the internally contracted averaged coupled-pair-functional level of theory yield a dissociation energy (Do) for Ni2(+) that is 0.17 eV larger than that of Ni2. This finding is consistent with the collision-induced dissociation experiments of Lian, Su, and Armentrout, but rules out the results from the resonant two-photon dissociation experiments of Lessen and Brucat, which predict that the Do value of Ni2(+) is about 1 eV larger than that of Ni2.

  6. Accurate bond energies of biodiesel methyl esters from multireference averaged coupled-pair functional calculations.

    PubMed

    Oyeyemi, Victor B; Keith, John A; Carter, Emily A

    2014-09-04

    Accurate bond dissociation energies (BDEs) are important for characterizing combustion chemistry, particularly the initial stages of pyrolysis. Here we contribute to evaluating the thermochemistry of biodiesel methyl ester molecules using ab initio BDEs derived from a multireference averaged coupled-pair functional (MRACPF2)-based scheme. Having previously validated this approach for hydrocarbons and a variety of oxygenates, herein we provide further validation for bonds within carboxylic acids and methyl esters, finding our scheme predicts BDEs within chemical accuracy (i.e., within 1 kcal/mol) for these molecules. Insights into BDE trends with ester size are then analyzed for methyl formate through methyl crotonate. We find that the carbonyl group in the ester moiety has only a local effect on BDEs. C═C double bonds in ester alkyl chains are found to increase the strengths of bonds adjacent to the double bond. An important exception are bonds beta to C═C or C═O bonds, which produce allylic-like radicals upon dissociation. The observed trends arise from different degrees of geometric relaxation and resonance stabilization in the radicals produced. We also compute BDEs in various small alkanes and alkenes as models for the long hydrocarbon chain of actual biodiesel methyl esters. We again show that allylic bonds in the alkenes are much weaker than those in the small methyl esters, indicating that hydrogen abstractions are more likely at the allylic site and even more likely at bis-allylic sites of alkyl chains due to more electrons involved in π-resonance in the latter. Lastly, we use the BDEs in small surrogates to estimate heretofore unknown BDEs in large methyl esters of biodiesel fuels.

  7. PM6 study of free radical scavenging mechanisms of flavonoids: why does O-H bond dissociation enthalpy effectively represent free radical scavenging activity?

    PubMed

    Amić, Dragan; Stepanić, Višnja; Lučić, Bono; Marković, Zoran; Dimitrić Marković, Jasmina M

    2013-06-01

    It is well known that the bond dissociation enthalpy (BDE) of the O-H group is related to the hydrogen atom transfer (HAT) mechanism of free radical scavenging that is preferred in gas-phase and non-polar solvents. The present work shows that the BDE may also be related to radical scavenging processes taking place in polar solvents, i.e., single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). This is so because the total energy requirements related to the SET-PT [sum of the ionization potential (IP) and proton dissociation enthalpy (PDE)] and the SPLET [sum of the proton affinity (PA) and electron transfer enthalpy (ETE)] are perfectly correlated with the BDE. This could explain why the published data for polyphenolic antioxidant activity measured by various assays are better correlated with the BDE than with other reaction enthalpies involved in radical scavenging mechanisms, i.e., the IP, PDE, PA and ETE. The BDE is fairly well able to rank flavonoids as antioxidants in any medium, but to conclude which radical scavenging mechanism represents the most probable reaction pathway from the thermodynamic point of view, the IP and PA (ETE) should also be considered. This is exemplified in the case of the radical scavenging activity of 25 flavonoids.

  8. Mechanistic examination of Cβ-Cγ bond cleavages of tryptophan residues during dissociations of molecular peptide radical cations.

    PubMed

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [G(n)W](•+) (n = 2-4) and [GXW](•+) (X = C, S, L, F, Y, Q) species. The C(β)-C(γ) bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO(2)](•+)) can generate [M - CO(2) - 116](+), [M - CO(2) - 117](•+), and [1H-indole](•+) (m/z 117) species as possible product ions. Competition between the formation of [M - CO(2) - 116](+) and [1H-indole](•+) systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2, the decarboxylated species that is active against C(β)-C(γ) bond cleavage, can efficiently isomerize to form a more stable π-radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The C(β)-C(γ) bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WG(n)R](•+) (n = 1-3) radical cations consistently resulted in predominant formation of [M - 116](+) product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote C(β)-C(γ) bond cleavage to prevail over the charge-directed one. DFT calculations predicted that the barrier for the former is 6.2 kcal mol(-1) lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  9. Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

    SciTech Connect

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  10. Effects of carbonyl bond, metal cluster dissociation, and evaporation rates on predictions of nanotube production in high-pressure carbon monoxide

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Smalley, Richard E.

    2003-01-01

    The high-pressure carbon monoxide (HiPco) process for producing single-wall carbon nanotubes (SWNTs) uses iron pentacarbonyl as the source of iron for catalyzing the Boudouard reaction. Attempts using nickel tetracarbonyl led to no production of SWNTs. This paper discusses simulations at a constant condition of 1300 K and 30 atm in which the chemical rate equations are solved for different reaction schemes. A lumped cluster model is developed to limit the number of species in the models, yet it includes fairly large clusters. Reaction rate coefficients in these schemes are based on bond energies of iron and nickel species and on estimates of chemical rates for formation of SWNTs. SWNT growth is measured by the conformation of CO2. It is shown that the production of CO2 is significantly greater for FeCO because of its lower bond energy as compared with that of NiCO. It is also shown that the dissociation and evaporation rates of atoms from small metal clusters have a significant effect on CO2 production. A high rate of evaporation leads to a smaller number of metal clusters available to catalyze the Boudouard reaction. This suggests that if CO reacts with metal clusters and removes atoms from them by forming MeCO, this has the effect of enhancing the evaporation rate and reducing SWNT production. The study also investigates some other reactions in the model that have a less dramatic influence.

  11. Hyperthermal Energy Collisions of CF3 + Ions with Modified Surfaces: Surface-Induced Dissociation

    SciTech Connect

    Rezayat, T.; Shukla, A.

    2004-01-01

    Collisions of low-energy ions, especially polyatomic ions, with surfaces have become an active area of research due to their numerous applications in chemistry, physics and material sciences. An interesting aspect of such collisions is the dissociation of ions which has been successfully exploited for the characterization of colliding ions, especially high mass ions from biological molecules. However, detailed studies of the energy transfer and dissociation have been performed only for a few simple systems and hence the mechanism(s) of ions’ excitation and dissociation are not as well understood even for small ions. We have therefore undertaken a study of the dissociation of a small polyatomic ion, CF3+, at several collision energies between 28.8 eV and 159 eV in collision with fluorinated alkyl thiol on gold 111 crystal and a LiF surface. These experiments were performed using a custom built tandem mass spectrometer where the energy and intensity distributions of the scattered fragment ions were measured as a function of the fragment ion mass and scattering angle. In contrast with the previous studies of the dissociation of ethanol and acetone cations where the inelastically scattered primary ions dominated the collision process (up to ~50 eV maximum energy used in those experiments), we did not observe a measurable abundance of inelastically scattered undissociated CF3+ ions at all energies studied here. We observed all fragment ions, CF2+, CF+, F+ and C+ at all energies studied with the relative intensity of the highest energy pathway, C+, increasing with collision energy. Also, the dissociation efficiency decreased significantly as the collision energy was increased from to 159 eV. The energy distributions of nearly all the fragment ions showed two distinct components, one corresponding to the loss of nearly all of the kinetic energy and scattered over a broad angular range while the other corresponding to smaller kinetic energy losses and scattered closer to

  12. Low-Energy Collision-Induced Dissociation Mass Spectra of Protonated p-Toluenesulfonamides Derived from Aliphatic Amines

    NASA Astrophysics Data System (ADS)

    Bialecki, Jason B.; Weisbecker, Carl S.; Attygalle, Athula B.

    2014-06-01

    Collision-induced fragmentation of protonated N-alkyl- p-toluenesulfonamides primarily undergo either an elimination of the amine to form CH3-(C6H4)-SO2 + cation ( m/z 155) or an alkene to form a cation for the protonated p-toluenesulfonamide ( m/z 172). To comprehend the fragmentation pathways, several deuterated analogs of N-decyl- p-toluenesulfonamides were prepared and evaluated. Hypothetically, two mechanisms, both of which involve ion-neutral complexes, can be envisaged. In one mechanism, the S-N bond fragments to produce an intermediate [sulfonyl cation/amine] complex, which dissociates to afford the m/z 155 cation (Pathway A). In the other mechanism, the C-N bond dissociates to produce a different intermediate complex. The fragmentation of this [ p-toluenesulfonamide/carbocation] complex eliminates p-toluenesulfonamide and releases the carbocation (Pathway B). Computations carried out by the Hartree-Fock method suggested that the Pathway B is more favorable. However, a peak for the carbocation is observed only when the carbocation formed is relatively stable. For example, the spectrum of N-phenylethyl- p-toluenesulfonamide is dominated by the peak at m/z 105 for the incipient phenylethyl cation, which rapidly isomerizes to the remarkably stable methylbenzyl cation. The peaks for the carbocations are weak or absent in the spectra of most of N-alkyl- p-toluenesulfonamides because alkyl carbocations, such as the decyl cation, rearrange to more stable secondary cations by 1,2-hydride and alkyl shifts. The energy freed is not dissipated, but gets internalized, causing the carbocation to dissociate either by transferring a proton to the sulfonamide or by releasing smaller alkenes to form smaller carbocations. The loss of the positional integrity in this way was proven by deuterium labeling experiments.

  13. Dissociative-recombination product states and the dissociation energy D0 of Ne2+

    SciTech Connect

    Hardy, K. A.; Peterson, J. R.; Ramos, G.; Sheldon, J. W.

    1998-02-28

    Final product states of Ne2+ dissociative recombination were studied using time-of-flight spectroscopy to determine the kinetic energies released. The dissociative recombination occurred in a sustained discharge in the presence of a variable magnetic field and discharge voltage, at pressures of 5-15 mTorr. Under different conditions various excited states were observed ranging from the lowest 3s metastable states to higher Rydbcrg states within 0.000 54 eV of the dissociation limit. From their narrow widths, it is deduced that these higher states arose from Ne2+ ions with subthermal energies. From two of these narrow distributions, we obtain an improved value for the dissociation limit D0(Ne2+)= 1.26±0.02 eV.

  14. Dissociation energy of the ground state of the CuH molecule

    NASA Astrophysics Data System (ADS)

    Rao, V. M.; Rao, M. L. P.; Rao, P. T.

    1981-06-01

    The dissociation energy of the ground state of the CuH molecule, which is observed in sun spots and in 19 Piscium, is evaluated by fitting the Hulburt-Hirschfelder function to the RKRV curve. The Hulburt-Hirschfelder potential is shown to reproduce the true curve more accurately than does the Lippincott function. The value obtained for the dissociation energy is 2.84 eV, while the values reported by Herzberg (1950) and Beckel et al. (1971) are less than 2.89 eV and 2.80 + or - 0.12 eV, respectively.

  15. A critical evaluation of the factors determining the effect of intramolecular hydrogen bonding on the O-H bond dissociation enthalpy of catechol and of flavonoid antioxidants.

    PubMed

    Lucarini, Marco; Pedulli, Gian Franco; Guerra, Maurizio

    2004-02-20

    New experimental results on the determination of the bond dissociation enthalpy (BDE) value of 3,5-di-tert-butylcatechol, a model compound for flavonoid antioxidants, by the EPR radical equilibration technique are reported. By measurement of the equilibrium constant for the reaction between 3,5-di-tert-butylcatechol and the 2,6-di-tert-butyl-4-methylphenoxyl radical, in UV irradiated isooctane solutions at different temperatures, it has been shown that the thermodynamic parameters for this reaction are DeltaH degrees = -2.8+/-0.1 kcal mol(-1) and DeltaS degrees = +1.3+/-0.2 cal mol(-1) K(-1). This demonstrates that the entropic variations in the hydrogen exchange reaction between phenols and the corresponding phenoxyl radicals are also negligible when one of the reacting species is a polyphenol and that the EPR radical equilibration technique also allows the determination of the Obond;H BDEs in intramolecularly hydrogen-bonded polyphenols. The BDE of 3,5-di-tert-butylcatechol (78.2 kcal mol(-1)) was determined to be identical to that of alpha-tocopherol. Through use of the group additivity rule, this piece of data was also used to calculate the strength of the intramolecular hydrogen bond between the hydroxyl proton and the oxygen radical centre in the corresponding semiquinone radical (5.6 kcal mol(-1)), which is responsible both for the excellent antioxidant properties of catechols and for the BDE of catechol (81.8 kcal mol(-1)). These values are in poor agreement with those predicted by DFT calculations reported in the literature (9.5 kcal mol(-1) and 77.6 kcal mol(-1), respectively). Extensive theoretical calculations indicate that the BDE of catechol is reproduced well (81.6 kcal mol(-1)) by use of diffuse functions on oxygen and the CCSD method.

  16. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

    1997-01-01

    The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

  17. Trajectory study of energy transfer and unimolecular dissociation of highly excited allyl with argon.

    PubMed

    Conte, Riccardo; Houston, Paul L; Bowman, Joel M

    2014-09-11

    The influence of rotational excitation on energy transfer in single collisions of allyl with argon and on allyl dissociation is investigated. About 90,000 classical scattering simulations are performed in order to determine collision-induced changes in internal energy and in allyl rotational angular momentum. Dissociation is studied by means of about 50,000 additional trajectories evolved for the isolated allyl under three different conditions: allyl with no angular momentum (J = 0); allyl with the same microcanonically sampled initial conditions used for the collisions (J*); allyl evolving from the corresponding exit conditions after the collision. The potential energy surface is the sum of an intramolecular potential and an interaction one, and it has already been used in a previous work on allyl-argon scattering (Conte, R.; Houston, P. L.; Bowman, J. M. J. Phys. Chem. A 2013, 117, 14028-14041). Energy transfer data show that increased initial rotation favors, on average, increased relaxation of the excited molecule. The availability of a high-level intramolecular potential energy surface permits us to study the dependence of energy transfer on the type of starting allyl isomer. A turning point analysis is presented, and highly efficient collisions are detected. Collision-induced variations in the allyl rotational angular momentum may be quite large and are found to be distributed according to three regimes. The roles of rotational angular momentum, collision, and type of isomer on allyl unimolecular dissociation are considered by looking at dissociations times, kinetic energies of the fragments, and branching ratios. Generally, rotational angular momentum has a strong influence on the dissociation dynamics, while the single collision and the type of starting isomer are less influential.

  18. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    PubMed Central

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-01-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation. PMID:27731375

  19. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    NASA Astrophysics Data System (ADS)

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-10-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.

  20. Dissociative Recombination of N2H+: Evidence for Fracture of the NN Bond

    NASA Astrophysics Data System (ADS)

    Geppert, W. D.; Thomas, R.; Semaniak, J.; Ehlerding, A.; Millar, T. J.; Österdahl, F.; af Ugglas, M.; Djurić, N.; Paál, A.; Larsson, M.

    2004-07-01

    Branching ratios and absolute cross sections have been measured for the dissociative recombination of N2H+ using the CRYRING ion storage ring. It has been found that the channel N2H++e--->N2+H accounts for only 36% of the total reaction and that the branching into the other exoergic pathway, N2H++e--->NH+N, consequently amounts to 64%. The cross section of the reaction could be fitted by the expression σ=(2.4+/-0.4)×10-16E-1.04+/-0.02 cm2, which leads to a thermal reaction rate of k(T)=(1.0+/-0.2)×10-7(T/300)-0.51+/-0.02 cm3 s-1, in favorable agreement with previous flowing afterglow Langmuir probe measurements at room temperature, although our temperature dependence is very different. The implications of these measurements for the chemistry of interstellar clouds are discussed. A standard model calculation for a dark cloud predicts a slight increase of N2H+ in the dark clouds but a five- to sevenfold increase of the NH concentration as steady state is reached.

  1. Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation.

    PubMed

    Mormann, Michael; Eble, Johannes; Schwöppe, Christian; Mesters, Rolf M; Berdel, Wolfgang E; Peter-Katalinić, Jasna; Pohlentz, Gottfried

    2008-11-01

    Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.

  2. Structure, magnetism, and dissociation energy of small bimetallic cobalt-chromium oxide cluster cations: A density-functional-theory study

    NASA Astrophysics Data System (ADS)

    Pham, Hung Tan; Cuong, Ngo Tuan; Tam, Nguyen Minh; Lam, Vu Dinh; Tung, Nguyen Thanh

    2016-01-01

    We study CoxCryOm+ (x + y = 2, 3 and 1 ≤ m ≤ 4) clusters by means of density-functional-theory calculations. It is found that the clusters grow preferentially through maximizing the number of metal-oxygen bonds with a favor on Cr sites. The size- and composition-dependent magnetic behavior is discussed in relation with the local atomic magnetic moments. While doped species show an oscillatory magnetic behavior, the total magnetic moment of pure cobalt and chromium oxide clusters tends to enhance or reduce as increasing the oxygen content, respectively. The dissociation energies for different evaporation channels are also calculated to suggest the stable patterns, as fingerprints for future photofragmentation experiments.

  3. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

    PubMed

    Munafò, A; Panesi, M; Magin, T E

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

  4. Efficient calculation of low energy statistical rates for gas phase dissociation using umbrella sampling

    NASA Astrophysics Data System (ADS)

    Mella, Massimo

    2006-03-01

    Monte Carlo (MC) simulations can be used to compute microcanonical statistical rates of gas phase dissociation reactions. Unfortunately, the MC approach may suffer from a slow convergence and large statistical errors for energies just above the dissociation threshold. In this work, umbrella sampling is proposed as a device to reduce the statistical error of MC rate constants. The method is tested by computing the classical dissociation rate for the reaction [H5O2+]*→H2O+H3O+ over the range of internal energy 38dissociation process of the Zundel cation (H5O2+) at all energies.

  5. Classical dynamics of dissociative adsorption for a nonactivated system: The role of zero point energy

    NASA Astrophysics Data System (ADS)

    Busnengo, H. F.; Crespos, C.; Dong, W.; Rayez, J. C.; Salin, A.

    2002-05-01

    We present dissociative adsorption probabilities of H2 on Pd(111) computed with the classical trajectory method. We perform both classical (C) and quasiclassical (QC) calculations, the latter including, by contrast with the former, the initial zero point energy (ZPE) of H2. We analyze in detail the role played by the ZPE and demonstrate the strong and weak points of both C and QC calculations. We show that ZPE is crucial in accelerating the molecules toward the surface through vibrational softening. However, at low energies, dynamic trapping is quenched in QC calculations by processes of vibration to rotation energy transfer that would be associated with closed channels in a quantum approach. In this study we use a new representation of the H2/Pd(111) potential energy surface (obtained by interpolation of ab initio data) with a significantly better accuracy in the entrance channel region which plays a decisive role in the dissociation dynamics.

  6. Noncatalytic dissociation of MgO by laser pulses towards sustainable energy cycle

    NASA Astrophysics Data System (ADS)

    Yabe, T.; Mohamed, M. S.; Uchida, S.; Baasandash, C.; Sato, Y.; Tsuji, M.; Mori, Y.

    2007-06-01

    We succeeded in dissociating MgO using laser pulses without a reducing agent. The energy efficiency from laser to magnesium reaction energy exceeded 42.5%. Although 1kW CO2 cw laser and Nd-YAG pulse laser are used in this experiment, the laser can be pumped by natural resources such as solar light or wind power. Thus natural resources are stored in the form of magnesium, which can be used through the reaction with water whenever we need the energy, and thus a renewable energy system will be established. This paper reports the preliminary experiments of MgO reduction toward a sustainable energy cycle.

  7. X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond

    SciTech Connect

    de Serrano, V.S.; Davis, M.F.; Gaff, J.F.; Zhang, Q.; Chen, Z.; D'Antonio, E.L.; Bowden, E.F.; Rose, R.; Franzen, S.

    2010-11-09

    X-ray crystal structures of the metcyano form of dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata (DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN{sup -}) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocket of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN{sup -} or O{sub 2} in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN{sup -} or O{sub 2} in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S-O{sub 2} form of DHP [de Serrano et al. (2007), Acta Cryst. D63, 1094-1101], it is concluded that CN{sup -} is gradually replaced by O{sub 2} as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHP A compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN{sup -} at 100 K suggests that the distal pocket of DHP A has greater flexibility than most other hemoglobins.

  8. Predictive Models for the Free Energy of Hydrogen Bonded Complexes with Single and Cooperative Hydrogen Bonds.

    PubMed

    Glavatskikh, Marta; Madzhidov, Timur; Solov'ev, Vitaly; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2016-12-01

    In this work, we report QSPR modeling of the free energy ΔG of 1 : 1 hydrogen bond complexes of different H-bond acceptors and donors. The modeling was performed on a large and structurally diverse set of 3373 complexes featuring a single hydrogen bond, for which ΔG was measured at 298 K in CCl4 . The models were prepared using Support Vector Machine and Multiple Linear Regression, with ISIDA fragment descriptors. The marked atoms strategy was applied at fragmentation stage, in order to capture the location of H-bond donor and acceptor centers. Different strategies of model validation have been suggested, including the targeted omission of individual H-bond acceptors and donors from the training set, in order to check whether the predictive ability of the model is not limited to the interpolation of H-bond strength between two already encountered partners. Successfully cross-validating individual models were combined into a consensus model, and challenged to predict external test sets of 629 and 12 complexes, in which donor and acceptor formed single and cooperative H-bonds, respectively. In all cases, SVM models outperform MLR. The SVM consensus model performs well both in 3-fold cross-validation (RMSE=1.50 kJ/mol), and on the external test sets containing complexes with single (RMSE=3.20 kJ/mol) and cooperative H-bonds (RMSE=1.63 kJ/mol).

  9. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time- and Energy-Resolved Surface-Induced Dissociation Studies

    SciTech Connect

    Laskin, Julia

    2006-07-01

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation in a Fourier transform ion cyclotron resonance mass spectrometer specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM-based approach developed at the Environmental Molecular Sciences Laboratory (EMSL).

  10. Theoretical investigation on the bond dissociation enthalpies of phenolic compounds extracted from Artocarpus altilis using ONIOM(ROB3LYP/6-311++G(2df,2p):PM6) method

    NASA Astrophysics Data System (ADS)

    Thong, Nguyen Minh; Duong, Tran; Pham, Linh Thuy; Nam, Pham Cam

    2014-10-01

    Theoretical calculations have been performed to predict the antioxidant property of phenolic compounds extracted from Artocarpus altilis. The Osbnd H bond dissociation enthalpy (BDE), ionization energy (IE), and proton dissociation enthalpy (PDE) of the phenolic compounds have been computed. The ONIOM(ROB3LYP/6-311++G(2df,2p):PM6) method is able to provide reliable evaluation for the BDE(Osbnd H) in phenolic compounds. An important property of antioxidants is determined via the BDE(Osbnd H) of those compounds extracted from A. altilis. Based on the BDE(Osbnd H), compound 12 is considered as a potential antioxidant with the estimated BDE value of 77.3 kcal/mol in the gas phase.

  11. Do Bond Functions Help for the Calculation of Accurate Bond Energies?

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)

    1998-01-01

    The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.

  12. Identification of general linear relationships between activation energies and enthalpy changes for dissociation reactions at surfaces.

    PubMed

    Michaelides, Angelos; Liu, Z-P; Zhang, C J; Alavi, Ali; King, David A; Hu, P

    2003-04-02

    The activation energy to reaction is a key quantity that controls catalytic activity. Having used ab inito calculations to determine an extensive and broad ranging set of activation energies and enthalpy changes for surface-catalyzed reactions, we show that linear relationships exist between dissociation activation energies and enthalpy changes. Known in the literature as empirical Brønsted-Evans-Polanyi (BEP) relationships, we identify and discuss the physical origin of their presence in heterogeneous catalysis. The key implication is that merely from knowledge of adsorption energies the barriers to catalytic elementary reaction steps can be estimated.

  13. Dissociation energies of six NO2 isotopologues by laser induced fluorescence spectroscopy and zero point energy of some triatomic molecules.

    PubMed

    Michalski, G; Jost, R; Sugny, D; Joyeux, M; Thiemens, M

    2004-10-15

    We have measured the rotationless photodissociation threshold of six isotopologues of NO2 containing 14N, 15N, 16O, and 18O isotopes using laser induced fluorescence detection and jet cooled NO2 (to avoid rotational congestion). For each isotopologue, the spectrum is very dense below the dissociation energy while fluorescence disappears abruptly above it. The six dissociation energies ranged from 25 128.56 cm(-1) for 14N16O2 to 25 171.80 cm(-1) for 15N18O2. The zero point energy for the NO2 isotopologues was determined from experimental vibrational energies, application of the Dunham expansion, and from canonical perturbation theory using several potential energy surfaces. Using the experimentally determined dissociation energies and the calculated zero point energies of the parent NO2 isotopologue and of the NO product(s) we determined that there is a common De = 26 051.17+/-0.70 cm(-1) using the Born-Oppenheimer approximation. The canonical perturbation theory was then used to calculate the zero point energy of all stable isotopologues of SO2, CO2, and O3, which are compared with previous determinations.

  14. Variational Energy Decomposition Analysis of Chemical Bonding. 1. Spin-Pure Analysis of Single Bonds.

    PubMed

    Levine, Daniel S; Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-10-11

    We have designed an energy decomposition analysis (EDA) to gain a deeper understanding of single chemical bonds, that is, those in which the interacting fragments are doublet open-shell systems but the supersystem is closed-shell. The method is a spin-pure extension of the absolutely localized molecular orbital (ALMO) EDA to the one-pair perfect pairing energy (equivalently to an active space of two electrons in two orbitals). The total interaction energy is broken up into four terms: frozen interactions, spin-coupling, polarization, and charge-transfer. A variety of single bonds are analyzed and, in addition, we use this method to show how solvation changes the nature of bonds, producing different results in the gas-phase and with explicit solvent molecules.

  15. Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

    NASA Astrophysics Data System (ADS)

    Mikhailov, G. P.; Lazarev, V. V.

    2016-07-01

    The effect the number of chitosan monomer units CTS n ( n = 1-5), the protonation of chitosan dimers, and the interaction between CTS n ( n = 1-3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS n is 2 n - 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.

  16. Hyperthermal Energy Collisions of CF3+ Ions With Modified Surfaces: Surface-Induced Dissociation

    SciTech Connect

    Rezayat, Talayeh; Shukla, Anil K.

    2004-12-01

    The dissociative scattering of low-energy ions, especially polyatomic ions, from surfaces has become an active area of research in chemistry, physics and material sciences. The interaction between an ion and a surface is more complicated than ion and gaseous neutral collisions and needs to be explored in detail to understand the ion excitation and dissociation phenomena associated with Surface-induced dissociation (SID) of ions, a technique used for the analysis of high mass ions from biological molecules. However, dynamics studies of SID have been performed only for a few simple systems, viz., ethanol, acetone, benzene and carbon disulfide ions. We have therefore undertaken a study of the SID of a small polyatomic ion, CF3+, at several collision energies between 28.8 eV and 159 eV in collision with fluorinated alkyl thiol on gold 111 crystal. These experiment were performed using a custom built tandem mass spectrometer where the energy and intensity distributions of the scattered fragment ions were measured as a function of the fragment mass and scattering angle. In contrast with the previous studies of the SID of ethanol and acetone cations where the inelastically scattered primary ions dominated the collision process (up to {approx}50 eV maximum energy used in those experiments), we did not observe a measurable abundance of inelastically scattered undissociated CF3+ ions up to the lowest energy studied here. We observed all fragment ions, CF2+, CF+, F+ and C+ at all energies studied with the relative intensity of the highest energy pathway, C+, increasing with collision energy. Also, the SID efficiency decreased significantly as the collision energy was increased from 106 eV to 159 eV. The energy distributions of all the fragment ions showed two distinct components, one corresponding to the loss of nearly all of the kinetic energy and scattered over a broad angular range while the other corresponding to smaller kinetic energy losses and scattered closer to the

  17. A Unified Kinetics and Equilibrium Experiment: Rate Law, Activation Energy, and Equilibrium Constant for the Dissociation of Ferroin

    ERIC Educational Resources Information Center

    Sattar, Simeen

    2011-01-01

    Tris(1,10-phenanthroline)iron(II) is the basis of a suite of four experiments spanning 5 weeks. Students determine the rate law, activation energy, and equilibrium constant for the dissociation of the complex ion in acid solution and base dissociation constant for phenanthroline. The focus on one chemical system simplifies a daunting set of…

  18. Covalent bonding: the fundamental role of the kinetic energy.

    PubMed

    Bacskay, George B; Nordholm, Sture

    2013-08-22

    This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.

  19. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation.

    PubMed

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A; Lambrecht, Marlies A; Koehler, Peter; Delcour, Jan A

    2015-07-20

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing.

  20. The Dissociation Energies of AlH2 and AlAr

    NASA Technical Reports Server (NTRS)

    Ricca, Alessandra; Partridge, Harry; Bauschlicher, Charles W., Jr.; Visscher, Luuk; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The D(sub 0) values for AlH2 and AlAr are computed using the coupled cluster approach in conjunction with large basis sets. Basis set superposition and spin-orbit effects are accounted for as they are sizeable due to the small binding energy. The computed dissociation energy for AlAr is 101 /cm , which is 83% of the experimental value (122.4/ cm). Our best estimate for the H2 binding energy in AlH2 is 40 +/- 28 /cm.

  1. Storing Renewable Energy in Chemical Bonds

    SciTech Connect

    Helm, Monte; Bullock, Morris

    2013-03-27

    With nearly 7 billion people, the world's population is demanding more electricity every year. Improved technologies are bringing wind and solar power to our electrical grid. However, wind turbines and solar panels only work when the wind blows or the sun shines. PNNL scientists discuss catalysis approaches for storing and releasing energy on demand.

  2. Storing Renewable Energy in Chemical Bonds

    ScienceCinema

    Helm, Monte; Bullock, Morris

    2016-07-12

    With nearly 7 billion people, the world's population is demanding more electricity every year. Improved technologies are bringing wind and solar power to our electrical grid. However, wind turbines and solar panels only work when the wind blows or the sun shines. PNNL scientists discuss catalysis approaches for storing and releasing energy on demand.

  3. Elementary Steps of Syngas Reactions on Mo2C(001): Adsorption Thermochemistry and Bond Dissociation

    SciTech Connect

    Medford, Andrew

    2012-02-16

    Density functional theory (DFT) and ab initio thermodynamics are applied in order to investigate the most stable surface and subsurface terminations of Mo{sub 2}C(001) as a function of chemical potential and in the presence of syngas. The Mo-terminated (001) surface is then used as a model surface to evaluate the thermochemistry and energetic barriers for key elementary steps in syngas reactions. Adsorption energy scaling relations and Broensted-Evans-Polanyi relationships are established and used to place Mo{sub 2}C into the context of transition metal surfaces. The results indicate that the surface termination is a complex function of reaction conditions and kinetics. It is predicted that the surface will be covered by either C{sub 2}H{sub 2} or O depending on conditions. Comparisons to transition metals indicate that the Mo-terminated Mo{sub 2}C(001) surface exhibits carbon reactivity similar to transition metals such as Ru and Ir, but is significantly more reactive towards oxygen.

  4. Measurement of bonding energy in an anhydrous nitrogen atmosphere and its application to silicon direct bonding technology

    NASA Astrophysics Data System (ADS)

    Fournel, F.; Continni, L.; Morales, C.; Da Fonseca, J.; Moriceau, H.; Rieutord, F.; Barthelemy, A.; Radu, I.

    2012-05-01

    Bonding energy represents an important parameter for direct bonding applications as well as for the elaboration of physical mechanisms at bonding interfaces. Measurement of bonding energy using double cantilever beam (DCB) under prescribed displacement is the most used technique thanks to its simplicity. The measurements are typically done in standard atmosphere with relative humidity above 30%. Therefore, the obtained bonding energies are strongly impacted by the water stress corrosion at the bonding interfaces. This paper presents measurements of bonding energies of directly bonded silicon wafers under anhydrous nitrogen conditions in order to prevent the water stress corrosion effect. It is shown that the measurements under anhydrous nitrogen conditions (less than 0.2 ppm of water in nitrogen) lead to high stable debonding lengths under static load and to higher bonding energies compared to the values measured under standard ambient conditions. Moreover, the bonding energies of Si/SiO2 or SiO2/SiO2 bonding interfaces are measured overall the classical post bond annealing temperature range. These new results allow to revisit the reported bonding mechanisms and to highlight physical and chemical phenomena in the absence of stress corrosion effect.

  5. Modeling of dissociation and energy transfer in shock-heated nitrogen flows

    NASA Astrophysics Data System (ADS)

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-01

    This work addresses the modeling of dissociation and energy transfer processes in shock heated nitrogen flows by means of the maximum entropy linear model and a newly proposed hybrid bin vibrational collisional model. Both models aim at overcoming two of the main limitations of the state of the art non-equilibrium models: (i) the assumption of equilibrium between rotational and translational energy modes of the molecules and (ii) the reliance on the quasi-steady-state distribution for the description of the population of the internal levels. The formulation of the coarse-grained models is based on grouping the energy levels into bins, where the population is assumed to follow a Maxwell-Boltzmann distribution at its own temperature. Different grouping strategies are investigated. Following the maximum entropy principle, the governing equations are obtained by taking the zeroth and first-order moments of the rovibrational master equations. The accuracy of the proposed models is tested against the rovibrational master equation solution for both flow quantities and population distributions. Calculations performed for free-stream velocities ranging from 5 km/s to 10 km/s demonstrate that dissociation can be accurately predicted by using only 2-3 bins. It is also shown that a multi-temperature approach leads to an under-prediction of dissociation, due to the inability of the former to account for the faster excitation of high-lying vibrational states.

  6. Modeling of dissociation and energy transfer in shock-heated nitrogen flows

    SciTech Connect

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-15

    This work addresses the modeling of dissociation and energy transfer processes in shock heated nitrogen flows by means of the maximum entropy linear model and a newly proposed hybrid bin vibrational collisional model. Both models aim at overcoming two of the main limitations of the state of the art non-equilibrium models: (i) the assumption of equilibrium between rotational and translational energy modes of the molecules and (ii) the reliance on the quasi-steady-state distribution for the description of the population of the internal levels. The formulation of the coarse-grained models is based on grouping the energy levels into bins, where the population is assumed to follow a Maxwell-Boltzmann distribution at its own temperature. Different grouping strategies are investigated. Following the maximum entropy principle, the governing equations are obtained by taking the zeroth and first-order moments of the rovibrational master equations. The accuracy of the proposed models is tested against the rovibrational master equation solution for both flow quantities and population distributions. Calculations performed for free-stream velocities ranging from 5 km/s to 10 km/s demonstrate that dissociation can be accurately predicted by using only 2-3 bins. It is also shown that a multi-temperature approach leads to an under-prediction of dissociation, due to the inability of the former to account for the faster excitation of high-lying vibrational states.

  7. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

    SciTech Connect

    Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A.

    2014-09-14

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about −121 cm{sup −1} upon dimerization, somewhat more than in the anharmonic experiment (−111 cm{sup −1})

  8. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: harmonic constraints for methanol dimer.

    PubMed

    Heger, Matthias; Suhm, Martin A; Mata, Ricardo A

    2014-09-14

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about -121 cm(-1) upon dimerization, somewhat more than in the anharmonic experiment (-111 cm(-1)).

  9. Enthalpy of formation of anisole: implications for the controversy on the O-H bond dissociation enthalpy in phenol.

    PubMed

    Simões, Ricardo G; Agapito, Filipe; Diogo, Hermínio P; da Piedade, Manuel E Minas

    2014-11-20

    Significant discrepancies in the literature data for the enthalpy of formation of gaseous anisole, ΔfHmo(PhOCH3, g), have fueled an ongoing controversy regarding the most reliable enthalpy of formation of the phenoxy radical and of the gas phase O-H bond dissociation enthalpy, DHo(PhO-H), in phenol. In the present work ΔfHmo(PhOCH3, g) was reassessed using a combination of calorimetric determinations and high-level (W2-F12) ab initio calculations. Static-bomb combustion calorimetry led to the standard molar enthalpy of formation of liquid anisole at 298.15 K, ΔfHmo(PhOCH3, l) = −(117.1 ± 1.4) kJ·mol(-1). The corresponding enthalpy of vaporization was obtained as, ΔvapHmo(PhOCH3) = 46.41 ± 0.26 kJ·mol(-1), by Calvet-drop microcalorimetry. These results give ΔfHmo(PhOCH3, g) = −(70.7 ± 1.4) kJ·mol(-1), in excellent agreement with ΔfHmo(PhOCH3, g) = −(70.8 ± 3.2) kJ·mol(-1), obtained from the W2-F12 calculations. The ΔfHmo(PhOCH3, g) here recommended leads to ΔfHmo(PhO•, g) = 55.5 ± 2.4 kJ·mol(-)1 and DH°(PhO-H) = 368.1 ± 2.6 kJ·mol(-1).

  10. Enthalpy of Formation and O-H Bond Dissociation Enthalpy of Phenol: Inconsistency between Theory and Experiment.

    PubMed

    Dorofeeva, Olga V; Ryzhova, Oxana N

    2016-04-21

    Gas-phase O–H homolytic bond dissociation enthalpy in phenol, DH298°(C6H5O–H), is still disputed, despite a large number of experimental and computational studies. In estimating this value, the experimental enthalpy of formation of phenol, ΔfH298°(C6H5OH, g) = −96.4 ± 0.6 kJ/mol (Cox, J. D. Pure Appl. Chem. 1961, 2, 125−128), is often used assuming high accuracy of the experimental value. In the present work a substantially less negative value of ΔfH298°(C6H5OH, g) = −91.8 ± 2.5 kJ/mol was calculated combining G4 theory with an isodesmic reaction approach. A benchmark quality of this result was achieved by using a large number of reliable reference species in isodesmic reaction calculations. Among these are the most accurate ΔfH298° values currently available from the Active Thermochemical Tables (ATcT) for 36 species (neutral molecules, radicals, and ions), anisole with recently reassessed enthalpy of formation, and 13 substituted phenols. The internal consistency of the calculated ΔfH298°(C6H5OH, g) value with the experimental enthalpies of formation of more than 50 reference species suggests that the reported experimental enthalpy of formation of phenol is in error. Taking into account that the enthalpy of formation of phenol has not been investigated experimentally since 1961, the new measurements would be extremely valuable. Using the accurate enthalpies of formation of C6H5OH and C6H5O• calculated in the present work, we obtained DH298°(C6H5O–H) = 369.6 ± 4.0 kJ/mol. This value is in satisfactory agreement with that determined from the most precise experimental measurement.

  11. Methods for associating or dissociating guest materials with a metal organic framework, systems for associating or dissociating guest materials within a series of metal organic frameworks, thermal energy transfer assemblies, and methods for transferring thermal energy

    DOEpatents

    McGrail, B. Peter; Brown, Daryl R.; Thallapally, Praveen K.

    2016-08-02

    Methods for releasing associated guest materials from a metal organic framework are provided. Methods for associating guest materials with a metal organic framework are also provided. Methods are provided for selectively associating or dissociating guest materials with a metal organic framework. Systems for associating or dissociating guest materials within a series of metal organic frameworks are provided. Thermal energy transfer assemblies are provided. Methods for transferring thermal energy are also provided.

  12. Methods for associating or dissociating guest materials with a metal organic framework, systems for associating or dissociating guest materials within a series of metal organic frameworks, thermal energy transfer assemblies, and methods for transferring thermal energy

    DOEpatents

    McGrail, B. Peter; Brown, Daryl R.; Thallapally, Praveen K.

    2014-08-05

    Methods for releasing associated guest materials from a metal organic framework are provided. Methods for associating guest materials with a metal organic framework are also provided. Methods are provided for selectively associating or dissociating guest materials with a metal organic framework. Systems for associating or dissociating guest materials within a series of metal organic frameworks are provided. Thermal energy transfer assemblies are provided. Methods for transferring thermal energy are also provided.

  13. The role of proton mobility in determining the energy-resolved vibrational activation/dissociation channels of N-glycopeptide ions.

    PubMed

    Kolli, Venkata; Roth, Heidi A; De La Cruz, Gabriela; Fernando, Ganga S; Dodds, Eric D

    2015-10-08

    Site-specific glycoproteomic analysis largely hinges on the use of tandem mass spectrometry (MS/MS) to identify glycopeptides. Experiments of this type are usually aimed at drawing connections between individual oligosaccharide structures and their specific sites of attachment to the polypeptide chain. These determinations inherently require ion dissociation methods capable of interrogating both the monosaccharide and amino acid connectivity of the glycopeptide. Collision-induced dissociation (CID) shows potential to satisfy this requirement, as the vibrational activation/dissociation of protonated N-glycopeptides has been observed to access cleavage of either glycosidic bonds of the glycan or amide bonds of the peptide in an energy-resolved manner. Nevertheless, the relative energy requirement for these fragmentation pathways varies considerably among analytes. This research addresses the influence of proton mobility on the vibrational energy necessary to achieve either glycan or peptide cleavage in a collection of protonated N-glycopeptide ions. While greater proton mobility of the precursor ion was found to correlate with lower energy requirements for precursor ion depletion and appearance of glycosidic fragments, the vibrational energy deposition necessary for appearance of peptide backbone fragments showed no relation to the precursor ion proton mobility. These results are consistent with observations suggesting that peptide fragments arise from an intermediate fragment which is generally of lower proton mobility than the precursor ion. Such findings have potential to facilitate the rational selection of CID conditions which are best suited to provide either glycan or peptide cleavage products in MS/MS based N-glycoproteomic analysis.

  14. Astrophysical molecules of A1H and CaH - RKR potential and dissociation energies

    NASA Astrophysics Data System (ADS)

    Narasimhamurthy, B.; Rajamanickam, N.

    1983-03-01

    The true potential energy curves for the electronic ground states of astrophysically important AlH and CaH molecules are constructed by the Rydberg-Klein-Rees method. Empirical potential functions, of three-parameters by Lippincott, of five-parameters by Hulburt and Hirschfelder and, of electronegativity by Szöke and Baitz, are examined for the adequacy to represent the true curve. From the best-fitting function, the dissociation energies D00 of AlH and CaH molecules are estimated to be 2.99±0.08 and 2.72±0.06 eV respectively.

  15. Formation and reactivity of a porphyrin iridium hydride in water: acid dissociation constants and equilibrium thermodynamics relevant to Ir-H, Ir-OH, and Ir-CH2- bond dissociation energetics.

    PubMed

    Bhagan, Salome; Wayland, Bradford B

    2011-11-07

    Aqueous solutions of group nine metal(III) (M = Co, Rh, Ir) complexes of tetra(3,5-disulfonatomesityl)porphyrin [(TMPS)M(III)] form an equilibrium distribution of aquo and hydroxo complexes ([(TMPS)M(III)(D(2)O)(2-n)(OD)(n)]((7+n)-)). Evaluation of acid dissociation constants for coordinated water show that the extent of proton dissociation from water increases regularly on moving down the group from cobalt to iridium, which is consistent with the expected order of increasing metal-ligand bond strengths. Aqueous (D(2)O) solutions of [(TMPS)Ir(III)(D(2)O)(2)](7-) react with dihydrogen to form an iridium hydride complex ([(TMPS)Ir-D(D(2)O)](8-)) with an acid dissociation constant of 1.8(0.5) × 10(-12) (298 K), which is much smaller than the Rh-D derivative (4.3 (0.4) × 10(-8)), reflecting a stronger Ir-D bond. The iridium hydride complex adds with ethene and acetaldehyde to form organometallic derivatives [(TMPS)Ir-CH(2)CH(2)D(D(2)O)](8-) and [(TMPS)Ir-CH(OD)CH(3)(D(2)O)](8-). Only a six-coordinate carbonyl complex [(TMPS)Ir-D(CO)](8-) is observed for reaction of the Ir-D with CO (P(CO) = 0.2-2.0 atm), which contrasts with the (TMPS)Rh-D analog which reacts with CO to produce an equilibrium with a rhodium formyl complex ([(TMPS)Rh-CDO(D(2)O)](8-)). Reactivity studies and equilibrium thermodynamic measurements were used to discuss the relative M-X bond energetics (M = Rh, Ir; X = H, OH, and CH(2)-) and the thermodynamically favorable oxidative addition of water with the (TMPS)Ir(II) derivatives.

  16. Empirical equations for the bond energies and vibrational frequencies at chemisorptive bonds on surfaces

    NASA Astrophysics Data System (ADS)

    Chang, Chin-An

    1982-09-01

    Empirical equations derived for bond energies and force constants of gaseous molecules are applied to chemisorptive bonds on surfaces. For two adsorbed atoms from the same family of the periodic table, A and B, the chemisorptive bond energies, E, to the same metal, M, can be approximated by EA-M/ EB-M ≈ ( EA 2/ EB 2) 1/2, where EA 2 and EB 2 are the bonds energies of diatomic molecules A 2 and B 2, respectively The corresponding vibrational frequencies, ν, can be approximated by ν 2A-M/ν 2B-M ≈ ( mB/ mA)( FA 2/ FB 2) 1/2 · mA and mB are the masses of atoms A and B, respectively; FA 2 and FB 2 are the force constants of molecules A 2 and B 2, respectively. These relations are applied to the chemisorption of halogens on metals and showed good agreement with experiment.

  17. Improving collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD) fourier transform MS/MS degradome-peptidome identifications using high accuracy mass information.

    PubMed

    Shen, Yufeng; Tolić, Nikola; Purvine, Samuel O; Smith, Richard D

    2012-02-03

    MS dissociation methods, including collision induced dissociation (CID), high energy collision dissociation (HCD), and electron transfer dissociation (ETD), can each contribute distinct peptidome identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant informatics challenges. In this work, we explored utilization of high accuracy fragment ion mass measurements, in this case provided by Fourier transform MS/MS, to improve peptidome peptide data set size and consistency relative to conventional descriptive and probabilistic scoring methods. For example, we identified 20-40% more peptides than SEQUEST, Mascot, and MS_GF scoring methods using high accuracy fragment ion information and the same false discovery rate (FDR) from CID, HCD, and ETD spectra. Identified species covered >90% of the collective identifications obtained using various conventional peptide identification methods, which significantly addresses the common issue of different data analysis methods generating different peptide data sets. Choice of peptide dissociation and high-precision measurement-based identification methods presently available for degradomic-peptidomic analyses needs to be based on the coverage and confidence (or specificity) afforded by the method, as well as practical issues (e.g., throughput). By using accurate fragment information, >1000 peptidome components can be identified from a single human blood plasma analysis with low peptide-level FDRs (e.g., 0.6%), providing an improved basis for investigating potential disease-related peptidome components.

  18. Toward the development of the potential with angular distortion for halogen bond: a comparison of potential energy surfaces between halogen bond and hydrogen bond.

    PubMed

    Wang, Lili; Gao, Jun; Bi, Fuzhen; Song, Bo; Liu, Chengbu

    2014-10-02

    As noncovalent intermolecular interactions, hydrogen bond (HB) and halogen bond (XB) are attracting increasing attention. In this work, the potential energy surfaces (PESs) of hydrogen and halogen bonds are compared. Twelve halogen-bonded and three hydrogen-bonded models are scanned for analysis using the MP2 level of theory. This work indicates that potential energy surfaces of both HB and XB have angular distortion. The potential well of XB is narrower than that of HB. With the elongation of the bond length, the potential energy surfaces get flatter. The best fitting functions for angular distortion and the flattening character of angular terms are also combined into a modified Buckingham potential. The testing results show that the essential features of the PES, including angular distortion and flattening character, have been reproduced. These results provide a better understanding of halogen and hydrogen bonds and the optimization of halogen bond force fields.

  19. Effective coordination number: A simple indicator of activation energies for NO dissociation on Rh(100) surfaces

    SciTech Connect

    Ghosh, Prasenjit; Pushpa, Raghani; Gironcoli, Stefano de

    2009-12-15

    We have used density-functional theory to compute the activation energy for the dissociation of NO on two physical and two hypothetical systems: unstrained and strained Rh(100) surfaces and monolayers of Rh atoms on strained and unstrained MgO(100) surfaces. We find that the activation energy, relative to the gas phase, is reduced when a monolayer of Rh is placed on MgO, due both to the chemical nature of the substrate and the strain imposed by the substrate. The former effect is the dominant one, though both effects are of the same order of magnitude. We find that both effects are encapsulated in a simple quantity which we term as the 'effective coordination number'(n{sub e}); the activation energy is found to vary linearly with n{sub e}. We have compared the performance of n{sub e} as a predictor of activation energy of NO dissociation on the above-mentioned Rh surfaces with the two well-established indicators, namely, the position of the d-band center and the coadsorption energy of N and O. We find that for the present systems n{sub e} performs as well as the other two indicators.

  20. Binding Energy and Dissociation Barrier: Experimental Determination of the Key Parameters of the Potential Energy Curve of Diethyl Ether on Si(001).

    PubMed

    Reutzel, Marcel; Lipponer, Marcus; Dürr, Michael; Höfer, Ulrich

    2015-10-01

    The key parameters of the potential energy curve of organic molecules on semiconductor surfaces, binding energy of the intermediate state and dissociation barrier, were experimentally investigated for the model system of diethyl ether (Et2O) on Si(001). Et2O adsorbs via a datively bonded intermediate from which it converts via ether cleavage into a covalently attached final state. This thermally activated conversion into the final state was followed in real-time by means of optical second-harmonic generation (SHG) at different temperatures and the associated energy barrier ϵa = 0.38 ± 0.05 eV and pre-exponential factor νa = 10(4±1) s(-1) were determined. From molecular beam experiments on the initial sticking probability, the difference between the desorption energy ϵd and ϵa was extracted and thus the binding energy of the intermediate state was determined (0.62 ± 0.08 eV). The results are discussed in terms of general chemical trends as well as with respect to a wider applicability on adsorbate reactions on semiconductor surfaces.

  1. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

    NASA Astrophysics Data System (ADS)

    Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v

  2. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions.

    PubMed

    Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V

    2015-08-07

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability

  3. Breaking the carbon dimer: the challenges of multiple bond dissociation with full configuration interaction quantum Monte Carlo methods.

    PubMed

    Booth, George H; Cleland, Deidre; Thom, Alex J W; Alavi, Ali

    2011-08-28

    The full configuration interaction quantum Monte Carlo (FCIQMC) method, as well as its "initiator" extension (i-FCIQMC), is used to tackle the complex electronic structure of the carbon dimer across the entire dissociation reaction coordinate, as a prototypical example of a strongly correlated molecular system. Various basis sets of increasing size up to the large cc-pVQZ are used, spanning a fully accessible N-electron basis of over 10(12) Slater determinants, and the accuracy of the method is demonstrated in each basis set. Convergence to the FCI limit is achieved in the largest basis with only O[10(7)] walkers within random errorbars of a few tenths of a millihartree across the binding curve, and extensive comparisons to FCI, CCSD(T), MRCI, and CEEIS results are made where possible. A detailed exposition of the convergence properties of the FCIQMC methods is provided, considering convergence with elapsed imaginary time, number of walkers and size of the basis. Various symmetries which can be incorporated into the stochastic dynamic, beyond the standard abelian point group symmetry and spin polarisation are also described. These can have significant benefit to the computational effort of the calculations, as well as the ability to converge to various excited states. The results presented demonstrate a new benchmark accuracy in basis-set energies for systems of this size, significantly improving on previous state of the art estimates.

  4. Structure, energetics, and bonding of novel potential high energy density materials Rh2(N5)4: A DFT study

    NASA Astrophysics Data System (ADS)

    Tang, Lihong; Bao, Shuangyou; Peng, Jinhui; Li, Kai; Ning, Ping; Guo, Huibin; Zhu, Tingting; Gu, Junjie; Li, Qianshu

    2015-10-01

    Theoretical studies examining a series of binuclear transition metal pentazolides Rh2(N5)4 predict paddle wheel type structures with very short metal-metal distances. Natural bonding orbital analysis indicated that the bonding between the metal atom and the five-membered ring is predominantly ionic for Rh2(N5)4 species, and a high-order metal-metal multiple bonding exists between the two metal atoms. In addition, the presence of the delocalized π orbital plays an important role in the stabilization of Rh2(N5)4. Nucleus independent chemical shift values confirm that the planar N5- exhibits aromaticity. The dissociation energies into mononuclear fragments are predicted for Rh2(N5)4.

  5. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    DOE PAGES

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; ...

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of thismore » support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.« less

  6. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    SciTech Connect

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.

  7. Water binding energies of [Pb(amino acid-H)H2O]+ complexes determined by blackbody infrared radiative dissociation.

    PubMed

    Burt, Michael B; Decker, Sarah G A; Fridgen, Travis D

    2012-11-21

    The water binding energies (E(0)) of eight deprotonated Pb(2+)-amino acid (Aa) complexes of the form [Pb(Aa-H)H(2)O](+) (Aa = Gly, Ala, Val, Leu, Ile, Phe, Glu, and Lys) were determined using blackbody infrared radiative dissociation (BIRD). A Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer was used to trap ions generated by electrospray ionization (ESI) in a "zero"-pressure (~10(-10) torr) cell where dissociation can only occur by absorption of thermally generated photons. Since the [Pb(Aa-H)H(2)O](+) complexes have relatively few vibrational degrees of freedom (36-78) and are within the slow-exchange kinetic limit, the master equation was solved to extract meaningful threshold dissociation energies and thermal unimolecular dissociation rate constants (k(uni)). The master equation analysis uses variable reaction coordinate transition state theory (VRC-TST) to minimize the Rice-Ramsperger-Kassel-Marcus (RRKM) dissociation rate constants. The determined water binding energies range from 76.6 to 113.6 kJ mol(-1), and agree well with 0 K dissociation energies calculated using the B3LYP/6-31+G(d,p) and MP2(full)/6-311++G(2d,2p)//B3LYP/6-31+G(d,p) methods. The relative strengths of the binding energies reflect the known structural isomers (A-, B-, C-, and D-type) of these [Pb(Aa-H)H(2)O](+) complexes.

  8. Tantalum surface oxidation: Bond relaxation, energy entrapment, and electron polarization

    NASA Astrophysics Data System (ADS)

    Guo, Yongling; Bo, Maolin; Wang, Yan; Liu, Yonghui; Sun, Chang Q.; Huang, Yongli

    2017-02-01

    A combination of photoelectron spectrometric analysis and density functional theory calculations has enabled reconciliation of the bond-energy-electron relaxation for the Ta(100, 110, 111) surfaces chemisorbed with oxygen at different coverages. Results show that increasing oxygen coverage lowers the adsorption energy associated with lattice reconstruction. Valence electrons transfer from Ta surface atoms to oxygen to create four excessive DOS features in terms of Osbnd Ta bonding, lone pairs of oxygen, Ta+ electron holes, and polarized Ta dipoles. Oxidation proceeds in the following dynamics: oxygen gets electrons from two neighboring Ta atoms left behind Ta+; the sp3-orbital hybridization takes place with additional two electron lone pairs, the lone pairs polarize the other two Ta neighbors becoming dipoles. X-ray photoelectron spectral analysis results in the 4f binding energy of an isolated Ta atom and its shift upon bond formation and oxidation. Exercises provide not only a promising numerical approach for the quantitative information about the bond and electronic behavior but also consistent insight into the electronic dynamics of metal oxidation.

  9. Dissociative double-photoionization of butadiene in the 25-45 eV energy range using 3-D multi-coincidence ion momentum imaging spectrometry

    SciTech Connect

    Oghbaie, Shabnam; Gisselbrecht, Mathieu; Laksman, Joakim; Månsson, Erik P.; Sankari, Anna; Sorensen, Stacey L.

    2015-09-21

    Dissociative double-photoionization of butadiene in the 25-45 eV energy range has been studied with tunable synchrotron radiation using full three-dimensional ion momentum imaging. Using ab initio calculations, the electronic states of the molecular dication below 33 eV are identified. The results of the measurement and calculation show that double ionization from π orbitals selectively triggers twisting about the terminal or central C–C bonds. We show that this conformational rearrangement depends upon the dication electronic state, which effectively acts as a gateway for the dissociation reaction pathway. For photon energies above 33 eV, three-body dissociation channels where neutral H-atom evaporation precedes C–C charge-separation in the dication species appear in the correlation map. The fragment angular distributions support a model where the dication species is initially aligned with the molecular backbone parallel to the polarization vector of the light, indicating a high probability for double-ionization to the “gateway states” for molecules with this orientation.

  10. Heats of Formation and Bond Energies in Group III Compounds

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Allendorf, Mark D.; Melius, Carl F.; Arnold, James O. (Technical Monitor)

    1999-01-01

    We present heats of formation and bond energies for Group-III compounds obtained from calculations of molecular ground-state I electronic energies. Data for compounds of the form MXn are presented, where M = B, Al, Ga, and In, X = He H, Cl, and CH3, and n = 1-3. Energies for the B, Al, and Ga compounds are obtained from G2 predictions, while those for the In compounds are obtained from CCSD(T)/CBS calculations; these are the most accurate calculations for indium-containing compounds published to date. In most cases, the calculated thermochemistry is in good agreement with published values derived from experiments for those species that have well-established heats of formation. Bond energies obtained from the heats of formation follow the expected trend (Cl much greater than CH3 approx. H). However, the CH3M-(CH3)2 bond energies obtained for trimethylgallium and trimethylindium are considerably stronger (greater than 15 kcal/mol) than currently accepted values.

  11. Photodissociation of CH2. I - Potential energy surfaces of the dissociation into CH and H

    NASA Technical Reports Server (NTRS)

    Bearda, Robert A.; Van Hemert, Marc C.; Van Dishoeck, Ewine F.

    1992-01-01

    The possible photodissociation pathways of the CH2 radical are studied using ab initio multireference configuration-interaction methods, and accurate photodissociation cross sections and branching ratios for the production of CH + H and C + H2 are obtained. Potential energy surfaces were calculated using the Wuppertal-Bonn self-consistent field plus a multireference single and double-excitation configuration interaction package of programs. Two-dimensional potential energy surfaces of the ten lowest triplet states correlating with the seven lowest states of CH were calculated as functions of bond angle and one C-H bond distance, keeping the other C-H bond distance fixed at the equilibrium CH2 value.

  12. Angular and energy distributions of fragment ions in dissociative double photoionization of acetylene molecules in the 31.9-50.0 eV photon energy range

    NASA Astrophysics Data System (ADS)

    Falcinelli, Stefano; Alagia, Michele; Farrar, James M.; Kalogerakis, Konstantinos S.; Pirani, Fernando; Richter, Robert; Schio, Luca; Stranges, Stefano; Rosi, Marzio; Vecchiocattivi, Franco

    2016-09-01

    The two-body dissociation reactions of the dication C2H2+2, initiated via double ionization of acetylene molecules by photons in the energy range 31.9-50.0 eV, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The angular distributions and kinetic energy of product ions, measured in the 31.9-50.0 eV energy range, exhibit significant differences for the three leading dissociation reactions with respect to a previous investigation carried out at a fixed energy of 39.0 eV, providing thus new information on the dynamical evolution of the system. The analysis of the results indicates that such dissociation reactions occur with a different mechanism. In particular, the symmetric dissociation in two CH+ ions is characterized by different dynamics, and the anisotropy of the angular distribution of ionic products increases with photon energy in a more pronounced way than the other two reactions. Moreover, the kinetic energy distribution of the symmetric dissociation reaction exhibits several components that change with photon energy. The new experimental findings cast light on the microscopic evolution of the system and can provide a laboratory reference for new theoretical calculations on specific features of the multidimensional potential energy surface, namely, the structure, energy and symmetry of dication states, the electronic state of dissociation products, energy barriers and their dependence on the geometry of the intermediate state.

  13. Multireference coupled-cluster calculation of the dissociation energy profile of triplet ketene

    NASA Astrophysics Data System (ADS)

    Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki

    2011-07-01

    Triplet ketene exhibits a steplike structure in the experimentally observed photodissociation rates, but its mechanism is still unknown despite many theoretical efforts. Here we revisit this problem by calculating the potential energy profile of triplet ketene with the Adamowicz and Mukherjee multireference coupled-cluster (MRCC) theories. At the MRCCSD level, the imaginary frequency of the dissociation barrier is calculated to be about 300i cm-1, which is slightly smaller than the previous estimates but is still much greater than the expected maximum value for reproducing the observed steps (100i cm-1). This implies that other types of mechanisms (including nonadiabatic ones) may be more plausible for the observed steps.

  14. Electron energy loss spectroscopy of carbon in dissociated dislocations in tantalum carbide

    NASA Astrophysics Data System (ADS)

    Allison, Craig; Hoffman, Mark; Williams, Wendell S.

    1982-10-01

    The carbon concentration in individual stacking faults in dissociated dislocations in tantalum carbide (TaCx) was analyzed using electron energy loss spectroscopy. Although the faulted region is less than 10 nm wide, the small diameter electron beam (0.5 nm) of a dedicated scanning transmission electron microscope allowed the carbon K x-ray excitation edge from the faulted region to be distinguished from the corresponding signal from the unfaulted region. The 50-nm thick foil was prepared by grinding, polishing, and ion milling a specimen sawed from a single crystal of TaC0.78. The analysis showed a significantly lower value for the carbon concentration in the fault, in accordance with crystallographic and energy considerations. The stacking fault in NaCl-structure TaCx must exhibit hcp symmetry, but the appropriate hcp phase, Ta2C, contains less carbon. Hence diffusion of carbon away from the moving dislocation must accompany plastic deformation. However, in view of the high melting point and high activation energy for carbon migration, diffusion is slow below approximately 1600 °C. This temperature corresponds approximately with the brittle-ductile transition for TaC. The isomorphic compound TiC does not exhibit dissociated dislocations, and hence this form of Suzuki hardening should not occur. Indeed, gross plastic deformation in TiC can occur at temperatures as low as 800 °C.

  15. Dissociative Electron Attachment to chloroacetylene

    NASA Astrophysics Data System (ADS)

    Ngassam, V.; Orel, A. E.

    2007-06-01

    The production of two fragments with σ symmetry from electron-impact dissociation of C2H2, which has only a low lying &*circ; resonance at equilibrium geometry, has been explained by the existence of interactions with &*circ; resonances at bent geometries. We are investigating the presence of such multidimensional effects in the dissociative attachment of chloroacetylene (C2HCl). We have performed electron scattering calculations using the Complex Kohn variational method to determine the resonance energies and widths of the chloroacetylene resonances as a function of both the Cl--C2H bond distance as well as the variation with C-C stretch and bend. We will discuss our results and our prediction of the dissociation dynamics in comparison to the findings for for C2H2. This work was supported by the U.S. DOE Office of Basic Energy Sciences, Division of Chemical Sciences and the National Science Foundation, PHY-05-55401.

  16. Determination of CD- and CH-bond energies in d-chloroform and fluoroform from vibrational spectra using the Morse potential

    SciTech Connect

    Apostolova, E.S.; Tulub, A.V.

    1995-04-01

    Based on the six-parametric model energy operator containing Morse potentials, the spectrum of valence vibrations of d-chloroform and fluoroform is calculated to the vibrational quantum number v= 2 with an accuracy of 5 and 6.3 cm{sup -1}, respectively. Upon HCCl{sub 3}{r_arrow} DCC1{sub 3} isotopic substitution, the CH-bond dissociation energy increases by 25.2 kJ/mol, which agrees with experimental estimates. The CH-bond dissociation energy 444.2 kJ/mol in the HCF{sub 3} molecule is quite close to its experimental value of 446.4 {+-} 4.2 kJ/mol. The influence of the high-frequency laser field on the vibrational spectrum of HCC{sub 3} is considered using averaging over the vibration period.

  17. Energy-based analysis of biochemical cycles using bond graphs.

    PubMed

    Gawthrop, Peter J; Crampin, Edmund J

    2014-11-08

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks.

  18. Energy-based analysis of biochemical cycles using bond graphs

    PubMed Central

    Gawthrop, Peter J.; Crampin, Edmund J.

    2014-01-01

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks. PMID:25383030

  19. Argon hydrochloride, Ar.HCl, bond energy by infrared spectroscopy

    NASA Technical Reports Server (NTRS)

    Miziolek, A. W.; Pimentel, G. C.

    1976-01-01

    The infrared absorption of argon (200 to 760 torr) and hydrogen chloride (2 to 6 torr) mixtures is reexamined in the missing Q branch region (spectral region between 2860 and 3010 wavelength/cm) at temperatures ranging from 195 to 298 K. The temperature dependence of two absorption features of the argon hydrogen chloride complex, at 2887 and 2879 wavelength/cm, leads to a bond energy estimate that depends on the assumptions made about the internal degrees of freedom of the complex. It is shown that agreement with experiment can be reached for well depths near 1.2 kcal/mole. This result is relatively insensitive to the choice of the vibrational frequencies and anharmonicities, but does depend on the extent to which the energy level manifolds are truncated to avoid molecular excitation in excess of the bond energy. The bond energy is found to deviate from the commonly accepted value of 0.4 kcal/mole. Possible causes for the discrepancy are considered.

  20. Free energy barrier for dissociation of the guanosine monophosphate anion in water

    NASA Astrophysics Data System (ADS)

    Cornetta, Lucas M.; Coutinho, Kaline; Canuto, Sylvio; Varella, Márcio T. do N.

    2016-08-01

    We report free energy barriers for the ground-state dissociation of the guanosine nucleotide anion in solution, employing implicit and explicit solvation models. The latter was based on the Free Energy Perturbation technique and Monte Carlo simulations. For the lowest-energy structure, both solvation models indicate a solvent-induced transition from a dipole-bound state in the gas phase to a π∗ valence state in solution. The free barrier estimates obtained from explicit and implicit solvation are in fair agreement with each other, although significantly overestimated in comparison to a previously reported explicit solvation model based on ab initio molecular dynamics simulations. Accounting for corrections related to the different DFT functionals used in the present and previous studies significantly improves the agreement. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

  1. Effects of Exchange Energy and Spin-Orbit Coupling on Bond Energies

    ERIC Educational Resources Information Center

    Smith, Derek W.

    2004-01-01

    Since chemical reactions involve the breaking and making of bonds, understanding the relative strengths of bonds is of paramount importance in the study, teaching, and practice of chemistry. Further, it is showed that free atoms having p(super n) configuration with n = 2,3, or 4 are stabilized by exchange energy, and by spin-orbit coupling for n =…

  2. Free energy landscapes for S-H bonds in Cp*2Mo2S4 complexes.

    PubMed

    Appel, Aaron M; Lee, Suh-Jane; Franz, James A; DuBois, Daniel L; DuBois, M Rakowski

    2009-04-15

    An extensive family of thermochemical data is presented for a series of complexes derived from Cp*Mo(mu-S)(2)(mu-SMe)(mu-SH)MoCp* and Cp*Mo(mu-S)(2)(mu-SH)(2)MoCp*. These data include electrochemical potentials, pK(a) values, homolytic solution bond dissociation free energies (SBDFEs), and hydride donor abilities in acetonitrile. Thermochemical data ranged from +0.6 to -2.0 V vs FeCp(2)(+/o) for electrochemical potentials, 5 to 31 for pK(a) values, 43 to 68 kcal/mol for homolytic SBDFEs, and 44 to 84 kcal/mol for hydride donor abilities. The observed values for these thermodynamic parameters are comparable to those of many transition metal hydrides, which is consistent with the many parallels in the chemistry of these two classes of compounds. The extensive set of thermochemical data is presented in free energy landscapes as a useful approach to visualizing and understanding the relative stabilities of all of the species under varying conditions of pH and H(2) overpressure. In addition to the previously studied homogeneous reactivity and catalysis, Mo(2)S(4) complexes are also models for heterogeneous molybdenum sulfide catalysts, and therefore, the present results demonstrate the dramatic range of S-H bond strengths available in both homogeneous and heterogeneous reaction pathways.

  3. IR Spectra and Bond Energies Computed Using DFT

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles; Andrews, Lester; Arnold, James (Technical Monitor)

    2000-01-01

    The combination of density functional theory (DFT) frequencies and infrared (IR) intensities and experimental spectra is a very powerful tool in the identification of molecules and ions. The computed and measured isotopic ratios make the identification much more secure than frequencies and intensities alone. This will be illustrated using several examples, such as Mn(CO)n and Mn(CO)n-. The accuracy of DFT metal-ligand bond energies will also be discussed.

  4. Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni*

    PubMed Central

    Scott, Nichollas E.; Parker, Benjamin L.; Connolly, Angela M.; Paulech, Jana; Edwards, Alistair V. G.; Crossett, Ben; Falconer, Linda; Kolarich, Daniel; Djordjevic, Steven P.; Højrup, Peter; Packer, Nicolle H.; Larsen, Martin R.; Cordwell, Stuart J.

    2011-01-01

    Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous

  5. Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni.

    PubMed

    Scott, Nichollas E; Parker, Benjamin L; Connolly, Angela M; Paulech, Jana; Edwards, Alistair V G; Crossett, Ben; Falconer, Linda; Kolarich, Daniel; Djordjevic, Steven P; Højrup, Peter; Packer, Nicolle H; Larsen, Martin R; Cordwell, Stuart J

    2011-02-01

    Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous

  6. Guided ion beam studies of the reactions of Con+ (n=1-18) with N2: Cobalt cluster mononitride and dinitride bond energies

    NASA Astrophysics Data System (ADS)

    Liu, Fuyi; Li, Ming; Tan, Lin; Armentrout, P. B.

    2008-05-01

    The reactions of Con+ (n=1-18) with N2 are measured as a function of kinetic energy over a range of 0-15eV in a guided ion beam tandem mass spectrometer. A variety of Com+, ComN+, and ComN2+ (m⩽n) product ions are observed, all in endothermic processes, with collision-induced dissociation dominating the products for all clusters. Bond dissociation energies for both cobalt cluster nitrides and dinitrides are derived from threshold analysis of the energy dependence of the endothermic reactions using several different approaches. These values show only a mild dependence on cluster size over the range studied, although the Co13+-N bond energy is relatively weak. The bond energies of Con+-N for larger clusters suggest that a reasonable value for the desorption energy of atomic nitrogen from bulk phase cobalt is 6.3±0.2eV, which is somewhat lower than the only available value in the literature, an estimate based on the enthalpy of formation of bulk cobalt nitride. The trends in the cobalt nitride thermochemistry are also compared to previously determined metal-metal bond energies, D0(Con+-Co), and to D0(Fen+-N). Implications for catalytic ammonia production using cobalt versus iron are discussed.

  7. Tandem mass spectrometry acquisition approaches to enhance identification of protein-protein interactions using low-energy collision-induced dissociative chemical crosslinking reagents.

    PubMed

    Soderblom, Erik J; Bobay, Benjamin G; Cavanagh, John; Goshe, Michael B

    2007-01-01

    Chemical crosslinking combined with mass spectrometry is a useful tool for studying the topological organization of multiprotein interactions, but it is technically challenging to identify peptides involved in a crosslink using tandem mass spectrometry (MS/MS) due to the presence of product ions originating from both peptides within the same crosslink. We have previously developed a novel set of collision-induced dissociative chemical crosslinking reagents (CID-CXL reagents) that incorporate a labile bond within the linker which readily dissociates at a single site under low-energy collision-induced dissociation (CID) to enable independent isolation and sequencing of the crosslinked peptides by traditional MS/MS and database searching. Alternative low-energy CID events were developed within the in-source region by increasing the multipole DC offset voltage (ISCID) or within the ion trap by increasing the collisional excitation (ITCID). Both dissociation events, each having their unique advantages, occur without significant backbone fragmentation to the peptides, thus permitting subsequent CID to be applied to these distinct peptide ions for generation of suitable product ion spectra for database searching. Each approach was developed and applied to a chemical crosslinking study involving the N-terminal DNA-binding domain of AbrB (AbrBN), a transition-state regulator in Bacillus subtilis. A total of thirteen unique crosslinks were identified using the ITCID approach which represented a significant improvement over the eight unique crosslinks identified using the ISCID approach. The ability to segregate intrapeptide and interpeptide crosslinks using ITCID represents the first step towards high-throughput analysis of protein-protein crosslinks using our CID-CXL reagents.

  8. Effects of density functionals and dispersion interactions on geometries, bond energies and harmonic frequencies of Etbnd UX3 (E = N, P, CH; X = H, F, Cl)

    NASA Astrophysics Data System (ADS)

    Pandey, Krishna Kumar; Patidar, Pankaj; Patidar, Sunil Kumar; Vishwakarma, Ravi

    2014-12-01

    Quantum-chemical calculations have been performed to evaluate the geometries, bonding nature and harmonic frequencies of the compounds [Etbnd UX3] at DFT, DFT-D3, DFT-D3(BJ) and DFT-dDSc levels using different density functionals BP86, BLYP, PBE, revPBE, PW91, TPSS and M06-L. The stretching frequency of Utbnd N bond in [Ntbnd UF3] calculated with DFT/BLYP closely resembles with the experimental value. The performance of different density functionals for accurate Utbnd N vibrational frequencies follows the order BLYP > revPBE > BP86 > PW91 > TPSS > PBE > M06-L. The BLYP functional gives accurate value of the Utbnd E bond distances. The uranium atom in the studied compounds [Etbnd UX3] is positively charged. Upon going from [Etbnd UF3] to [Etbnd UCl3], the partial Hirshfeld charge on uranium atom decreases because of the lower electronegativity of chlorine compared to flourine. The Gopinathan-Jug bond order for Utbnd E bonds ranges from 2.90 to 3.29. The Utbnd E bond dissociation energies vary with different density functionals as M06-L < TPSS < BLYP < revPBE < BP86 < PBE ≈ PW91. The orbital interactions ΔEorb, in all studied compounds [Etbnd UX3] are larger than the electrostatic interaction ΔEelstat, which means the Utbnd N bonds in these compound have greater degree of covalent character (in the range 63.8-77.2%). The Usbnd E σ-bonding interaction is the dominant bonding interaction in the nitride and methylidyne complexes while it is weaker in [Ptbnd UX3]. The dispersion energy contributions to the total bond dissociation energies are rather small. Compared to the Grimme's D3(BJ) corrections, the Corminboeuf's dispersion corrections are larger with metaGGA functionals (TPSS, M06-L) while smaller with GGA functionals.

  9. Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculation.

    PubMed

    Pak, Alireza; Lesage, Denis; Gimbert, Yves; Vékey, Károly; Tabet, Jean-Claude

    2008-04-01

    The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom 'DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta-Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (V(c)) were linearly correlated with the mean internal energy values () carried by desolvated ions. These mean internal energy values seem to be slightly dependent on the size of the studied ion. ESI mass spectra and CID spectra were then simulated using the MassKinetics software to propose an empirical equation for the mean internal energy () versus cone voltage (V(c)) for different source temperatures (T): < E(int) > = [405 x 10(-6) - 480 x 10(-9) (DOF)] V(c)T + E(therm)(T). In this equation, the E(therm)(T) parameter is the mean internal energy due to the source temperature at 0 V(c).

  10. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides.

    PubMed

    Aboufazeli, Forouzan; Kolli, Venkata; Dodds, Eric D

    2015-04-01

    Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

  11. A Comparison of Energy-Resolved Vibrational Activation/Dissociation Characteristics of Protonated and Sodiated High Mannose N-Glycopeptides

    NASA Astrophysics Data System (ADS)

    Aboufazeli, Forouzan; Kolli, Venkata; Dodds, Eric D.

    2015-04-01

    Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.

  12. Improved morphed potentials for Ar-HBr including scaling to the experimentally determined dissociation energy.

    PubMed

    Wang, Z; McIntosh, A L; McElmurry, B A; Walton, J R; Lucchese, R R; Bevan, J W

    2005-09-15

    A lead salt diode infrared laser spectrometer has been employed to investigate the rotational predissociation in Ar-HBr for transitions up to J' = 79 in the v(1) HBr stretching vibration of the complex using a slit jet and static gas phase. Line-shape analysis and modeling of the predissociation lifetimes have been used to determine a ground-state dissociation energy D(0) of 130(1) cm(-1). In addition, potential energy surfaces based on ab initio calculations are scaled, shifted, and dilated to generate three-dimensional morphed potentials for Ar-HBr that reproduce the measured value of D(0) and that have predictive capabilities for spectroscopic data with nearly experimental uncertainty. Such calculations also provide a basis for making a comprehensive comparison of the different morphed potentials generated using the methodologies applied.

  13. The Trouble with Chemical Energy: Why Understanding Bond Energies Requires an Interdisciplinary Systems Approach

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Klymkowsky, Michael W.

    2013-01-01

    Helping students understand "chemical energy" is notoriously difficult. Many hold inconsistent ideas about what energy is, how and why it changes during the course of a chemical reaction, and how these changes are related to bond energies and reaction dynamics. There are (at least) three major sources for this problem: 1) the way biologists talk…

  14. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation

    PubMed Central

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A.; Koehler, Peter; Delcour, Jan A.

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  15. Measuring the energy landscape of complex bonds using AFM

    NASA Astrophysics Data System (ADS)

    Mayyas, Essa; Hoffmann, Peter; Runyan, Lindsay

    2009-03-01

    We measured rupture force of a complex bond of two interacting proteins with atomic force microscopy. Proteins of interest were active and latent Matrix metalloproteinases (MMPs), type 2 and 9, and their tissue inhibitors TIMP1 and TIMP2. Measurements show that the rupture force depends on the pulling speed; it ranges from 30 pN to 150 pN at pulling speeds 30nm/s to 48000nm/s. Analyzing data using an extended theory enabled us to understand the mechanism of MMP-TIMP interaction; we determined all physical parameters that form the landscape energy of the interaction, in addition to the life time of the bond and its length. Moreover, we used the pulling experiment to study the interaction of TIMP2 with the receptor MT1-MMP on the surface of living cells.

  16. Energy dependence of dissociative J/ψ photoproduction as a signature of gluon saturation at the LHC

    NASA Astrophysics Data System (ADS)

    Cepila, J.; Contreras, J. G.; Tapia Takaki, J. D.

    2017-03-01

    We have developed a model in which the quantum fluctuations of the proton structure are characterised by hot spots, whose number grows with decreasing Bjorken-x. Our model reproduces the F2 (x ,Q2) data from HERA at the relevant scale, as well as the exclusive and dissociative J / ψ photoproduction data from H1 and ALICE. Our model predicts that for Wγp ≈ 500 GeV, the dissociative J / ψ cross section reaches a maximum and then decreases steeply with energy, which is in qualitatively good agreement to a recent observation that the dissociative J / ψ background in the exclusive J / ψ sample measured in photoproduction by ALICE decreases as energy increases. Our prediction provides a clear signature for gluon saturation at LHC energies.

  17. Excitation energy transfer in covalently bonded porphyrin heterodimers

    NASA Astrophysics Data System (ADS)

    Paschenko, V. Z.; Konovalova, N. V.; Bagdashkin, A. L.; Gorokhov, V. V.; Tusov, V. B.; Yuzhakov, V. I.

    2012-04-01

    We describe the photophysical properties of heterodimers that are formed by the free base 2-(2-carboxyvinyl)-5,10,15,20-tetraphenylporphyrin and the zinc complex of 5-( p-aminophenyl)-10,15,20-triphenylporphyrin and that are covalently bonded by the amide link. These dimers differ in the configuration of the double bond in the spacer group. We determine fluorescence quantum yields of heterodimers and their porphyrin components. The energy transfer rate constants have been estimated from the measured fluorescence lifetimes and fluorescence excitation spectra and, also, they have been calculated from the steady-state absorption and fluorescence spectra according to the Förster theory. We have found that the efficiency of the intramolecular energy transfer in heterodimers is 0.97-0.99, and the energy migration rate constants have been found to be (1.82-4.49) × 1010 s-1. The results of our investigation show that synthesized heterodimers can be used as efficient light-harvesting elements in solar energy conversion devices.

  18. Controlling the bond scission sequence of oxygenates for energy applications

    NASA Astrophysics Data System (ADS)

    Stottlemyer, Alan L.

    The so called "Holy Grail" of heterogeneous catalysis is a fundamental understanding of catalyzed chemical transformations which span multidimensional scales of both length and time, enabling rational catalyst design. Such an undertaking is realizable only with an atomic level understanding of bond formation and destruction with respect to intrinsic properties of the metal catalyst. In this study, we investigate the bond scission sequence of small oxygenates (methanol, ethanol, ethylene glycol) on bimetallic transition metal catalysts and transition metal carbide catalysts. Oxygenates are of interest both as hydrogen carriers for reforming to H2 and CO and as fuels in direct alcohol fuel cells (DAFC). To address the so-called "materials gap" and "pressure gap" this work adopted three parallel research approaches: (1) ultra high vacuum (UHV) studies including temperature programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) on polycrystalline surfaces; (2) DFT studies including thermodynamic and kinetic calculations; (3) electrochemical studies including cyclic voltammetry (CV) and chronoamperometry (CA). Recent studies have suggested that tungsten monocarbide (WC) may behave similarly to Pt for the electrooxidation of oxygenates. TPD was used to quantify the activity and selectivity of oxygenate decomposition for WC and Pt-modifiedWC (Pt/WC) as compared to Pt. While decomposition activity was generally higher on WC than on Pt, scission of the C-O bond resulted in alkane/alkene formation on WC, an undesired product for DAFC. When Pt was added to WC by physical vapor deposition C-O bond scission was limited, suggesting that Pt synergistically modifies WC to improve the selectivity toward C-H bond scission to produce H2 and CO. Additionally, TPD confirmed WC and Pt/WC to be more CO tolerant than Pt. HREELS results verified that surface intermediates were different on Pt/WC as compared to Pt or WC and evidence of aldehyde

  19. Dissociation and multiple ionization energies for five polycyclic aromatic hydrocarbon molecules

    NASA Astrophysics Data System (ADS)

    Holm, A. I. S.; Johansson, H. A. B.; Cederquist, H.; Zettergren, H.

    2011-01-01

    We have performed density functional theory calculations for a range of neutral, singly, and multiply charged polycyclic aromatic hydrocarbons (PAHs), and their fragmentation products for H-, H^+-, C_2H_2-, and C_2H_2^+-emissions. The adiabatic and vertical ionization energies follow linear dependencies as functions of charge state for all five intact PAHs (naphthalene, biphenylene, anthracene, pyrene, and coronene). First estimates of the total ionization and fragmentation cross sections in ion-PAH collisions display markedly different size dependencies for pericondensed and catacondensed PAH species, reflecting differences in their first ionization energies. The dissociation energies show that the PAH^{q+}-molecules are thermodynamically stable for q ⩽ 2 (naphthalene, biphenylene, and anthracene), q ⩽ 3 (pyrene), and q ⩽ 4 (coronene). PAHs in charge states above these limits may also survive experimental time scales due to the presence of reaction barriers as deduced from explorations of the potential energy surface regions for H^+-emissions from all five PAHs and for C_2H_2+-emission from naphthalene - the smallest PAH.

  20. Energetics and dynamics of fragmentation of protonated leucine enkephalin from time- and energy-resolved surface-induced dissociation studies.

    PubMed

    Laskin, Julia

    2006-07-13

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM-based approach developed in our laboratory. The following threshold energies and activation entropies were determined in this study: E(0) = 1.20 eV and DeltaS++ = -20 eu(1) (MH(+)-->b(5)); E(0) = 1.14 eV and DeltaS++ = -14.7 eu (MH(+)-->b(4)); E(0) = 1.42 eV and DeltaS++ = -2.5 eu (MH(+)-->b(3)); E(0) = 1.30 eV and DeltaS++ = -4.1 eu (MH(+)-->a(4)); E(0) = 1.37 eV and DeltaS++ = -5.2 eu (MH(+)-->y ions); E(0) = 1.50 eV and DeltaS++ = 1.6 eu (MH(+)-->internal fragments); E(0) = 1.62 eV and DeltaS++ = 5.2 eu (MH(+)-->F). Comparison with Arrhenius activation energies reported in the literature demonstrated for the first time the reversal of the order of activation energies as compared to threshold energies for dissociation.

  1. The molecular dissociation of formaldehyde at medium photoexcitation energies: A quantum chemistry and direct quantum dynamics study

    SciTech Connect

    Araujo, Marta; Magalhaes, Alexandre L.; Lasorne, Benjamin; Worth, Graham A.; Bearpark, Michael J.; Robb, Michael A.

    2009-10-14

    The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into H{sub 2} and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the S{sub 1}, T{sub 1}, and S{sub 0} states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from S{sub 1} followed by dissociation of vibrationally hot H{sub 2}CO in S{sub 0}. We recently proposed a novel mechanism [M. Araujo et al., J. Phys. Chem. A 112, 7489 (2008)] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between S{sub 1} and S{sub 0} after the system has passed through an S{sub 1} transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in S{sub 1}. At lower energy, an alternative scheme to internal conversion involves intersystem crossing via T{sub 1} to regenerate the reactant before the S{sub 0} barrier to dissociation. We propose here a previously unidentified mechanism leading directly to H{sub 2} and CO products via T{sub 1}. This channel opens at medium energies, near or above the T{sub 1} barrier to dissociation and still lower than the S{sub 1} barrier, thus making T{sub 1} a possible shortcut to molecular dissociation.

  2. Higher energy collision dissociation (HCD) product ion-triggered electron transfer dissociation (ETD) mass spectrometry for the analysis of N-linked glycoproteins.

    PubMed

    Singh, Charandeep; Zampronio, Cleidiane G; Creese, Andrew J; Cooper, Helen J

    2012-09-07

    Large scale mass spectrometry analysis of N-linked glycopeptides is complicated by the inherent complexity of the glycan structures. Here, we evaluate a mass spectrometry approach for the targeted analysis of N-linked glycopeptides in complex mixtures that does not require prior knowledge of the glycan structures or pre-enrichment of the glycopeptides. Despite the complexity of N-glycans, the core of the glycan remains constant, comprising two N-acetylglucosamine and three mannose units. Collision-induced dissociation (CID) mass spectrometry of N-glycopeptides results in the formation of the N-acetylglucosamine (GlcNAc) oxonium ion and a [mannose+GlcNAc] fragment (in addition to other fragments resulting from cleavage within the glycan). In ion-trap CID, those ions are not detected due to the low m/z cutoff; however, they are detected following the beam-type CID known as higher energy collision dissociation (HCD) on the orbitrap mass spectrometer. The presence of these product ions following HCD can be used as triggers for subsequent electron transfer dissociation (ETD) mass spectrometry analysis of the precursor ion. The ETD mass spectrum provides peptide sequence information, which is unobtainable from HCD. A Lys-C digest of ribonuclease B and trypsin digest of immunoglobulin G were separated by ZIC-HILIC liquid chromatography and analyzed by HCD product ion-triggered ETD. The data were analyzed both manually and by search against protein databases by commonly used algorithms. The results show that the product ion-triggered approach shows promise for the field of glycoproteomics and highlight the requirement for more sophisticated data mining tools.

  3. Structure-Energy Relationships of Halogen Bonds in Proteins.

    PubMed

    Scholfield, Matthew R; Ford, Melissa Coates; Carlsson, Anna-Carin Cecilia; Butta, Hawera; Mehl, Ryan A; Ho, Pui Shing

    2017-03-27

    The structures and stabilities of proteins are defined by a series of weak non-covalent electrostatic, van der Waals, and hydrogen bond (HB) interactions. In this study, we have designed and engineered halogen bonds (XBs) site-specifically in order to study their structure-energy relationship in a model protein, T4 lysozyme. The evidence for XBs is the displacement of the aromatic side chain towards an oxygen acceptor, at distances that are at or less than the sums of their respective van der Waals radii, when the hydroxyl substituent of the wildtype tyrosine is replaced by an iodine. In addition, thermal melting studies show that the iodine XB rescues the stabilization energy from an otherwise destabilizing substitution (at an equivalent non-interacting site), indicating that the interaction is also present in solution. Quantum chemical calculations show that the XB complements an HB at this site and that solvent structure must also be considered in trying to design molecular interactions such as XBs into biological systems. A bromine substitution also shows displacement of the side chain, but the distances and geometries do not indicate formation of an XB. Thus, we have dissected the contributions from various non-covalent interactions of halogens introduced into proteins, to drive the application of XBs, particularly in biomolecular design.

  4. Relative Proton Affinities from Kinetic Energy Release Distributions for Dissociation of Proton-Bound Dimers

    SciTech Connect

    Hache, John J.; Laskin, Julia ); Futrell, Jean H. )

    2002-12-19

    Kinetic energy release distributions (KERDs) upon dissociation of proton-bound dimers are utilized along with Finite Heat Bath theory analysis to obtain relative proton affinities of monomeric species composing the dimer. The proposed approach allows accurate measurement of relative proton affinities based on KERD measurements for the compound with unknown thermochemical properties versus a single reference base. It also allows distinguishing the cases when dissociation of proton-bound dimers is associated with reverse activation barrier, for which both our approach and the kinetic method become inapplicable. Results are reported for the n-butanol-n-propanol dimer, for which there is no significant difference in entropy effects for two reactions and for the pyrrolidine-1,2-ethylenediamine dimer, which is characterized by a significant difference in entropy effects for the two competing reactions. Relative protonation affinities of -1.0?0.3 kcal/mol for the n-butanol-n-propanol pair and 0.27?0.10 kcal/mol for the pyrrolidine-1,2-ethylenediamine pair are in good agreement with literature values. Relative reaction entropies were extracted from the branching ratio and KERD measurements. Good correspondence was found between the relative reaction entropies for the n-butanol-n-propanol dimer (D(DS?)=-0.3?1.5 cal/mol K) and the relative protonation entropy for the two monomers (D(DSp)=0). However, the relative reaction entropy for the pyrrolidine-1,2-ethylenediamine dimer is higher than the difference in protonation entropies (D(DS?)=8.2?0.5 cal/mol K vs. D(DSp)=5 cal/mol K).

  5. Full-dimensional diabatic potential energy surfaces including dissociation: the ²E″ state of NO₃.

    PubMed

    Eisfeld, Wolfgang; Vieuxmaire, Olivier; Viel, Alexandra

    2014-06-14

    A scheme to produce accurate full-dimensional coupled diabatic potential energy surfaces including dissociative regions and suitable for dynamical calculations is proposed. The scheme is successfully applied to model the two-sheeted surface of the (2)E″ state of the NO3 radical. An accurate potential energy surface for the NO₃⁻ anion ground state is developed as well. Both surfaces are based on high-level ab initio calculations. The model consists of a diabatic potential matrix, which is expanded to higher order in terms of symmetry polynomials of symmetry coordinates. The choice of coordinates is key for the accuracy of the obtained potential energy surfaces and is discussed in detail. A second central aspect is the generation of reference data to fit the expansion coefficients of the model for which a stochastic approach is proposed. A third ingredient is a new and simple scheme to handle problematic regions of the potential energy surfaces, resulting from the massive undersampling by the reference data unavoidable for high-dimensional problems. The final analytical diabatic surfaces are used to compute the lowest vibrational levels of NO₃⁻ and the photo-electron detachment spectrum of NO₃⁻ leading to the neutral radical in the (2)E″ state by full dimensional multi-surface wave-packet propagation for NO3 performed using the Multi-Configuration Time Dependent Hartree method. The achieved agreement of the simulations with available experimental data demonstrates the power of the proposed scheme and the high quality of the obtained potential energy surfaces.

  6. Reduction in database search space by utilization of amino acid composition information from electron transfer dissociation and higher-energy collisional dissociation mass spectra.

    PubMed

    Hansen, Thomas A; Kryuchkov, Fedor; Kjeldsen, Frank

    2012-08-07

    With high-mass accuracy and consecutively obtained electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS), reliable (≥97%) and sensitive fragment ions have been extracted for identification of specific amino acid residues in peptide sequences. The analytical benefit of these specific amino acid composition (AAC) ions is to restrict the database search space and provide identification of peptides with higher confidence and reduced false negative rates. The 6706 uniquely identified peptide sequences determined with a conservative Mascot score of >30 were used to characterize the AAC ions. The loss of amino acid side chains (small neutral losses, SNLs) from the charge reduced peptide radical cations was studied using ETD. Complementary AAC information from HCD spectra was provided by immonium ions. From the ETD/HCD mass spectra, 5162 and 6720 reliable SNLs and immonium ions were successfully extracted, respectively. Automated application of the AAC information during database searching resulted in an average 3.5-fold higher confidence level of peptide identification. In addition, 4% and 28% more peptides were identified above the significance level in a standard and extended search space, respectively.

  7. Statistical Characterization of the Charge State and Residue Dependence of Low Energy CID Peptide Dissociation Patterns

    PubMed Central

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2013-01-01

    Data mining was performed on 28,330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pair-wise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly-charged Arg- and Lys- ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially-mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton(s) and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton(s). When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions and/or y ions depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially-mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  8. Near-threshold continuum structure and the dissociation energies of H[sub 2], HD, and D[sub 2

    SciTech Connect

    Eyler, E.E.; Melikechi, N. )

    1993-07-01

    Using laser double-resonance spectroscopy, we have studied the second dissociation limit of all three stable isotopic variants of molecular hydrogen. Just above threshold, the vibrational continuum exhibits considerable fine-grained structure, differing greatly between isotopes because of varying nonadiabatic couplings between the [ital B], [ital B][prime], and [ital C] states. Significantly improved values of the dissociation energies are obtained from the continuum onsets. We also report preliminary investigations of atomic 2[ital S]:2[ital P] branching ratios very near threshold.

  9. Identification of lanthionine and lysinoalanine in heat-treated wheat gliadin and bovine serum albumin using tandem mass spectrometry with higher-energy collisional dissociation.

    PubMed

    Rombouts, Ine; Lambrecht, Marlies A; Carpentier, Sebastien C; Delcour, Jan A

    2016-04-01

    The present manuscript reports on the identification of various dehydroamino acid-derived bonds and cross-links resulting from thermal treatment (excess water, 240 min, 130 °C) of two model food proteins, bovine serum albumin, and wheat gliadin. S-Carbamidomethylated tryptic and chymotryptic digests of unheated (control) and heated serum albumin and gliadin, respectively, were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-ESI-MS/MS) with higher-energy collisional dissociation (HCD). Heat-induced β-elimination of cystine, serine and threonine, and subsequent Michael addition of cysteine and lysine to dehydroalanine and 3-methyl-dehydroalanine were demonstrated. Lanthionine, lysinoalanine, 3-methyl-lanthionine, and 3-methyl-lysinoalanine were identified. The detection of inter-chain lanthionine in both bovine serum albumin and wheat gliadin suggests the significance of these cross-links for food texture.

  10. Dissociation of multiple hydrogen molecules on the non-planar aluminium cluster: stationary points on the Al6 + nH2 potential energy surface

    NASA Astrophysics Data System (ADS)

    Moc, Jerzy

    2013-02-01

    Compared to clusters of transition metal atoms, H-H bond activation by main Group metal clusters is much less known. Here, we have examined a potential new way of obtaining a novel alane Al6H8 through addition of multiple H2 molecules to the aluminium hexamer, i.e., Al6 + nH2 (n=1-4) reactions. To this end, systematic high level quantum chemical modeling calculations using density functional theory (DFT) and coupled-cluster singles-doubles-perturbative triples (CCSD(T)) method in conjunction with the aug-cc-pVTZ basis set were performed to identify the lowest energy barrier paths for the consecutive dissociation of several hydrogen molecules on Al6, the smallest aluminium cluster with a three-dimensional ground-state structure. These computational results are relevant to the issues of hydrogen storage and novel stable alanes.

  11. Energy-resolved collision-induced dissociation studies of 1,10-phenanthroline complexes of the late first-row divalent transition metal cations: determination of the third sequential binding energies.

    PubMed

    Nose, Holliness; Chen, Yu; Rodgers, M T

    2013-05-23

    The third sequential binding energies of the late first-row divalent transition metal cations to 1,10-phenanthroline (Phen) are determined by energy-resolved collision-induced dissociation (CID) techniques using a guided ion beam tandem mass spectrometer. Five late first-row transition metal cations in their +2 oxidation states are examined including: Fe(2+), Co(2+), Ni(2+), Cu(2+), and Zn(2+). The kinetic energy dependent CID cross sections for loss of an intact Phen ligand from the M(2+)(Phen)3 complexes are modeled to obtain 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of the internal energy of the complexes, multiple ion-neutral collisions, and unimolecular decay rates. Electronic structure theory calculations at the B3LYP, BHandHLYP, and M06 levels of theory are employed to determine the structures and theoretical estimates for the first, second, and third sequential BDEs of the M(2+)(Phen)x complexes. B3LYP was found to deliver results that are most consistent with the measured values. Periodic trends in the binding of these complexes are examined and compared to the analogous complexes to the late first-row monovalent transition metal cations, Co(+), Ni(+), Cu(+), and Zn(+), previously investigated.

  12. On the Dissociation of Methyl Orange: Spectrophotometric Investigation in Aqueous Solutions from 10 to 90ºC and Theoretical Evidence for Intramolecular Dihydrogen Bonding

    SciTech Connect

    Boily, Jean F.; Seward, Terry M.

    2005-12-01

    The dissociation of methyl orange was investigated by spectrophotometry in aqueous solutions from 10 to 90°C and by quantum chemical calculations. Combined chemometric and thermodynamic analyses of the spectrophotometric data were used to simultaneously extract the thermodynamic stabilities and the spectrophotometric attributes of the dominant methyl orange species in solutions containing less than 20.00 mmol kg-1 perchloric acid and submicromolal concentrations of methyl orange. The analyses revealed the presence of only one monomeric deprotonated and one monomeric protonated species. The spectra did not reveal any evidence for the presence of tautomeric equilibria between the protonated azo and ammonium species in the experimental range studied. Thermodynamic analyses of the temperature dependent dissociation constants showed the reactions to be endothermic and enthalpy driven reaction with increasing acidity and increasing temperature. All molar absorption coefficients in the 275-375 nm range can be adequately reproduced in the 10-90°C range with a set of Gauss-Lorentz parameters and used to predict the absorption spectra for any desired condition. The dominant features of the spectrophotometric attributes of the methyl orange species could also be retrieved in Time Dependent-Density Functional Theory (TD-DFT) calculations. Topological analyses of the electron density also revealed the formation of a dihydrogen bond between the azo proton and an adjacent phenyl ring hydridic hydrogen which increases the stability of the azo molecules relative to the ammonium molecule.

  13. N-H Bond Dissociation Enthalpies and Facile H Atom Transfers for Early Intermediates of Fe-N2 and Fe-CN Reductions.

    PubMed

    Rittle, Jonathan; Peters, Jonas C

    2017-03-01

    Fe-mediated biological nitrogen fixation is thought to proceed via either a sequence of proton and electron transfer steps, concerted H atom transfer steps, or some combination thereof. Regardless of the specifics and whether the intimate mechanism for N2-to-NH3 conversion involves a distal pathway, an alternating pathway, or some hybrid of these limiting scenarios, Fe-NxHy intermediates are implicated that feature reactive N-H bonds. Thermodynamic knowledge of the N-H bond strengths of such species is scant, and is especially difficult to obtain for the most reactive early stage candidate intermediates (e.g., Fe-N═NH, Fe═N-NH2, Fe-NH═NH). Such knowledge is essential to considering various mechanistic hypotheses for biological (and synthetic) nitrogen fixation and to the rational design of improved synthetic N2 fixation catalysts. We recently reported several reactive complexes derived from the direct protonation of Fe-N2 and Fe-CN species at the terminal N atom (e.g., Fe═N-NH2, Fe-C≡NH, Fe≡C-NH2). These same Fe-N2 and Fe-CN systems are functionally active for N2-to-NH3 and CN-to-CH4/NH3 conversion, respectively, when subjected to protons and electrons, and hence provide an excellent opportunity for obtaining meaningful N-H bond strength data. We report here a combined synthetic, structural, and spectroscopic/analytic study to estimate the N-H bond strengths of several species of interest. We assess the reactivity profiles of species featuring reactive N-H bonds and estimate their homolytic N-H bond enthalpies (BDEN-H) via redox and acidity titrations. Very low N-H bond dissociation enthalpies, ranging from 65 (Fe-C≡NH) to ≤37 kcal/mol (Fe-N═NH), are determined. The collective data presented herein provide insight into the facile reactivity profiles of early stage protonated Fe-N2 and Fe-CN species.

  14. Evaluation of one-dimensional potential energy surfaces for prediction of spectroscopic properties of hydrogen bonds in linear bonded complexes.

    PubMed

    Jouypazadeh, Hamidreza; Farrokhpour, Hossein; Solimannejad, Mohammad

    2017-05-01

    This work evaluated the reliability of the one-dimensional potential energy surface for calculating the spectroscopic properties (rovibrational constants and rotational line energies) of hydrogen bonds in linear bonded complexes by comparing theoretical results with the corresponding experimental results. For this purpose, two hydrogen bonded complexes were selected: the HCN···HCN homodimer and the HCN···HF heterodimer. The one-dimensional potential energy surfaces related to the hydrogen bonds in these complexes were calculated using different computational methods and basis sets. The calculated potential curve of each complex was fitted to an analytical one-dimensional potential function to obtain the potential parameters. The obtained analytical potential function of each complex was used in a two-particle Schrödinger equation to obtain the rovibrational energy levels of the hydrogen bond. Using the calculated rovibrational levels, the rovibrational spectra and constants of each complex were calculated and compared with experimental data available from the literature. Compared with experimental data, the calculated one-dimensional potential energy surface at the QCISD/aug-cc-pVDZ level of theory was found to predict the spectroscopic properties of hydrogen bonds better than the potential curves obtained using other computational methods, especially for the HCN···HCN homodimer complex. Generally, the results obtained for the HCN···HCN homodimer complex were closer to experimental data than those obtained for the HCN···HF heterodimer complex. The investigation performed in this work showed that the one-dimensional potential curve related to the hydrogen bond between two linear molecules can be used to predict the spectroscopic constants of hydrogen bonds. Graphical abstract Potential energy curves of HCN···HCN and HCN···HF complexes calculated at the different computational levels.

  15. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111)

    NASA Astrophysics Data System (ADS)

    Geweke, Jan; Shirhatti, Pranav R.; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M.

    2016-08-01

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed—presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]—50 times smaller than those reported here—were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  16. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111).

    PubMed

    Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M

    2016-08-07

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  17. The kinetic energy spectrum of protons produced by the dissociative ionization of H2 by electron impact

    NASA Technical Reports Server (NTRS)

    Khakoo, M. A.; Srivastava, S. K.

    1985-01-01

    The kinetic energy spectra of protons resulting from the dissociative ionization of H2 by electron impact have been measured for electron impact energies from threshold (approximately 17 eV) to 160 eV at 90 deg and 30 deg detection angles, using a crossed-beam experimental arrangement. To check reliability, two separate proton energy analysis methods have been employed, i.e., a time-of-flight proton energy analysis and an electrostatic hemispherical energy analyzer. The present results are compared with previous measurements.

  18. Presolvated Low Energy Electron Attachment to Peptide Methyl esters in Aqueous Solution: C-O Bond Cleavage at 77K

    PubMed Central

    Kheir, Jeanette; Chomicz, Lidia; Engle, Alyson; Rak, Janusz; Sevilla, Michael D.

    2013-01-01

    In this study, the reactions of presolvated electrons with glycine methyl ester and N-acetylalanylalanine methyl ester (N-aAAMe) are investigated by electron spin resonance (ESR) spectroscopy and DFT calculations. Electrons were produced by gamma irradiation in neutral 7.5 M LiCl-D2O aqueous glasses at low temperatures. For glycine methyl ester electron addition at 77K results in both N-terminal deamination to form a glycyl radical and C-O ester bond cleavage to form methyl radicals. For samples of N-acetylalanylalanine methyl ester electrons are found to add to the peptide bonds at 77K and cleave the carboxyl ester groups to produce methyl radicals. On annealing to 160K electron adducts at the peptide links undergo chain scission to produce alanyl radicals and further annealing to 170K α-carbon peptide backbone radicals are produced by hydrogen abstraction. DFT calculations for electron addition to the methyl ester portion of N-aAAMe show the cleavage reaction is highly favorable (free energy equals to −30.7 kcal/mol) with the kinetic barrier of only 9.9 kcal/mol. A substantial electron affinity of the ester link (38.0 kcal/mol) provides more than sufficient energy to overcome this small barrier. Protonated peptide bond electron adducts, also show favorable N-C chain cleavage reactions of −12.7 to −15.5 kcal/mol with a barrier from 7.4 to 10.0 kcal/mol. The substantial adiabatic electron affinity (AEA) of the peptide bond and ester groups provides sufficient energy for the bond dissociation. PMID:23406302

  19. Presolvated low energy electron attachment to peptide methyl esters in aqueous solution: C-O bond cleavage at 77 K.

    PubMed

    Kheir, Jeanette; Chomicz, Lidia; Engle, Alyson; Rak, Janusz; Sevilla, Michael D

    2013-03-14

    In this study, the reactions of presolvated electrons with glycine methyl ester and N-acetylalanylalanine methyl ester (N-aAAMe) are investigated by electron spin resonance (ESR) spectroscopy and DFT calculations. Electrons were produced by γ-irradiation in neutral 7.5 M LiCl-D2O aqueous glasses at low temperatures. For glycine methyl ester, electron addition at 77 K results in both N-terminal deamination to form a glycyl radical and C-O ester bond cleavage to form methyl radicals. For samples of N-acetylalanylalanine methyl ester, electrons are found to add to the peptide bonds at 77 K and cleave the carboxyl ester groups to produce methyl radicals. On annealing to 160 K, electron adducts at the peptide links undergo chain scission to produce alanyl radicals and on further annealing to 170 K α-carbon peptide backbone radicals are produced by hydrogen abstraction. DFT calculations for electron addition to the methyl ester portion of N-aAAMe show the cleavage reaction is highly favorable (free energy equals to -30.7 kcal/mol) with the kinetic barrier of only 9.9 kcal/mol. A substantial electron affinity of the ester link (38.0 kcal/mol) provides more than sufficient energy to overcome this small barrier. Protonated peptide bond electron adducts also show favorable N-C chain cleavage reactions of -12.7 to -15.5 kcal/mol with a barrier from 7.4 to 10.0 kcal/mol. The substantial adiabatic electron affinity (AEA) of the peptide bond and ester groups provides sufficient energy for the bond dissociation.

  20. Metallic bond effects on mean excitation energies for stopping powers

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Xu, Y. J.

    1982-01-01

    Mean excitation energies for first row metals are evaluated by means of the local plasma approximation. Particle corrections based on Pines' (1953) procedure and the Wigner Seitz (1934) model of the metallic state are included. The agreement with experimental values is remarkably good. In contrast to previous work, the calculations given here estimate shifts in the plasma frequency according to the theory for plane wave states in an extended plasma as calculated by Pines. It is demonstrated that the effects of the metallic bond in lithium and beryllium are quite large and that they appear mainly as a result of collective oscillations in the 'free' electron gas formed from the valence electrons. The usefulness of the plasma frequency shift derived for a degenerate electron gas in predicting the plasma frequency shift within the ion core is considered surprising.

  1. Resonant structure of low-energy H{sub 3}{sup +} dissociative recombination

    SciTech Connect

    Petrignani, Annemieke; Altevogt, Simon; Berg, Max H.; Bing, Dennis; Grieser, Manfred; Hoffmann, Jens; Jordon-Thaden, Brandon; Krantz, Claude; Mendes, Mario B.; Novotny, Oldrich; Novotny, Steffen; Buhr, Henrik; Kreckel, Holger; Kokoouline, Viatcheslav; Greene, Chris H.; Orlov, Dmitry A.; Repnow, Roland; Sorg, Tobias; Stuetzel, Julia; Wolf, Andreas

    2011-03-15

    High-resolution dissociative recombination rate coefficients of rotationally cool and hot H{sub 3}{sup +} in the vibrational ground state have been measured with a 22-pole trap setup and a Penning ion source, respectively, at the ion storage-ring TSR. The experimental results are compared with theoretical calculations to explore the dependence of the rate coefficient on ion temperature and to study the contributions of different symmetries to probe the rich predicted resonance spectrum. The kinetic energy release was investigated by fragment imaging to derive internal temperatures of the stored parent ions under differing experimental conditions. A systematic experimental assessment of heating effects is performed which, together with a survey of other recent storage-ring data, suggests that the present rotationally cool rate-coefficient measurement was performed at 380{sub -130}{sup +50} K and that this is the lowest rotational temperature so far realized in storage-ring rate-coefficient measurements on H{sub 3}{sup +}. This partially supports the theoretical suggestion that temperatures higher than assumed in earlier experiments are the main cause for the large gap between the experimental and the theoretical rate coefficients. For the rotationally hot rate-coefficient measurement a temperature of below 3250 K is derived. From these higher-temperature results it is found that increasing the rotational ion temperature in the calculations cannot fully close the gap between the theoretical and the experimental rate coefficients.

  2. Intrinsic errors in several ab initio methods. The dissociation energy of N{sub 2}

    SciTech Connect

    Peterson, K.A. |; Dunning, T.H. Jr.

    1995-03-23

    Using sequences of correlation consistent basis sets, complete basis set (CBS) limits for the dissociation energy D{sub c} of N{sub 2} have been estimated for a variety of commonly used electron correlation methods. After extrapolation to the CBS limit, the difference between theory and experiment corresponds to the error intrinsic to the chosen theoretical method. Correlated wave functions (valence electrons correlated only) for which intrinsic errors have been estimated include internally contracted multireference configuration interaction (CMRCI), singles and doubles coupled cluster theory with and without perturbative triple excitations [CCSD, CCSD(T)], and second-, third-, and fourth-order Moller-Plesset perturbation theory (MP2, MP3, MP4). For CMRCI and CCSD(T), D{sub c} converges smoothly from below the experimental value and yields the smallest intrinsic errors, -0.8 and -1.6 kcal/mol, respectively. In contrast, for MP2 and MP4, D{sub c} exhibits fortuitously good agreement with experiment for small basis sets but leads to CBS limits that are 11.6 and 3.4 kcal/mol larger than experiment, respectively. Correlation of the 1s core electrons is predicted to yield intrinsic errors of less than 1 kcal/mol for CMRCI and CCSD(T), while those for MP2 and MP4 increase still further. 38 refs., 1 fig., 1 tab.

  3. Low-energy collisionally activated dissociation of pentose-borate complexes

    NASA Astrophysics Data System (ADS)

    Pepi, Federico; Garzoli, Stefania; Tata, Alessandra; Giacomello, Pierluigi

    2010-01-01

    Pentose-borate 1:1 complexes were generated in the ESI source of a triple quadrupole and ion trap mass spectrometer by electrospray ionization of Na2B4O7 and pentose (arabinose, lyxose, ribose, xylose) 2:1 solution in CH3CN/H2O. The study of their low-energy collisionally activated dissociation (CAD) demonstrated that ribose and lyxose are preferentially complexed at the C2-C3 cis-diol function whereas arabinose and xylose are esterified at the C1-C2 hydroxyl groups. No evidence was found of the stronger affinity for ribose to borate. The ribose probiotic rule can be explained by considering its peculiar capability, among the investigated pentoses, to almost totally complex the borate anion at the C2-C3 hydroxyl group, thus enabling the subsequent stages of nucleotide assembly, such as phosphorylation and linkage to the nucleobases. Finally, the differences observed in the pentose-borate complex CAD spectra can be used for the mass spectrometric discrimination of isomeric pentoses in complex mixtures.

  4. Theoretical study of the dissociation energy and the red and violet band systems of CN

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1987-01-01

    The dissociation energy (D sub O) of CN is determined to be 7.65 + or - 0.06 eV. This corresponds to delta H sub f (CN) = 105.3 + or - 1.5 kcal/mole, in excellent agreement with Engleman and Rouse (1975), but considerably larger than the recent value deduced from shock-tube studies by Colket (1984). The result is obtained not only from extensive ab initio MRCI calculations using a very large Gaussian basis set, but also from extrapolation of the directly computed value by comparison of computed and experimental results fo NO, C2, and N2. As an additional calibration of the methods, the D sub O value for CN was computed from the corresponding value for CN(-) using the experimental electron affinity data. The lifetime of the nu prime = 0 level of the violet (B 2 sigma + yields X 2 sigma +) system was computed to be 62.4 ns, in good agreement with both experiment and previous calculations. Lifetimes for the red (A 2 pi yields X 2 sigma +) system decrease with increasing nu prime, which is consistent both with the recent experiment and calculations. While the computed lifetimes are significantly longer that those obtained from the experiment, they are shorter than those deduced from an analysis of the solar spectrum. However the D sub O and f (sub OO) are consistent with Lambert's model for the solar spectrum.

  5. Recoil energy distributions for dissociation of the van der Waals molecule p-difluorobenzene-Ar with 450-3000 cm(-1) excess energy.

    PubMed

    Bellm, Susan M; Lawrance, Warren D

    2005-03-08

    Velocity map imaging has been used to measure the distributions of translational energy released in the dissociation of p-difluorobenzene-Ar van der Waals complexes from the 5(1), 3(1), 5(2), 3(1)5(1), 5(3), 3(2), and 3(2)5(1) states. These states span 818-3317 cm(-1) of vibrational energy and correspond to a range of energies above dissociation of 451-2950 cm(-1). The translational energy release (recoil energy) distributions are remarkably similar, peaking at very low energy (10-20 cm(-1)) and decaying in an exponential fashion to approach zero near 300 cm(-1). The average translational energy released is small, shows no dependence on the initial vibrational energy, and spans the range 58-72 cm(-1) for the vibrational levels probed. The average value for the seven levels studied is 63 cm(-1). The low fraction of transfer to translation is qualitatively in accord with Ewing's momentum gap model [G. E. Ewing, Faraday Discuss. 73, 325 (1982)]. No evidence is found in the distributions for a high energy tail, although it is likely that the experiment is not sufficiently sensitive to detect a low fraction of transfer at high translational energies. The average translational energy released is lower than has been seen in comparable systems dissociating from triplet and cation states.

  6. Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation

    SciTech Connect

    Cao, Li; Tolic, Nikola; Qu, Yi; Meng, Da; Zhao, Rui; Zhang, Qibin; Moore, Ronald J.; Zink, Erika M.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Wu, Si

    2014-01-15

    Simultaneous elucidation of the glycan structure and the glycosylation site are needed to reveal the biological function of protein glycosylation. In this study, we employed a recent type of fragmentation termed higher energy collisional dissociation (HCD) to examine fragmentation patterns of intact glycopeptides generated from a mixture of standard glycosylated proteins. The normalized collisional energy (NCE) value for HCD was varied from 30% to 60% to evaluate the optimal conditions for the fragmentation of peptide backbones and glycoconjugates. Our results indicated that HCD with lower NCE valuespreferentially fragmented the sugar chains attached to the peptides to generate a ladder of neutral loss of monosaccharides, thus enabling the putative glycan structure characterization. Also, detection of the oxonium ions enabled unambiguous differentiation of glycopeptides from non-glycopeptides. On the contrary, HCD with higher NCE values preferentially fragmented the peptide backbone and thus provided information needed for confident peptide identification. We evaluated the HCD approach with alternating NCE parameters for confident characterization of intact N-linked and O-linked glycopeptides in a single liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. In addition, we applied a novel data analysis pipeline, so-called GlycoFinder, to form a basis for automated data analysis. Overall, 38 unique intact glycopeptides corresponding to eight glycosylation sites (including six N-linked and two O-linked sites) were confidently identified from a standard protein mixture. This approach provided concurrent characterization of both, the peptide and the glycan, thus enabling comprehensive structural characterization of glycoproteins in a single LC-MS/MS analysis.

  7. The trouble with chemical energy: why understanding bond energies requires an interdisciplinary systems approach.

    PubMed

    Cooper, Melanie M; Klymkowsky, Michael W

    2013-06-01

    Helping students understand "chemical energy" is notoriously difficult. Many hold inconsistent ideas about what energy is, how and why it changes during the course of a chemical reaction, and how these changes are related to bond energies and reaction dynamics. There are (at least) three major sources for this problem: 1) the way biologists talk about chemical energy (which is also the way we talk about energy in everyday life); 2) the macroscopic approach to energy concepts that is common in physics and physical sciences; and 3) the failure of chemistry courses to explicitly link molecular with macroscopic energy ideas. From a constructivist perspective, it is unlikely that students can, without a coherent understanding of such a central concept, attain a robust and accurate understanding of new concepts. However, changes are on the horizon, guided by the increasing understanding that difficult concepts require coherent, well-designed learning progressions and the new National Research Council Framework for K-12 Science Education. We provide supporting evidence for our assertions and suggestions for an interdisciplinary learning progression designed to better approach the concept of bond energies, a first step in an understanding chemical energy and behavior of reaction systems that is central to biological systems.

  8. Collision-induced dissociation of fatty acid [M - 2H + Na]- ions: charge-directed fragmentation and assignment of double bond position.

    PubMed

    Thomas, Michael C; Altvater, Jens; Gallagher, Thomas J; Nette, Geoffrey W

    2014-11-01

    The collision-induced dissociation (CID) of cationic fatty acid-metal ion complexes has been extensively studied and, in general, provides rich structural information. In particular, charge-remote fragmentation processes are commonly observed allowing the assignment of double bond position. In a previous manuscript, we presented two methods to doubly deprotonate polyunsaturated fatty acids to form anionic fatty acid-sodium ion complexes, referred to as [M - 2H + Na] (-) ions. In the current manuscript, the CID behavior of these [M - 2H + Na] (-) ions is investigated for the first time. Significantly, we also present a deuterium-labeling experiment, which excludes the possibility that deprotonation occurs predominately at the α-carbon in the formation of fatty acid [M - H + NaF](-) ions. This supports our original proposal where deprotonation occurs at the bis-allylic positions of polyunsaturated fatty acids. CID spectra of polyunsaturated fatty acid [M - 2H + Na](-) ions display abundant product ions arising from acyl chain cleavages. Through the examination of fatty acid isomers, it is demonstrated that double bond position may be unequivocally determined for methylene-interrupted polyunsaturated fatty acids with three or more carbon-carbon double bonds. In addition, CID of [M - 2H + Na](-) ions was applied to 18:3 isomers of Nannochloropsis oculata and three isomers were tentatively identified: ∆(9,12,15)18:3, ∆(6,9,12)18:3, and ∆(5,8,11)18:3. We propose that structurally-informative product ions are formed via charge-driven fragmentation processes at the site of the resonance-stabilized carbanion as opposed to charge-remote fragmentation processes, which could be inferred if deprotonation occurred predominately at the α-carbon.

  9. Calculation of activation energies for hydrogen-atom abstractions by radicals containing carbon triple bonds

    NASA Technical Reports Server (NTRS)

    Brown, R. L.; Laufer, A. H.

    1981-01-01

    Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.

  10. Dissociation energies of Ag–RG (RG = Ar, Kr, Xe) and AgO molecules from velocity map imaging studies

    SciTech Connect

    Cooper, Graham A.; Gentleman, Alexander S.; Iskra, Andreas; Wijk, Robert van; Mackenzie, Stuart R.; Kartouzian, Aras

    2015-09-28

    The near ultraviolet photodissociation dynamics of silver atom—rare gas dimers have been studied by velocity map imaging. Ag–RG (RG = Ar, Kr, Xe) species generated by laser ablation are excited in the region of the C ({sup 2}Σ{sup +})←X ({sup 2}Σ{sup +}) continuum leading to direct, near-threshold dissociation generating Ag* ({sup 2}P{sub 3/2}) + RG ({sup 1}S{sub 0}) products. Images recorded at excitation wavelengths throughout the C ({sup 2}Σ{sup +})←X ({sup 2}Σ{sup +}) continuum, coupled with known atomic energy levels, permit determination of the ground X ({sup 2}Σ{sup +}) state dissociation energies of 85.9 ± 23.4 cm{sup −1} (Ag–Ar), 149.3 ± 22.4 cm{sup −1} (Ag–Kr), and 256.3 ± 16.0 cm{sup −1} (Ag–Xe). Three additional photolysis processes, each yielding Ag atom photoproducts, are observed in the same spectral region. Two of these are markedly enhanced in intensity upon seeding the molecular beam with nitrous oxide, and are assigned to photodissociation of AgO at the two-photon level. These features yield an improved ground state dissociation energy for AgO of 15 965 ± 81 cm{sup −1}, which is in good agreement with high level calculations. The third process results in Ag atom fragments whose kinetic energy shows anomalously weak photon energy dependence and is assigned tentatively to dissociative ionization of the silver dimer Ag{sub 2}.

  11. Energy and temperature dependent dissociation of the Na(+)(benzene)1,2 clusters: importance of anharmonicity.

    PubMed

    Kolakkandy, Sujitha; Paul, Amit K; Pratihar, Subha; Kohale, Swapnil C; Barnes, George L; Wang, Hai; Hase, William L

    2015-01-28

    Chemical dynamics simulations were performed to study the unimolecular dissociation of randomly excited Na(+)(Bz) and Na(+)(Bz)2 clusters; Bz = benzene. The simulations were performed at constant energy, and temperatures in the range of 1200-2200 K relevant to combustion, using an analytic potential energy surface (PES) derived in part from MP2/6-311+G* calculations. The clusters decompose with exponential probabilities, consistent with RRKM unimolecular rate theory. Analyses show that intramolecular vibrational energy redistribution is sufficiently rapid within the clusters that their unimolecular dynamics is intrinsically RRKM. Arrhenius parameters, determined from the simulations of the clusters, are unusual in that Ea is ∼10 kcal/mol lower the Na(+)(Bz) → Na(+) + Bz dissociation energy and the A-factor is approximately two orders-of-magnitude too small. Analyses indicate that temperature dependent anharmonicity is important for the Na(+)(Bz) cluster's unimolecular rate constants k(T). This is consistent with the temperature dependent anharmonicity found for the Na(+)(Bz) cluster from a Monte Carlo calculation based on the analytic PES used for the simulations. Apparently temperature dependent anharmonicity is quite important for unimolecular dissociation of the Na(+)(Bz)1,2 clusters.

  12. Theoretical Electron Density Distributions for Fe- and Cu-Sulfide Earth Materials: A Connection between Bond Length, Bond Critical Point Properties, Local Energy Densities, and Bonded Interactions

    SciTech Connect

    Gibbs, Gerald V.; Cox, David F.; Rosso, Kevin M.; Ross, Nancy L.; Downs, R. T.; Spackman, M. A.

    2007-03-01

    Bond critical point and local energy density properties together with net atomic charges were calculated for theoretical electron density distributions, F(r), generated for a variety of Fe and Cu metal-sulfide materials with high- and low-spin Fe atoms in octahedral coordination and high-spin Fe atoms in tetrahedral coordination. The electron density, F(rc), the Laplacian, 32F(rc), the local kinetic energy, G(rc), and the oxidation state of Fe increase as the local potential energy density, V(rc), the Fe-S bond lengths, and the coordination numbers of the Fe atoms decrease. The properties of the bonded interactions for the octahedrally coordinated low-spin Fe atoms for pyrite and marcasite are distinct from those for high-spin Fe atoms for troilite, smythite, and greigite. The Fe-S bond lengths are shorter and the values of F(rc) and 32F(rc) are larger for pyrite and marcasite, indicating that the accumulation and local concentration of F(r) in the internuclear region are greater than those involving the longer, high-spin Fe-S bonded interactions. The net atomic charges and the bonded radii calculated for the Fe and S atoms in pyrite and marcasite are also smaller than those for sulfides with high-spin octahedrally coordinated Fe atoms. Collectively, the Fe-S interactions are indicated to be intermediate in character with the low-spin Fe-S interactions having greater shared character than the highspin interactions. The bond lengths observed for chalcopyrite together with the calculated bond critical point properties are consistent with the formula Cu+Fe3+S2. The bond length is shorter and the F(rc) value is larger for the FeS4 tetrahedron displayed by metastable greigite than those displayed by chalcopyrite and cubanite, consistent with a proposal that the Fe atom in greigite is tetravalent. S-S bond paths exist between each of the surface S atoms of adjacent slabs of FeS6 octahedra comprising the layer sulfide smythite, suggesting that the neutral Fe3S4 slabs are

  13. Theoretical electron density distributions for Fe- and Cu-sulfide earth materials: a connection between bond length, bond critical point properties, local energy densities, and bonded interactions.

    PubMed

    Gibbs, G V; Cox, D F; Rosso, K M; Ross, N L; Downs, R T; Spackman, M A

    2007-03-01

    Bond critical point and local energy density properties together with net atomic charges were calculated for theoretical electron density distributions, rho(r), generated for a variety of Fe and Cu metal-sulfide materials with high- and low-spin Fe atoms in octahedral coordination and high-spin Fe atoms in tetrahedral coordination. The electron density, rho(rc), the Laplacian, triangle down2rho(rc), the local kinetic energy, G(rc), and the oxidation state of Fe increase as the local potential energy density, V(rc), the Fe-S bond lengths, and the coordination numbers of the Fe atoms decrease. The properties of the bonded interactions for the octahedrally coordinated low-spin Fe atoms for pyrite and marcasite are distinct from those for high-spin Fe atoms for troilite, smythite, and greigite. The Fe-S bond lengths are shorter and the values of rho(rc) and triangle down2rho(rc) are larger for pyrite and marcasite, indicating that the accumulation and local concentration of rho(r) in the internuclear region are greater than those involving the longer, high-spin Fe-S bonded interactions. The net atomic charges and the bonded radii calculated for the Fe and S atoms in pyrite and marcasite are also smaller than those for sulfides with high-spin octahedrally coordinated Fe atoms. Collectively, the Fe-S interactions are indicated to be intermediate in character with the low-spin Fe-S interactions having greater shared character than the high-spin interactions. The bond lengths observed for chalcopyrite together with the calculated bond critical point properties are consistent with the formula Cu+Fe3+S2. The bond length is shorter and the rho(rc) value is larger for the FeS4 tetrahedron displayed by metastable greigite than those displayed by chalcopyrite and cubanite, consistent with a proposal that the Fe atom in greigite is tetravalent. S-S bond paths exist between each of the surface S atoms of adjacent slabs of FeS6 octahedra comprising the layer sulfide smythite

  14. The Trouble with Chemical Energy: Why Understanding Bond Energies Requires an Interdisciplinary Systems Approach

    PubMed Central

    Cooper, Melanie M.; Klymkowsky, Michael W.

    2013-01-01

    Helping students understand “chemical energy” is notoriously difficult. Many hold inconsistent ideas about what energy is, how and why it changes during the course of a chemical reaction, and how these changes are related to bond energies and reaction dynamics. There are (at least) three major sources for this problem: 1) the way biologists talk about chemical energy (which is also the way we talk about energy in everyday life); 2) the macroscopic approach to energy concepts that is common in physics and physical sciences; and 3) the failure of chemistry courses to explicitly link molecular with macroscopic energy ideas. From a constructivist perspective, it is unlikely that students can, without a coherent understanding of such a central concept, attain a robust and accurate understanding of new concepts. However, changes are on the horizon, guided by the increasing understanding that difficult concepts require coherent, well-designed learning progressions and the new National Research Council Framework for K–12 Science Education. We provide supporting evidence for our assertions and suggestions for an interdisciplinary learning progression designed to better approach the concept of bond energies, a first step in an understanding chemical energy and behavior of reaction systems that is central to biological systems. PMID:23737636

  15. Interstellar Isomers: The Importance of Bonding Energy Differences

    NASA Technical Reports Server (NTRS)

    Remijan, Anthony J.; Hollis, J. M.; Lovas, F. J.; Plusquellic, D. F.; Jewell, P. R.

    2005-01-01

    We present strong detections of methyl cyanide (CH3CN), vinyl cyanide (CH2CHCN), ethyl cyanide (CH3CH2CN) and cyanodiacetylene (HC4CN) molecules with the Green Bank Telescope (GBT) toward the Sgr B2(N) molecular cloud. Attempts to detect the corresponding isocyanide isomers were only successful in the case of methyl isocyanide (CH3NC) for its J(sub K) = 1(sub 0) - 0(sub 0) transition, which is the first interstellar report of this line. To determine the spatial distribution of CH3NC, we used archival Berkeley-Illinois-Maryland Association (BIMA) array data for the J(sub K) = 1(sub 0) - 0(sub 0) transitions but no emission was detected. From ab initio calculations, the bonding energy difference between the cyanide and isocyanide molecules is greater than 8500 per centimeter (greater than 12,000 K). Thus, cyanides are the more stable isomers and would likely be formed more preferentially over their isocyanide counterparts. That we detect CH3NC emission with a single antenna (Gaussian beamsize(omega(sub B))=1723 arcsec(sup 2)) but not with an interferometer (omega(sub b)=192 arcsec(sup 2)), strongly suggests that CH3NC has a widespread spatial distribution toward the Sgr B2(N) region. Other investigators have shown that CH3CN is present both in the LMH hot core of Sgr B2(N) and in the surrounding medium, while we have shown that CH3NC appears to be deficient in the LMH hot core. Thus, largescale, non-thermal processes in the surrounding medium may account for the conversion of CH3CN to CH3NC while the LMH hot core, which is dominated by thermal processes, does not produce a significant amount of CH3NC. Ice analog experiments by other investigators have shown that radiation bombardment of CH3CN can produce CH3NC, thus supporting our observations. We conclude that isomers separated by such large bonding energy differences are distributed in different interstellar environments, making the evaluation of column density ratios between such isomers irrelevant unless it can

  16. An isomer-specific high-energy collision-induced dissociation MS/MS database for forensic applications: a proof-of-concept on chemical warfare agent markers.

    PubMed

    Subramaniam, Raja; Östin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; Åstot, Crister

    2011-09-01

    Spectra database search has become the most popular technique for the identification of unknown chemicals, minimizing the need for authentic reference chemicals. In the present study, an isomer-specific high-energy collision-induced dissociation (CID) MS/MS spectra database of 12 isomeric O-hexyl methylphosphonic acids (degradation markers of nerve agents) was created. Phosphonate anions were produced by the electrospray ionization of phosphonic acids or negative-ion chemical ionization of their fluorinated derivatives and were analysed in a hybrid magnetic-sector-time-of-flight tandem mass spectrometer. A centre-of-mass energy (E(com)) of 65 eV led to an optimal sequential carbon-carbon bond breakage, which was interpreted in terms of charge remote fragmentation. The proposed mechanism is discussed in comparison with the routinely used low-energy CID MS/MS. Even-mass (odd-electron) charge remote fragmentation ion series were diagnostic of the O-alkyl chain structure and can be used to interpret unknown spectra. Together with the odd-mass ion series, they formed highly reproducible, isomer-specific spectra that gave significantly higher database matches and probability factors (by 1.5 times) than did the EI MS spectra of the trimethylsilyl derivatives of the same isomers. In addition, ionization by negative-ion chemical ionization and electrospray ionization resulted in similar spectra, which further highlights the general potential of the high-energy CID MS/MS technique.

  17. Performance of an integrated approach for prediction of bond dissociation enthalpies of phenols extracted from ginger and tea

    NASA Astrophysics Data System (ADS)

    Nam, Pham Cam; Chandra, Asit K.; Nguyen, Minh Tho

    2013-01-01

    Integration of the (RO)B3LYP/6-311++G(2df,2p) with the PM6 method into a two-layer ONIOM is found to produce reasonably accurate BDE(O-H)s of phenolic compounds. The chosen ONIOM model contains only two atoms of the breaking bond as the core zone and is able to provide reliable evaluation for BDE(O-H) for phenols and tocopherol. Deviation of calculated values from experiment is ±(1-2) kcal/mol. BDE(O-H) of several curcuminoids and flavanoids extracted from ginger and tea are computed using the proposed model. The BDE(O-H) values of enol curcumin and epigallocatechin gallate are predicted to be 83.3 ± 2.0 and 76.0 ± 2.0 kcal/mol, respectively.

  18. Compact two-electron wave function for bond dissociation and Van der Waals interactions: A natural amplitude assessment

    SciTech Connect

    Giesbertz, Klaas J. H.; Leeuwen, Robert van

    2014-05-14

    Electron correlations in molecules can be divided in short range dynamical correlations, long range Van der Waals type interactions, and near degeneracy static correlations. In this work, we analyze for a one-dimensional model of a two-electron system how these three types of correlations can be incorporated in a simple wave function of restricted functional form consisting of an orbital product multiplied by a single correlation function f (r{sub 12}) depending on the interelectronic distance r{sub 12}. Since the three types of correlations mentioned lead to different signatures in terms of the natural orbital (NO) amplitudes in two-electron systems, we make an analysis of the wave function in terms of the NO amplitudes for a model system of a diatomic molecule. In our numerical implementation, we fully optimize the orbitals and the correlation function on a spatial grid without restrictions on their functional form. Due to this particular form of the wave function, we can prove that none of the amplitudes vanishes and moreover that it displays a distinct sign pattern and a series of avoided crossings as a function of the bond distance in agreement with the exact solution. This shows that the wave function ansatz correctly incorporates the long range Van der Waals interactions. We further show that the approximate wave function gives an excellent binding curve and is able to describe static correlations. We show that in order to do this the correlation function f (r{sub 12}) needs to diverge for large r{sub 12} at large internuclear distances while for shorter bond distances it increases as a function of r{sub 12} to a maximum value after which it decays exponentially. We further give a physical interpretation of this behavior.

  19. Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system.

    PubMed

    Liu, Cui; Zhao, Dong-Xia; Yang, Zhong-Zhi

    2012-02-05

    The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.

  20. On the activation of σ-bonds by electric fields: A Valence Bond perspective

    NASA Astrophysics Data System (ADS)

    Rincón, Luis; Mora, Jose R.; Torres, F. Javier; Almeida, Rafael

    2016-09-01

    The activation of non-polar σ -bonds induced by an electric field is studied from the perspective of the Valence Bond theory. As representative examples we study the dissociation of the H-H and C-H bonds of molecular hydrogen and methane, respectively, under the experience of an homogeneous as well as an heterogeneous field oriented along the bond axis. For all cases, the increase in the electric field have similar effects: (i) the stabilization of the potential energy, (ii) an increment of the equilibrium bond length and (iii) the transition from an homolytic dissociation mechanism to an heterolytic one when the bond is subjected under a strong enough field. These general observations are thoroughly explained using a simple Valence Bond model that involve the increment of the resonance energy between the covalent and the ionic structures, and the curve crossing between the two structures after some field strength.

  1. Evaluation of the Rh(II)-Rh(II) bond dissociation enthalpy for [(TMTAA)Rh]2 by 1H NMR T2 measurements: application in determining the Rh-C(O)- BDE in [(TMTAA)Rh]2C═O.

    PubMed

    Imler, Gregory H; Zdilla, Michael J; Wayland, Bradford B

    2013-10-07

    Toluene solutions of the rhodium(II) dimer of dibenzotetramethylaza[14]annulene ([(TMTAA)Rh]2; (1)) manifest an increase in the line widths for the singlet methine and methyl (1)H NMR resonances with increasing temperature that result from the rate of dissociation of the diamagnetic Rh(II)-Rh(II) bonded dimer (1) dissociating into paramagnetic Rh(II) monomers (TMTAA) Rh (2). Temperature dependence of the rates of Rh(II)-Rh(II) dissociation give the activation parameters for bond homolysis ΔH(‡)(app) = 24(1) kcal mol(-1) and ΔS(‡)(app) = 10 (1) cal K(-1) mol(-1) and an estimate for the Rh(II)-Rh(II) bond dissociation enthalpy (BDE) of 22 kcal mol(-1). Thermodynamic values for reaction of 1 with CO to form (TMTAA)Rh-C(O)-Rh(TMTAA) (3) ΔH1° = -14 (1) kcal mol(-1), ΔS1°= -30(3) cal K(-1) mol(-1)) were used in deriving a (TMTAA)Rh-C(O)- BDE of 53 kcal mol(-1).

  2. Structures, energies and bonding in neutral and charged Li microclusters.

    PubMed

    Yepes, Diana; Kirk, Steven Robert; Jenkins, Samantha; Restrepo, Albeiro

    2012-09-01

    Structural and chemical properties of charged and neutral Lithium microclusters are investigated for [Formula: see text]. A total of 18 quantum conformational spaces are randomly walked to produce candidate structures for local minima. Very rich potential energy surfaces are produced, with the largest structural complexity predicted for anionic clusters. Analysis of the electron charge distributions using the quantum theory of atoms in molecules (QTAIM) predicts major stabilizing roles of Non-nuclear attractors (NNAs) via NNA···Li interactions with virtually no direct Li···Li interactions, except in the least stable configurations. A transition in behavior for clusters containing more than seven nuclei is observed by using the recently introduced quantum topology to determine in a quantum mechanically consistent fashion the number of spatial dimensions each cluster has. We experiment with a novel scheme for extracting persistent structural motifs with increase in cluster size. The new structural motifs correlate well with the energetic stability, particularly in highlighting the least stable structures. Quantifying the degree of covalent character in Lithium bonding independently agrees with the observation in the transition in cluster behavior for lithium clusters containing more than seven nuclei. Good correlation with available experimental data is obtained for all properties reported in this work.

  3. Classification of metal-oxide bonded interactions based on local potential- and kinetic-energy densities

    SciTech Connect

    Gibbs, Gerald V.; Cox, David; Crawford, T Daniel; Rosso, Kevin M.; Ross, Nancy; Downs, R. T.

    2006-02-28

    A classification of the HF bonded interactions comprising a large number of molecules has been proposed by Espinosa et al. [J. Chem. Phys. 117, 5529 (2002)] based on the ratio |V(rc)|/G(rc) where |V(rc)| is the magnitude of the local potential energy density and G(rc) is the local kinetic density evaluated at the bond critical points, rc. A calculation of the ratio for the MO bonded interactions comprising a relatively large number of molecules and earth materials, together with the constraints imposed by the values of Ñ2ρ(rc) and the local electronic energy density H(rc) = G(rc) + V(rc) in the HF study, yielded the same classification for the oxides as found for the fluorides. This is true despite the different trends of the bond critical point and local energy properties with the bond length displayed by the HF and MO bonded interactions. LiO, NaO and MgO bonded interactions classify as closed shell ionic bonds, BeO, AlO, SiO, BO and PO bonded interactions classify as bonds of intermediate character and NO bonded interactions classify as shared covalent bonds. CO and SO bonded interactions classify as both intermediate and covalent bonded interactions. The CO triple bonded interaction classifies as a bond of intermediate character and the CO single bonded interaction classifies as a covalent bond whereas their H(rc) value indicates that they are both covalent bonds. The |V(rc)|/G(rc) ratios for the BeO, AlO and SiO bonded interactions indicate that they have a substantial component of ionic character despite their classification as bonds of intermediate character. The trend between |V(rc)|/G(rc) and the character of the bonded interaction is consistent with trends expected from electronegativity considerations. The connection between the net charges and the experimental SiO bond length evaluated for the Si and O atoms comprising two orthosilicates are examined in terms of the |V(rc)|/G(rc) values.

  4. The role of cold carriers and the multiple-carrier process of Si-H bond dissociation for hot-carrier degradation in n- and p-channel LDMOS devices

    NASA Astrophysics Data System (ADS)

    Sharma, Prateek; Tyaginov, Stanislav; Jech, Markus; Wimmer, Yannick; Rudolf, Florian; Enichlmair, Hubert; Park, Jong-Mun; Ceric, Hajdin; Grasser, Tibor

    2016-01-01

    We apply our hot-carrier degradation (HCD) model, which uses the information about the carrier energy distribution, to represent HCD data measured in n- and p-channel LDMOS transistors. In the first version of our model we use the spherical harmonics expansion approach to solve the Boltzmann transport equation (BTE), while in the second version we employ the drift-diffusion scheme. In the latter case the carrier energy distribution function is approximated by an analytic expression with parameters found using the drift-diffusion scheme. The model, which has already been verified with nLDMOS transistors, is used to represent the carrier distribution functions, interface state density profiles, and changes of the drain currents vs. stress time in pLDMOS transistor. Particular attention is paid to study the role of the cold fraction of the carrier ensemble. We check the validity of the model by neglecting the effect of cold carriers in HCD modeling in the case of nLDMOS devices stressed at high voltages. In our model, cold carriers are represented by the corresponding term in the analytic formula for the carrier distribution function as well as by the multiple-carrier process of the Si-H bond dissociation. We show that even in high-voltage devices stressed at high drain voltages the thermalized carriers still have a substantial contribution to HCD.

  5. Vibrational and Electronic Energy Transfer and Dissociation of Diatomic Molecules by Electron Collisions

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    At high altitudes and velocities equal to or greater than the geosynchronous return velocity (10 kilometers per second), the shock layer of a hypersonic flight will be in thermochemical nonequilibrium and partially ionized. The amount of ionization is determined by the velocity. For a trans atmospheric flight of 10 kilometers per second and at an altitude of 80 kilometers, a maximum of 1% ionization is expected. At a velocity of 12 - 17 kilometer per second, such as a Mars return mission, up to 30% of the atoms and molecules in the flow field will be ionized. Under those circumstances, electrons play an important role in determining the internal states of atoms and molecules in the flow field and hence the amount of radiative heat load and the distance it takes for the flow field to re-establish equilibrium. Electron collisions provide an effective means of transferring energy even when the electron number density is as low as 1%. Because the mass of an electron is 12,760 times smaller than the reduced mass of N2, its average speed, and hence its average collision frequency, is more than 100 times larger. Even in the slightly ionized regime with only 1% electrons, the frequency of electron-molecule collisions is equal to or larger than that of molecule-molecule collisions, an important consideration in the low density part of the atmosphere. Three electron-molecule collision processes relevant to hypersonic flows will be considered: (1) vibrational excitation/de-excitation of a diatomic molecule by electron impact, (2) electronic excitation/de-excitation, and (3) dissociative recombination in electron-diatomic ion collisions. A review of available data, both theory and experiment, will be given. Particular attention will be paid to tailoring the molecular physics to the condition of hypersonic flows. For example, the high rotational temperatures in a hypersonic flow field means that most experimental data carried out under room temperatures are not applicable. Also

  6. Collision-induced dissociation products of the protonated dipeptide carnosine: structural elucidation, fragmentation pathways and potential energy surface analysis.

    PubMed

    Moustafa, Eslam M; Ritacco, Ida; Sicilia, Emilia; Russo, Nino; Shoeib, Tamer

    2015-05-21

    Collision-induced dissociation (CID) experiments on protonated carnosine, [carnosine + H](+), with several collision energies were shown to yield eleven different fragment ions with the generation of product ions [carnosine-H2O + H](+) and [carnosine-NH3 + H](+) being the lowest energy processes. Energy-resolved CID showed that at slightly higher collision energies the ions [histidine + H](+) and [histidine-H2O-CO + H](+) are formed. At even higher energies four other product ions were observed, however, attained relatively lower abundances. Quantum chemistry calculations, carried out at different levels of theory, were employed to probe fragmentation mechanisms that account for all the experimental data. All the adopted computational protocols give similar energetic trends, and the range of the calculated free energy barrier values for the generation of all the observed product ions is in agreement with the fragmentation mechanisms offered here.

  7. Strength of Chemical Bonds

    NASA Technical Reports Server (NTRS)

    Christian, Jerry D.

    1973-01-01

    Students are not generally made aware of the extraordinary magnitude of the strengths of chemical bonds in terms of the forces required to pull them apart. Molecular bonds are usually considered in terms of the energies required to break them, and we are not astonished at the values encountered. For example, the Cl2 bond energy, 57.00 kcal/mole, amounts to only 9.46 x 10(sup -20) cal/molecule, a very small amount of energy, indeed, and impossible to measure directly. However, the forces involved in realizing the energy when breaking the bond operate over a very small distance, only 2.94 A, and, thus, f(sub ave) approx. equals De/(r - r(sub e)) must be very large. The forces involved in dissociating the molecule are discussed in the following. In consideration of average forces, the molecule shall be assumed arbitrarily to be dissociated when the atoms are far enough separated so that the potential, relative to that of the infinitely separated atoms, is reduced by 99.5% from the potential of the molecule at the equilibrium bond length (r(sub e)) for Cl2 of 1.988 A this occurs at 4.928 A.

  8. Dissociative photoionization of 1,2-dichloroethane in intense near-infrared femtosecond laser field

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Yang, Yan; Li, Zhipeng; Zhang, Shian; Sun, Zhenrong

    2017-01-01

    We experimentally demonstrate the dissociative photoionization of 1,2-C2H4Cl2 molecules in femtosecond laser field by time-of-flight mass spectrum and dc-slice imaging technology. Our results show the low kinetic energy components are from the dissociative ionization process of singly charged molecular ions, and the positive charge assignment are greatly influenced by the appearance energy of the fragment ions. The high kinetic energy components result from Coulomb explosion of multi-charged molecular ions, and the different angular distribution of these fragments along Csbnd C and Csbnd Cl bond dissociation can be explained by the potential energy surfaces of the molecular ions.

  9. The effects of collision energy, vibrational mode, and vibrational angular momentum on energy transfer and dissociation in NO2+-rare gas collisions: an experimental and trajectory study.

    PubMed

    Liu, Jianbo; Uselman, Brady W; Boyle, Jason M; Anderson, Scott L

    2006-10-07

    A combined experimental and trajectory study of vibrationally state-selected NO2+ collisions with Ne, Ar, Kr, and Xe is presented. Ne, Ar, and Kr are similar in that only dissociation to the excited singlet oxygen channel is observed; however, the appearance energies vary by approximately 4 eV between the three rare gases, and the variation is nonmonotonic in rare gas mass. Xe behaves quite differently, allowing efficient access to the ground triplet state dissociation channel. For all four rare gases there are strong effects of NO2+ vibrational excitation that extend over the entire collision energy range, implying that vibration influences the efficiency of collision to internal energy conversion. Bending excitation is more efficient than stretching; however, bending angular momentum partially counters the enhancement. Direct dynamics trajectories for NO2+ + Kr reproduce both the collision energy and vibrational state effects observed experimentally and reveal that intracomplex charge transfer is critical for the efficient energy transfer needed to drive dissociation. The strong vibrational effects can be rationalized in terms of bending, and to a lesser extent, stretching distortion enhancing transition to the Kr+ -NO2 charge state.

  10. Reactions in 1,1,1-trifluoroacetone triggered by low energy electrons (0-10 eV): from simple bond cleavages to complex unimolecular reactions.

    PubMed

    Illenberger, Eugen; Meinke, Martina C

    2014-08-21

    The impact of low energy electrons (0-10 eV) to 1,1,1-trifluoroacetone yields a variety of fragment anions which are formed via dissociative electron attachment (DEA) through three pronounced resonances located at 0.8 eV, near 4 eV, and in the energy range 8-9 eV. The fragment ions arise from different reactions ranging from the direct cleavage of one single or double bond (formation of F(-), CF3(-), O(-), (M-H)(-), and M-F)(-)) to remarkably complex unimolecular reactions associated with substantial geometric and electronic rearrangement in the transitory intermediate (formation of OH(-), FHF(-), (M-HF)(-), CCH(-), and HCCO(-). The ion CCH(-), for example, is formed by an excision of unit from the target molecule through the concerted cleavage of four bonds and recombination to H2O within the neutral component of the reaction.

  11. Thermochemical properties of methyl-substituted cyclic alkyl ethers and radicals for oxiranes, oxetanes, and oxolanes: C-H bond dissociation enthalpy trends with ring size and ether site.

    PubMed

    Auzmendi-Murua, Itsaso; Charaya, Sumit; Bozzelli, Joseph W

    2013-01-17

    Cyclic ethers are an important product from the gas-phase reactions of hydrocarbon radicals with molecular oxygen in the atmospheric chemistry of diolefins and in low to moderate temperature combustion and oxidation reaction systems. They are also important in organic synthesis. Structures, and fundamental thermochemical parameters-enthalpy (ΔH°(f,298)), entropy (S°(298)), and heat capacity (C(p)(T))-have been calculated for a series of cyclic alkyl ethers and their carbon centered radicals. Enthalpies of formation (ΔH°(f,298)) are determined at the B3LYP/6-31G(d,p), B3LYP/6-31G(2d,2p), and CBS-QB3 levels using several work reactions for each species. Entropy (S) and heat capacity (C(p)(T)) values from vibration, translational, and external rotational contributions are calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional studies. Contributions from the internal methyl rotors are substituted for torsion frequencies. Calculated enthalpies of formation for a series of 12 cyclic ethers and methyl substituted cyclic ethers are in good agreement with available literature values. C-H bond dissociation enthalpies are reported for 28 carbon sites of 3 to 5 member ring cyclic ethers for use in understanding effects of the ring and the ether oxygen on kinetics and stability. Trends in carbon-hydrogen bond energies for the ring and methyl substituents relative to ring size and to distance from the ether group are described.

  12. A variational algebraic method used to study the full vibrational spectra and dissociation energies of some specific diatomic systems.

    PubMed

    Zhang, Yi; Sun, Weiguo; Fu, Jia; Fan, Qunchao; Ma, Jie; Xiao, Liantuan; Jia, Suotang; Feng, Hao; Li, Huidong

    2014-01-03

    The algebraic method (AM) proposed by Sun et al. is improved to be a variational AM (VAM) to offset the possible experimental errors and to adapt to the individual energy expansion nature of different molecular systems. The VAM is used to study the full vibrational spectra {Eυ} and the dissociation energies De of (4)HeH(+)-X(1)Σ(+), (7)Li2-1(3)Δg,Na2-C(1)Πu,NaK-7(1)Π, Cs2-B(1)Πu and (79)Br2-β1g((3)P2) diatomic electronic states. The results not only precisely reproduce all known experimental vibrational energies, but also predict correct dissociation energies and all unknown high-lying levels that may not be given by the original AM or other numerical methods or experimental methods. The analyses and the skill suggested here might be useful for other numerical simulations and theoretical fittings using known data that may carry inevitable errors.

  13. Energy-sensitive imaging detector applied to the dissociative recombination of D{sub 2}H{sup +}

    SciTech Connect

    Buhr, H.; Schwalm, D.; Mendes, M. B.; Novotny, O.; Berg, M. H.; Bing, D.; Krantz, C.; Orlov, D. A.; Sorg, T.; Stuetzel, J.; Varju, J.; Wolf, A.; Heber, O.; Rappaport, M. L.; Zajfman, D.

    2010-06-15

    We report on an energy-sensitive imaging detector for studying the fragmentation of polyatomic molecules in the dissociative recombination of fast molecular ions with electrons. The system is based on a large area (10x10 cm{sup 2}) position-sensitive, double-sided Si-strip detector with 128 horizontal and 128 vertical strips, whose pulse height information is read out individually. The setup allows us to uniquely identify fragment masses and is thus capable of measuring branching ratios between different fragmentation channels, kinetic energy releases, and breakup geometries as a function of the relative ion-electron energy. The properties of the detection system, which has been installed at the Test Storage Ring (TSR) facility of the Max-Planck Institute for Nuclear Physics in Heidelberg, is illustrated by an investigation of the dissociative recombination of the deuterated triatomic hydrogen cation D{sub 2}H{sup +}. A huge isotope effect is observed when comparing the relative branching ratio between the D{sub 2} + H and the HD + D channel; the ratio 2B(D{sub 2} + H)/B(HD + D), which is measured to be 1.27{+-}0.05 at relative electron-ion energies around 0 eV, is found to increase to 3.7{+-}0.5 at {approx}5 eV.

  14. Blackbody Infrared Radiative Dissociation of Protonated Oligosaccharides

    NASA Astrophysics Data System (ADS)

    Fentabil, Messele A.; Daneshfar, Rambod; Kitova, Elena N.; Klassen, John S.

    2011-12-01

    The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions of cellohexaose (Cel6), which is composed of β-(1 → 4)-linked glucopyranose rings, and five malto-oligosaccharides (Malx, where x = 4-8), which are composed of α-(1 → 4)-linked glucopyranose units. At the temperatures investigated (85-160 °C), the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions. The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water molecules from the smallest B ions (B1 and B2) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation parameters (Ea and A) were determined. The Ea and A-factors measured for protonated Malx (x > 4) are indistinguishable within error (~19 kcal mol-1, 1010 s-1), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated Cel6 (24 kcal mol-1, 1012 s-1) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or Y ion is formed upon glycosidic bond cleavage.

  15. Theoretical Electric Dipole Moments and Dissociation Energies for the Ground States of GaH-BrH

    NASA Technical Reports Server (NTRS)

    Pettersson, Lars G. M.; Langhoff, Stephen R.

    1986-01-01

    Reliable experimental diople moments are available for the ground states of SeH and BrH whereas no values have been reported for GaH and AsH a recently reported experimental dipole moment for GeH of 1.24 + or -0.01 D has been seriously questioned, and a much lower value of, 0.1 + or - 0.05 D, suggested. In this work, we report accurate theoretical dipole moments, dipole derivatives, dissociation energies, and spectroscopic constants (tau(sub e), omega(sub e)) for the ground states of GaH through BrH.

  16. A revised set of values of single-bond radii derived from the observed interatomic distances in metals by correction for bond number and resonance energy

    PubMed Central

    Pauling, Linus; Kamb, Barclay

    1986-01-01

    An earlier discussion [Pauling, L. (1947) J. Am. Chem. Soc. 69, 542] of observed bond lengths in elemental metals with correction for bond number and resonance energy led to a set of single-bond metallic radii with values usually somewhat less than the corresponding values obtained from molecules and complex ions. A theory of resonating covalent bonds has now been developed that permits calculation of the number of resonance structures per atom and of the effective resonance energy per bond. With this refined method of correcting the observed bond lengths for the effect of resonance energy, a new set of single-bond covalent radii, in better agreement with values from molecules and complex ions, has been constructed. PMID:16593698

  17. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    SciTech Connect

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  18. Dissociative Disorders

    MedlinePlus

    ... of continuity between thoughts, memories, surroundings, actions and identity. People with dissociative disorders escape reality in ways ... at bay. Symptoms — ranging from amnesia to alternate identities — depend in part on the type of dissociative ...

  19. Threshold collision-induced dissociation of Sr2+(H2O)x complexes (x=1-6): An experimental and theoretical investigation of the complete inner shell hydration energies of Sr2+

    NASA Astrophysics Data System (ADS)

    Carl, D. R.; Chatterjee, B. K.; Armentrout, P. B.

    2010-01-01

    The sequential bond energies of Sr2+(H2O)x complexes, where x =1-6, are determined by threshold collision-induced dissociation using a guided ion beam tandem mass spectrometer equipped with an electrospray ionization source. The electrospray source produces an initial distribution of Sr2+(H2O)x complexes, where x =6-9. Smaller Sr2+(H2O)x complexes, where x =1-5, are accessed using a recently developed in-source fragmentation technique that takes place in the high pressure region of a rf-only hexapole ion guide. This work constitutes the first experimental study for the complete inner shell of any multiply charged ion. The kinetic energy dependent cross sections are determined over a wide energy range to monitor all possible dissociation products and are modeled to obtain 0 and 298 K binding energies for loss of a single water molecule. These binding energies decrease monotonically for the Sr2+(H2O) complex to Sr2+(H2O)6. Our experimental results agree well with previous literature results obtained by equilibrium and kinetic studies for x =5 and 6. Because there has been limited theory for the hydration of Sr2+, we also present an in-depth theoretical study on the energetics of the Sr2+(H2O)x systems by employing several levels of theory with multiple effective core potentials for Sr and different basis sets for the water molecules.

  20. Energy level of the nitrogen dangling bond in amorphous silicon nitride

    SciTech Connect

    Warren, W.L. ); Kanicki, J. ); Robertson, J. ); Lenahan, P.M. )

    1991-09-30

    The composition dependence and room-temperature metastability of the paramagnetic nitrogen dangling-bond center is amorphous silicon nitride suggest that its energy level lies close to the N {ital p}{pi} states, in agreement with theoretical calculations.

  1. Dissociative Ionization Mechanism and Appearance Energies in Adipic Acid Revealed by Imaging Photoelectron Photoion Coincidence, Selective Deuteration, and Calculations.

    PubMed

    Heringa, Maarten F; Slowik, Jay G; Prévôt, André S H; Baltensperger, Urs; Hemberger, Patrick; Bodi, Andras

    2016-05-26

    Adipic acid, a model compound for oxygenated organic aerosol, has been studied at the VUV beamline of the Swiss Light Source. Internal energy selected cations were prepared by threshold photoionization using vacuum ultraviolet synchrotron radiation and imaging photoelectron photoion coincidence spectroscopy (iPEPICO). The threshold photoelectron spectrum yields a vertical ionization energy (IE) of 10.5 eV, significantly above the calculated adiabatic IE of 8.6 eV. The cationic minimum is accessible after vertical ionization by H-transfer from one of the γ-carbons to a carbonyl oxygen and is sufficiently energetic to decay by water loss at the ionization onset. The slope of the breakdown curves, quantum chemical calculations, and selective deuteration of the carboxylic hydrogens establish the dissociative photoionization mechanism. After ionization, one γ-methylene hydrogen and the two carboxylic hydrogens are randomized prior to H2O loss. On the basis of the deuteration degree in the H2O + CO-loss product at higher energies, a direct water-loss channel without complete randomization also exists. The breakdown diagram and center of gravity of the H2O + CO-loss peak were modeled to obtain 0 K appearance energies of 10.77, 10.32, and 11.53 eV for H2O + CO loss, CH2COOH loss, and H2O + CH2COOH loss from adipic acid. These agree well with the CBS-QB3 calculated values of 10.68, 10.45, and 11.57 eV, respectively, which shows that threshold photoionization can yield energetics data as long as the dissociation is statistical, even when the parent ion cannot be observed. The results can be used as a starting point for a deeper understanding of the ionization and low-energy fragmentation of organic aerosol components.

  2. Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose.

    PubMed

    Sørensen, Trine Holst; Cruys-Bagger, Nicolaj; Borch, Kim; Westh, Peter

    2015-09-04

    Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association.

  3. Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose*

    PubMed Central

    Sørensen, Trine Holst; Cruys-Bagger, Nicolaj; Borch, Kim; Westh, Peter

    2015-01-01

    Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association. PMID:26183776

  4. Axial spatial distribution focusing: improving MALDI-TOF/RTOF mass spectrometric performance for high-energy collision-induced dissociation of biomolecules

    PubMed Central

    Belgacem, O; Pittenauer, E; Openshaw, M E; Hart, P J; Bowdler, A; Allmaier, G

    2016-01-01

    Rationale For the last two decades, curved field reflectron technology has been used in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers, assisting in the generation of post-source-decay (PSD) or collision-induced dissociation (CID) without decelerating precursor ions, producing true high-energy CID spectra. The result was the generation of product ion mass spectra with product ions typical of high-energy (10 keV and beyond) collision processes. The disadvantage of this approach was the lack of resolution in CID spectra resulting from the excess laser energy deposition used to generate those MS/MS spectra. The work presented in this study overcomes this limitation and includes comprehensive examples of high-energy and high-resolution CID MALDI-MS/MS spectra of biomolecules. Methods The devices used in this study are TOF/RTOF instruments equipped with a high-vacuum MALDI ion source. High-resolution and high-energy CID spectra result from the use of axial spatial distribution focusing (ASDF) in combination with curved field reflectron technology. Results A CID spectrum of the P14R1 peptide exhibits product ion resolution in excess of 10,000 (FWHM) but at the same time yields typical high-energy product ions such as w- and [y–2]-type ion series. High-energy CID spectra of lipids, exemplified by a glycerophospholipid and triglyceride, demonstrate C–C backbone fragmentation elucidating the presence of a hydroxyl group in addition to double-bond positioning. A complex high mannose carbohydrate (Man)8(GlcNAc)2 was also studied at 20 keV collision energy and revealed further high-energy product ions with very high resolution, allowing unambiguous detection and characterization of cross-ring cleavage-related ions. Conclusions This is the first comprehensive study using a MALDI-TOF/RTOF instrument equipped with a curved field reflectron and an ASDF device prior to the reflectron. © 2015 The Authors. Rapid Communications in

  5. Hydrogen bonding Part 53. Correlation of differential scanning calorimetric data with IR and dissociation vapor pressure studies of transitions of hexamethonium chloride and bromide dihydrates and hexamethonium bromide monohydrate

    NASA Astrophysics Data System (ADS)

    Snider, Barbara L.; Harmon, Kenneth M.

    1994-03-01

    Differential scanning calorimetry of hexamethonium chloride dihydrate shows an endothermic transition of 2.70 kcal mol -1 at 36.81°C. This correlates well with the temperatures observed by IR spectra (36°C) and equilibrium dissociation vapor pressure studies (37°C) for the transition between Type I planar cluster and Type II extended linear HOH⋯Cl - hydrogen bonding, and with the value of 2.77 kcal mol -1 for this transition derived by Hess' law treatment of dissociation vapor pressure data. Differential scanning calorimetry of hexamethonium bromide shows a rapid endothermic transition of 2.38 kcal mol -1 at 35.15°C and a very slow endothermic transition of about 12-13 kcal mol -1 centered near 50°C. This latter endotherm corresponds to the transition between Type I and Type II HOH⋯Br - hydrogen bonding observed by IR and vapor pressure studies at 49°C. The nature of the 35.15°C endotherm is not known. Hexamethonium bromide also shows a third endotherm at 142.91°C, which presumably results from melting of hydrate in the sealed DSC cell. Combined analysis of differential scanning calorimetry and dissociation vapor pressure data predicts a value of about -13 kcal mol -1 for an exothermic disproportionation at 52°C of two hexamethonium bromide monohydrate to Type II dihydrate and anhydrous bromide.

  6. Hypovalency--a kinetic-energy density description of a 4c-2e bond.

    PubMed

    Jacobsen, Heiko

    2009-06-07

    A bond descriptor based on the kinetic energy density, the localized-orbital locator (LOL), is used to characterize the nature of the chemical bond in electron deficient multi-center bonds. The boranes B(2)H(6), B(4)H(4), B(4)H(10), [B(6)H(6)](2-), and [B(6)H(7)](-) serve as prototypical examples of hypovalent 3c-2e and 4c-2e bonding. The kinetic energy density is derived from a set of Kohn-Sham orbitals obtained from pure density functional calculations (PBE/TZVP), and the topology of LOL is analyzed in terms of (3,-3) attractors (Gamma). The B-B-B and B-H-B 3c-2e, and the B-B-H-B 4c-2e bonding situations are defined by their own characteristic LOL profiles. The presence of one attractor in relation to the three or four atoms that are engaged in electron deficient bonding provides sufficient indication of the type of 3c-2e or 4c-2e bond present. For the 4c-2e bond in [B(6)H(7)](-) the LOL analysis is compared to results from an experimental QTAIM study.

  7. Meaning and consequence of the coexistence of competitive hydrogen bond/salt forms on the dissociation orientation of non-covalent complexes.

    PubMed

    Darii, Ekaterina; Alves, Sandra; Gimbert, Yves; Perret, Alain; Tabet, Jean-Claude

    2017-03-15

    Non-covalent complexes (NCC) between hexose monophosphates (HexP) and arginine (R) were analyzed using ESI MS and MS/MS in negative mode under different (hard, HC and soft, SC) desolvation conditions. High resolution mass spectrometry (HRMS) revealed the presence of different ionic species, namely, homo- and heteromultimers of R and HexP. Deprotonated heterodimers and corresponding sodiated species were enhanced under HC likely due to a decrease in available charge number associated with the reduction of H(+)/Na(+) exchange. The quantum calculations showed that the formation of covalent systems is very little exothermic, therefore, such systems are disfavored. Desolvation dependent CID spectra of deprotonated [(HexP+R)‒H](-) complexes demonstrated that they can exist within the hydrogen bond (HB) and salt bridge (SB) forms, yielding either NCC separation or covalent bond cleavages, respectively. Although HB forms are the main species, they cannot survive under HC; therefore, the minor SB forms became detectable. Energy-resolved mass spectrometry (ERMS) experiments revealed diagnostic fragment ions from both SB and HB forms, providing evidence that these isomeric forms are inconvertible. SB formation should result from the ionic interactions of highly acidic group of HexP with strongly basic guanidine group of arginine and thus requires an arginine zwitterion (ZW) form. This was confirmed by quantum calculations. Ion-ion interactions are significantly affected by the presence of sodium cation as demonstrated by the fragmentation patterns of sodiated complex species. Regarding CID data, only SB between protonated amino group of R and deprotonated phosphate group of HexP could be suggested, but the primary amine is not enough basic then, the SB must be fleeting. Nevertheless, the observation of the covalent bond cleavages suggests the presence of structures with a free negative charge able to induce fragmentations. Indeed, according to quantum calculations, solvated

  8. Low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides.

    PubMed

    Borisov, Oleg V; Goshe, Michael B; Conrads, Thomas P; Rakov, V Sergey; Veenstra, Timothy D; Smith, Richard D

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue-containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of Deinococcus radiodurans, the presence of these label-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys residue, and to differentiate identical Cys-peptides labeled with either ICAT-d0 or ICAT-d8.

  9. Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides

    SciTech Connect

    Borisov, Oleg V.; Goshe, Michael B. ); Conrads, Thomas P. ); Rakov, Vsevolod S. ); Veenstra, Timothy D. ); Smith, Richard D. )

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of D. radiodurans, the presence of these labeled-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys-residue, and to differentiate identical Cys-peptides labeled with either ICAT-D0 or ICAT-D8.

  10. Bond Graph Modeling and Validation of an Energy Regenerative System for Emulsion Pump Tests

    PubMed Central

    Li, Yilei; Zhu, Zhencai; Chen, Guoan

    2014-01-01

    The test system for emulsion pump is facing serious challenges due to its huge energy consumption and waste nowadays. To settle this energy issue, a novel energy regenerative system (ERS) for emulsion pump tests is briefly introduced at first. Modeling such an ERS of multienergy domains needs a unified and systematic approach. Bond graph modeling is well suited for this task. The bond graph model of this ERS is developed by first considering the separate components before assembling them together and so is the state-space equation. Both numerical simulation and experiments are carried out to validate the bond graph model of this ERS. Moreover the simulation and experiments results show that this ERS not only satisfies the test requirements, but also could save at least 25% of energy consumption as compared to the original test system, demonstrating that it is a promising method of energy regeneration for emulsion pump tests. PMID:24967428

  11. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  12. Low-energy electron-induced dissociation in condensed-phase L-cysteine I: Desorption of anions from chemisorbed films

    NASA Astrophysics Data System (ADS)

    Alizadeh, E.; Massey, S.; Rowntree, P. A.; Sanche, L.

    2015-09-01

    Among amino acids, cysteine has been widely studied, becoming a standard for molecular self-assembly experiments, because its mercapto group (-SH) allows the formation of self-assembled monolayers (SAMs) on metal surfaces. Dissociative electron attachment (DEA) on L-cysteine SAMs is investigated utilizing a time-of-flight mass spectrometer coupled with a low-energy electron gun. The results show that electrons with kinetic energies of 3 to 15 eV attach to L-cysteine producing anionic fragments of different masses (e.g., H-, O-, OH-, S-, SH-) via dissociation of intermediate transient anions. The anion yield functions exhibited purely resonant behaviour with electron energies below 15 eV, indicating that the formation of transient anions is the predominant mechanism of production of anionic fragments from L-cysteine dissociation.

  13. Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene

    PubMed Central

    Bang, Junhyeok; Meng, Sheng; Sun, Yi-Yang; West, Damien; Wang, Zhiguo; Gao, Fei; Zhang, S. B.

    2013-01-01

    Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD that predict H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations. PMID:23277576

  14. Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene

    SciTech Connect

    Bang, Junhyeok; Meng, Sheng; Sun, Yi-Yang; West, Damien; Wang, Zhiguo; Gao, Fei; Zhang, Shengbai

    2013-01-15

    Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab-initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD which predicts H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations.

  15. Spectroscopic constants of diatomic molecules computed correcting Hartree-Fock or general-valence-bond potential-energy curves with correlation-energy functionals

    NASA Astrophysics Data System (ADS)

    Pérez-Jordá, José M.; San-Fabián, Emilio; Moscardó, Federico

    1992-04-01

    The Kohn-Sham energy with exact exchange [using the exact Hartree-Fock (HF) exchange but an approximate correlation-energy functional] may be computed very accurately by adding the correlation obtained from the HF density to the total HF energy. Three density functionals are used: local spin density (LSD), LSD with self-interaction correction, and LSD with generalized gradient correction. This scheme has been extended (Lie-Clementi, Colle-Salvetti, and Moscardo-San-Fabian) to be used with general-valence-bond (GVB) energies and wave functions, so that the extra correlation included in the GVB energy is not counted again. The effect of all these approximate correlations on HF or GVB spectroscopic constants (Re,ωe, and De) is studied. Approximate relations showing how correlation affects them are derived, and may be summarized as follows: (1) the effect on Re and ωe depends only on the correlation derivative at Re, and (2) the effect on De depends mainly on the correlation difference between quasidissociated and equilibrium geometries. A consequence is that all the correlation corrections tested here give larger ωe and De and shorter Re than the uncorrected HF or GVB values. This trend is correct for De for both HF and GVB. For Re and ωe, it is correct in most cases for GVB, but it often fails for the HF cases. A comparison is made with Kohn-Sham calculations with both exchange and correlation approximated. As a final conclusion, it is found that, within the present scheme, a qualitatively correct HF or GVB potential-energy curve, together with a correlation-energy approximation with correct dissociation behavior, is crucial for obtaining good estimates of spectroscopic constants.

  16. Dissociative disorders.

    PubMed

    Kihlstrom, John F

    2005-01-01

    The dissociative disorders, including "psychogenic" or "functional" amnesia, fugue, dissociative identity disorder (DID, also known as multiple personality disorder), and depersonalization disorder, were once classified, along with conversion disorder, as forms of hysteria. The 1970s witnessed an "epidemic" of dissociative disorder, particularly DID, which may have reflected enthusiasm for the diagnosis more than its actual prevalence. Traditionally, the dissociative disorders have been attributed to trauma and other psychological stress, but the existing evidence favoring this hypothesis is plagued by poor methodology. Prospective studies of traumatized individuals reveal no convincing cases of amnesia not attributable to brain insult, injury, or disease. Treatment generally involves recovering and working through ostensibly repressed or dissociated memories of trauma; at present, there are few quantitative or controlled outcome studies. Experimental studies are few in number and have focused largely on state-dependent and implicit memory. Depersonalization disorder may be in line for the next "epidemic" of dissociation.

  17. Dissociative amnesia.

    PubMed

    Staniloiu, Angelica; Markowitsch, Hans J

    2014-08-01

    Dissociative amnesia is one of the most enigmatic and controversial psychiatric disorders. In the past two decades, interest in the understanding of its pathophysiology has surged. In this report, we review new data about the epidemiology, neurobiology, and neuroimaging of dissociative amnesia and show how advances in memory research and neurobiology of dissociation inform proposed pathogenetic models of the disorder. Dissociative amnesia is characterised by functional impairment. Additionally, preliminary data suggest that affected people have an increased and possibly underestimated suicide risk. The prevalence of dissociative amnesia differs substantially across countries and populations. Symptoms and disease course also vary, indicating a possibly heterogeneous disorder. The accompanying clinical features differ across cultural groups. Most dissociative amnesias are retrograde, with memory impairments mainly involving the episodic-autobiographical memory domain. Anterograde dissociative amnesia occurring without significant retrograde memory impairments is rare. Functional neuroimaging studies of dissociative amnesia with prevailing retrograde memory impairments show changes in the network that subserves autobiographical memory. At present, no evidence-based treatments are available for dissociative amnesia and no broad framework exists for its rehabilitation. Further research is needed into its neurobiology, course, treatment options, and strategies to improve differential diagnoses.

  18. Homolytic S-S bond dissociation of 11 bis(thiocarbonyl)disulfides R-C(=S)-S-S-C(=S)R and prediction of a novel rubber vulcanization accelerator.

    PubMed

    Mak, Adrian Matthew; Steudel, Ralf; Wong, Ming Wah

    2008-06-02

    The structures and energetics of eight substituted bis(thiocarbonyl)disulfides (RCS(2))(2), their associated radicals RCS(2)(*), and their coordination compounds with a lithium cation have been studied at the G3X(MP2) level of theory for R = H, Me, F, Cl, OMe, SMe, NMe(2), and PMe(2). The effects of substituents on the dissociation of (RCS(2))(2) to RCS(2)(*) were analyzed using isodesmic stabilization reactions. Electron-donating groups with an unshared pair of electrons have a pronounced stabilization effect on both (RCS(2))(2) and RCS(2)(*). The S-S bond dissociation enthalpy of tetramethylthiuram disulfide (TMTD, R = NMe(2)) is the lowest in the above series (155 kJ mol(-1)), attributed to the particular stability of the formed Me(2)NCS(2)(*) radical. Both (RCS(2))(2) and the fragmented radicals RCS(2)(*) form stable chelate complexes with a Li(+) cation. The S-S homolytic bond cleavage in (RCS(2))(2) is facilitated by the reaction [Li(RCS(2))(2)](+)+Li(+)-->2 [Li(RCS(2))](*+). Three other substituted bis(thiocarbonyl) disulfides with the unconventional substituents R = OSF(5), Gu(1), and Gu(2) have been explored to find suitable alternative rubber vulcanization accelerators. Bis(thiocarbonyl)disulfide with a guanidine-type substituent, (Gu(1)CS(2))(2), is predicted to be an effective accelerator in sulfur vulcanization of rubber. Compared to TMTD, (Gu(1)CS(2))(2) is calculated to have a lower bond dissociation enthalpy and smaller associated barrier for the S-S homolysis.

  19. A Novel Method to Quantify Soil Aggregate Stability by Measuring Aggregate Bond Energies

    NASA Astrophysics Data System (ADS)

    Efrat, Rachel; Rawlins, Barry G.; Quinton, John N.; Watts, Chris W.; Whitmore, Andy P.

    2016-04-01

    Soil aggregate stability is a key indicator of soil quality because it controls physical, biological and chemical functions important in cultivated soils. Micro-aggregates are responsible for the long term sequestration of carbon in soil, therefore determine soils role in the carbon cycle. It is thus vital that techniques to measure aggregate stability are accurate, consistent and reliable, in order to appropriately manage and monitor soil quality, and to develop our understanding and estimates of soil as a carbon store to appropriately incorporate in carbon cycle models. Practices used to assess the stability of aggregates vary in sample preparation, operational technique and unit of results. They use proxies and lack quantification. Conflicting results are therefore drawn between projects that do not provide methodological or resultant comparability. Typical modern stability tests suspend aggregates in water and monitor fragmentation upon exposure to an un-quantified amount of ultrasonic energy, utilising a laser granulometer to measure the change in mean weight diameter. In this project a novel approach has been developed based on that of Zhu et al., (2009), to accurately quantify the stability of aggregates by specifically measuring their bond energies. The bond energies are measured operating a combination of calorimetry and a high powered ultrasonic probe, with computable output function. Temperature change during sonication is monitored by an array of probes which enables calculation of the energy spent heating the system (Ph). Our novel technique suspends aggregates in heavy liquid lithium heteropolytungstate, as opposed to water, to avoid exposing aggregates to an immeasurable disruptive energy source, due to cavitation, collisions and clay swelling. Mean weight diameter is measured by a laser granulometer to monitor aggregate breakdown after successive periods of calculated ultrasonic energy input (Pi), until complete dispersion is achieved and bond

  20. The Scalar Relativistic Contribution to Ga-Halide Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1998-01-01

    The one-electron Douglas Kroll (DK) and perturbation theory (+R) approaches are used to compute the scalar relativistic contribution to the atomization energies of GaFn. These results are compared with the previous GaCln results. While the +R and DK results agree well for the GaCln atom nation energies, they differ for GaFn. The present work suggests that the DK approach is more accurate than the +R approach. In addition, the DK approach is less sensitive to the choice of basis set. The computed atomization energies of GaF2 and GaF3 are smaller than the somewhat uncertain experiments. It is suggested that additional calibration calculations for the scalar relativistic effects in GaF2 and GaF3 would be valuable.

  1. Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

    SciTech Connect

    McGrath, Matthew; Kuo, I-F W.; Ngouana, Brice F.; Ghogomu, Julius N.; Mundy, Christopher J.; Marenich, Aleksandr; Cramer, Christopher J.; Truhlar, Donald G.; Siepmann, Joern I.

    2013-08-28

    The free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation quantum chemical approach at four temperatures between T = 300 and 450 K. The free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system’s potential energy. The latter free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation free energies agree very well with available experimental data. CJM was supported by the US Department of Energy,Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  2. Computed self-consistent field and singles and doubles configuration interaction spectroscopic data and dissociation energies for the diatomics B2, C2, N2, O2, F2, CN, CP, CS, PN, SiC, SiN, SiO, SiP, and their ions

    NASA Astrophysics Data System (ADS)

    McLean, A. D.; Liu, B.; Chandler, G. S.

    1992-12-01

    Results are presented for single-configuration self-consistent field (SCF) calculations near the Hartree-Fock limit. Singles and doubles configuration-interaction calculations from this single SCF configuration were performed for the ground states and selected excited states of the molecules B2, B2(+), C2, C2(+), N2, N2(+), O2, O2(+), F2, F2(+), CN, CN(-), CP, CS, PN, SiC, SiC(-), SiN, SiN(-), SiO, and SiP. Results include potential energy curves, equilibrium bond lengths, vibrational energies, ionization potentials, and dissociation energies.

  3. The spectroscopy of H3+3: low energy to dissociation

    NASA Astrophysics Data System (ADS)

    Ramanlal, Jayesh

    The H3" ion is the simplest and most fundamental of polyatomic molecules consisting of three protons and two electrons. H3 is an important molecule playing a key role in many areas of Physics, Chemistry and Astronomy. The astrophysical importance of H3" lies in the fact that most of the universe is made up of hydrogen, and molecular hydrogen in the cool regions. H3" is rapidly formed by the reaction H2 + H+-*H++H (1) Thus H3 is usually the dominant ion in environments containing molecular hydrogen. Further more, multiply deuterated species have been observed in the interstellar medium recently. These species are thought to have been formed via deuterium fractionation effects, in which the isotopomers H2D+ and D2H+ play a significant role. More than two decades have passed since Carrington and co-workers produced a remarkably rich spectrum of the H3". Over 27,000 absorption lines in a region between 872cm-1 to 1094cm""1. This experiment still remains largely unexplained. This work calculates intensities of transitions of states near dissociation. Thus will help illuminate the Carrington spectrum. Within this work I present a method of calculating line strengths for the H3" system. Several improvements on previous methods are presented, including the use discrete variable representation, symmetry and a parallel algorithm. The implementation of this method on massively parallel computers is also discussed. Several applications of the synthetic spectra of and isotopomers are presented. This will include where possible how they have aided other work and the results of this other work.

  4. Electron Scattering Resonances and Dissociative Attachment in Polyatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Olthoff, James Kenneth

    The electronic structure and bonding character of a molecule may be understood from the energies of the frontier molecular orbitals. Photoelectron spectroscopy has produced a wealth of information about the occupied molecular orbitals, but the unoccupied molecular orbitals have, until recently, been largely ignored. A relatively new technique, electron transmission spectroscopy, is now being used to investigate the unoccupied valence molecular orbitals of many chemical compounds. Electron transmission spectroscopy measures the energy of negative ion states which arise from electron capture into unoccupied molecular orbitals. Additional information about the unoccupied orbitals may be obtained if the negative ion decays by way of dissociation. Determination of the identity, kinetic energy, and production rates of stable ion fragments supplies information about the shape and position of the potential energy curves which describe the electronic states of the molecule and the anion. Used together, photoelectron, electron transmission, and dissociation data can produce a complete picture of a molecule's valence electronic structure. For this work a time-of-flight mass spectrometer has been attached to an electron transmission spectrometer to observe negative ion fragments due to dissociative attachment. The mass spectrometer measures the identity and kinetic energy of stable negative ions as a function of incident electron energy. Electron transmission spectra and ion production data have been acquired for many compounds in four chemical categories. Halogen-substituted unsaturated hydrocarbons have been studied to determine the relation between (pi)* anion states and stable ion production. Halogen substituted methanes were examined to determine how (sigma) bonding affects dissociative attachment. Spectra for a series of boron trihalides were obtained to determine correlations between electron transmission data and Lewis acidity. Lastly, substituted metal carbonyls were

  5. Experimental study on the initiation and energy release behavior of polymer bonded explosive materials

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Cai, Xuanming; Ye, Nan; Gao, Yubo

    2017-01-01

    In this paper, an initially sealed vented test chamber and a test projectile with polymer bonded explosive materials were designed to complete the experiments. As the initiation takes place on the interior, great amounts of thermo-chemical energy gases were vented through a hole formed by the penetration process. The gas pressure inside the chamber was used to evaluate the energy release behavior of polymer bonded explosive materials. The experimental results reveal that the impact velocity is significant to the energy release behavior, and in some extent the gas pressure improves with the velocity of the projectile. And the critical initiation velocity and the velocity as the polymer bonded explosive materials reached the maximum reactive efficiency were obtained.

  6. A physical picture for mechanical dissociation of biological complexes: from forces to free energies.

    PubMed

    Tapia-Rojo, Rafael; Marcuello, Carlos; Lostao, Anabel; Gómez-Moreno, Carlos; J Mazo, Juan; Falo, Fernando

    2017-02-08

    Single-molecule force spectroscopy is a powerful technique based on the application of controlled forces to macromolecules. In order to relate the measured response of the molecule to its equilibrium and dynamic properties, a suitable physical picture of the involved process is necessary. In this work, we introduce a plausible model for mechanical unbinding of some molecular complexes, based on a novel free energy profile. We combine two standard theoretical frameworks for analyzing force spectroscopy experiments on two protein:protein complexes, obtaining key magnitudes of the underlying free energy profile, which are only understood within the mentioned model. Additionally, we carry out detailed stochastic dynamics simulations to prove the validity of the analysis protocol and the reliability of the free energy profile. Remarkably, we can compare directly the obtained unbinding free energies with the previously known bulk binding free energies, bridging the gap between bulk and single molecule techniques.

  7. Electronic structure, molecular bonding and potential energy surfaces

    SciTech Connect

    Ruedenberg, K.

    1993-12-01

    By virtue of the universal validity of the generalized Born-Oppenheimer separation, potential energy surfaces (PES`) represent the central conceptual as well as quantitative entities of chemical physics and provide the basis for the understanding of most physicochemical phenomena in many diverse fields. The research in this group deals with the elucidation of general properties of PES` as well as with the quantitative determination of PES` for concrete systems, in particular pertaining to reactions involving carbon, oxygen, nitrogen and hydrogen molecules.

  8. Adsorption of water on O(2x2)/Ru(0001): thermal stability and inhibition of dissociation by H2O-O bonding

    SciTech Connect

    Mugarza, Aitor; Shimizu, Tomoko; Cabrera-Sanfelix, Pepa; Sanchez-Portal, Daniel; Arnau, Andres; Salmeron, Miquel

    2008-08-01

    The effect of preadsorbed oxygen on the subsequent adsorption and reactions of water on Ru(0001) has been studied using low temperature scanning tunneling microscopy and DFT calculations. Experiments were carried out for O coverages close to 0.25 ML. It was found that no dissociation of water takes place up to the desorption temperature of {approx}180-230 K. DFT calculations show that intact water on O(2x2)/Ru(0001) is {approx} 0.49 eV more stable than the dissociation products, H and OH, at their preferred fcc and top adsorption sites.

  9. Quantum dynamics study of fulvene double bond photoisomerization: The role of intramolecular vibrational energy redistribution and excitation energy

    SciTech Connect

    Blancafort, Lluis; Gatti, Fabien; Meyer, Hans-Dieter

    2011-10-07

    The double bond photoisomerization of fulvene has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method. Fulvene is a test case to develop optical control strategies based on the knowledge of the excited state decay mechanism. The decay takes place on a time scale of several hundred femtoseconds, and the potential energy surface is centered around a conical intersection seam between the ground and excited state. The competition between unreactive decay and photoisomerization depends on the region of the seam accessed during the decay. The dynamics are carried out on a four-dimensional model surface, parametrized from complete active space self-consistent field calculations, that captures the main features of the seam (energy and locus of the seam and associated branching space vectors). Wave packet propagations initiated by single laser pulses of 5-25 fs duration and 1.85-4 eV excitation energy show the principal characteristics of the first 150 fs of the photodynamics. Initially, the excitation energy is transferred to a bond stretching mode that leads the wave packet to the seam, inducing the regeneration of the reactant. The photoisomerization starts after the vibrational energy has flowed from the bond stretching to the torsional mode. In our propagations, intramolecular energy redistribution (IVR) is accelerated for higher excess energies along the bond stretch mode. Thus, the competition between unreactive decay and isomerization depends on the rate of IVR between the bond stretch and torsion coordinates, which in turn depends on the excitation energy. These results set the ground for the development of future optical control strategies.

  10. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies.

    PubMed

    Singh, Amit Raj; Granek, Rony

    2016-10-14

    We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

  11. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies

    NASA Astrophysics Data System (ADS)

    Singh, Amit Raj; Granek, Rony

    2016-10-01

    We study DNA denaturation by integrating elasticity — as described by the Gaussian network model — with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.

  12. Using Qualified Energy Conservation Bonds for Public Building Upgrades. Reducing Energy Bills in the City of Philadelphia

    SciTech Connect

    Zimring, Mark

    2012-07-18

    Qualified Energy Conservation Bonds (QECBs) are federally-subsidized bonds that enable state, tribal, and local government issuers to borrow money to fund a range of energy conservation projects, including public building upgrades that reduce energy use by at least 20 percent, at very attractive borrowing rates and long terms. As part of the American Recovery and Reinvestment Act (ARRA), the City of Philadelphia received a $15 million QECB award from the U.S. Department of the Treasury (Treasury). The city leveraged $6.25 million of its QECB allocation to finance half of a $12.6 million initiative to upgrade the energy efficiency of City buildings. The upgrades to four city facilities are expected to deliver over $10 million of net savings, and are a major step towards achieving the city’s goal of reducing government energy consumption by 30 percent by 2015.

  13. Evaluation of the surface bonding energy of an InP membrane bonded oxide-free to Si using instrumented nanoindentation

    NASA Astrophysics Data System (ADS)

    Pantzas, Konstantinos; Patriarche, Gilles; Le Bourhis, Eric; Troadec, David; Itawi, Ahmad; Beaudoin, Grégoire; Sagnes, Isabelle; Talneau, Anne

    2013-08-01

    Instrumented nanoindentation is used in conjunction with scanning transmission electron microscopy to evaluate the mechanical resistance at the bonding interface of a 450 nm thick InP membrane bonded oxide-free to Si. Indentation using a Berkovich tip is shown to cause the planes in InP to rotate by as much as 16°. The shear stress resulting from this rotation causes the InP membrane to buckle, forming a debonded blister around the indented zone. The geometry of this blister is used to compute the surface bond energy of InP bonded oxide-free to Si. An average surface bonding energy of 585 mJ m-2 is reported.

  14. Ab initio theoretical studies of potential energy surfaces in the photodissociation of the vinyl radical. I. Ã state dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Irle, Stephan; Morokuma, Keiji; Tschumper, Gregory S.

    2003-10-01

    The mechanism of photodissociation of the vinyl radical, C2H3, starting from the first doublet excited (D1,Ã) state was studied with high-level ab initio methods as well as with ab initio direct dynamics. Geometry optimizations of stationary points and surface crossing seams were performed with complete active space self-consistent field (CASSCF) method, and the energies were re-evaluated with single-point multireference single and double excitation configuration interaction (MRCISD) calculations. Both internal conversion and intersystem crossing channels, which could bring the excited vinyl radical down to the ground state potential energy surface leading to dissociation on the ground state, have been identified within planar Cs, twisted Cs and C2v symmetry. Direct dynamics calculation indicates that the most feasible reaction channel is the direct internal conversion from D1 to the ground state (D0) within planar Cs symmetry, through a minimum of seam of crossing (conical intersection) at an energy of about 80 kcal/mol (with respect to the ground-state equilibrium geometry). The other internal conversions from D1 to D0 through conical intersections within twisted Cs symmetry require energies of about 80 and 75 kcal/mol at the two minima of seam of crossing, respectively, and they are not favored dynamically without initial out-of-plane vibrational excitation. The intersystem crossing channels between D1 and the lowest quartet state (Q1) and D0 and Q1 within twisted Cs and C2v symmetry are not efficient due to the high energy of the minima of seam of crossing as well as the small spin-orbit coupling.

  15. Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

    SciTech Connect

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2005-09-01

    Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  16. Chemical bond as a test of density-gradient expansions for kinetic and exchange energies

    SciTech Connect

    Perdew, J.P.; Levy, M.; Painter, G.S.; Wei, S.; Lagowski, J.B.

    1988-01-15

    Errors in kinetic and exchange contributions to the molecular bonding energy are assessed for approximate density functionals by reference to near-exact Hartree-Fock values. From the molecular calculations of Allan et al. and of Lee and Ghosh, it is demonstrated that the density-gradient expansion does not accurately describe the noninteracting kinetic contribution to the bonding energy, even when this expansion is carried to fourth order and applied in its spin-density-functional form to accurate Hartree-Fock densities. In a related study, it is demonstrated that the overbinding of molecules such as N/sub 2/ and F/sub 2/, which occurs in the local-spin-density (LSD) approximation for the exchange-correlation energy, is not attributable to errors in the self-consistent LSD densities. Contrary to expectations based upon the Gunnarsson-Jones nodality argument, it is found that the LSD approximation for the exchange energy can seriously overbind a molecule even when bonding does not create additional nodes in the occupied valence orbitals. LSD and exact values for the exchange contribution to the bonding energy are displayed and discussed for several molecules.

  17. Threshold collision-induced dissociation measurements using a ring ion guide as the collision cell in a triple-quadrupole mass spectrometer.

    PubMed

    Romanov, Vladimir; Verkerk, Udo H; Siu, Chi-Kit; Hopkinson, Alan C; Siu, K W Michael

    2009-08-15

    A triple-quadrupole mass spectrometer has been modified for bond-dissociation energy measurements via threshold collision-induced dissociations (TCIDs) by replacing the conventional collision cell with a ring ion guide. Optimal operating conditions for the ring ion guide were determined or derived, and validated using a set of complexes for which bond dissociation energies are known. A comparison with reference data (within a range of 16-57 kcal/mol) indicates an accuracy approaching that of TCID determined on a guided ion-beam mass spectrometer. Complexes for which bond-dissociation energies were measured include metal ion complexes of simple ligands, amino acids and peptides, as well as of carbonic acid. There is excellent agreement between our experimental data and literature data, as well as theoretical data determined using a high-level computational method.

  18. High-Energy Collision-Induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

    2014-08-01

    A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

  19. Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene

    NASA Astrophysics Data System (ADS)

    Sand, Andrew M.; Truhlar, Donald G.; Gagliardi, Laura

    2017-01-01

    The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

  20. Molecular dynamics investigations of the dissociation of SiO2 on an ab initio potential energy surface obtained using neural network methods.

    PubMed

    Agrawal, Paras M; Raff, Lionel M; Hagan, Martin T; Komanduri, Ranga

    2006-04-07

    The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO(2) system. Unlike other similar NN studies, here, we studied the dissociation of SiO(2) without the initial use of any empirical potential. During the dissociation of SiO(2) into Si+O or Si+O(2), the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.

  1. Molecular dynamics investigations of the dissociation of SiO2 on an ab initio potential energy surface obtained using neural network methods

    NASA Astrophysics Data System (ADS)

    Agrawal, Paras M.; Raff, Lionel M.; Hagan, Martin T.; Komanduri, Ranga

    2006-04-01

    The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO2 system. Unlike other similar NN studies, here, we studied the dissociation of SiO2 without the initial use of any empirical potential. During the dissociation of SiO2 into Si +O or Si +O2, the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.

  2. A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems

    SciTech Connect

    Raupach, Marc; Tonner, Ralf

    2015-05-21

    The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the bonding energy between two fragments (e.g., the adsorption energy of a molecule on a surface) into several well-defined terms: preparation, electrostatic, Pauli repulsion, and orbital relaxation energies. This is complemented by consideration of dispersion interactions via a pairwise scheme. One major extension toward a previous implementation [Philipsen and Baerends, J. Phys. Chem. B 110, 12470 (2006)] lies in the separate discussion of electrostatic and Pauli and the addition of a dispersion term. The pEDA presented here for an implementation based on atomic orbitals can handle restricted and unrestricted fragments for 0D to 3D systems considering periodic boundary conditions with and without the determination of fragment occupations. For the latter case, reciprocal space sampling is enabled. The new method gives comparable results to established schemes for molecular systems and shows good convergence with respect to the basis set (TZ2P), the integration accuracy, and k-space sampling. Four typical bonding scenarios for surface-adsorbate complexes were chosen to highlight the performance of the method representing insulating (CO on MgO(001)), metallic (H{sub 2} on M(001), M = Pd, Cu), and semiconducting (CO and C{sub 2}H{sub 2} on Si(001)) substrates. These examples cover diverse substrates as well as bonding scenarios ranging from weakly interacting to covalent (shared electron and donor acceptor) bonding. The results presented lend confidence that the pEDA will be a powerful tool for the analysis of surface-adsorbate bonding in the future, enabling the transfer of concepts like ionic and covalent bonding, donor-acceptor interaction, steric repulsion, and others to extended systems.

  3. A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems.

    PubMed

    Raupach, Marc; Tonner, Ralf

    2015-05-21

    The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the bonding energy between two fragments (e.g., the adsorption energy of a molecule on a surface) into several well-defined terms: preparation, electrostatic, Pauli repulsion, and orbital relaxation energies. This is complemented by consideration of dispersion interactions via a pairwise scheme. One major extension toward a previous implementation [Philipsen and Baerends, J. Phys. Chem. B 110, 12470 (2006)] lies in the separate discussion of electrostatic and Pauli and the addition of a dispersion term. The pEDA presented here for an implementation based on atomic orbitals can handle restricted and unrestricted fragments for 0D to 3D systems considering periodic boundary conditions with and without the determination of fragment occupations. For the latter case, reciprocal space sampling is enabled. The new method gives comparable results to established schemes for molecular systems and shows good convergence with respect to the basis set (TZ2P), the integration accuracy, and k-space sampling. Four typical bonding scenarios for surface-adsorbate complexes were chosen to highlight the performance of the method representing insulating (CO on MgO(001)), metallic (H2 on M(001), M = Pd, Cu), and semiconducting (CO and C2H2 on Si(001)) substrates. These examples cover diverse substrates as well as bonding scenarios ranging from weakly interacting to covalent (shared electron and donor acceptor) bonding. The results presented lend confidence that the pEDA will be a powerful tool for the analysis of surface-adsorbate bonding in the future, enabling the transfer of concepts like ionic and covalent bonding, donor-acceptor interaction, steric repulsion, and others to extended systems.

  4. Ionic bond effects on the mean excitation energy for stopping power

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Chang, C. K.; Kamaratos, E.; Xu, Y. J.

    1982-01-01

    Molecular mean excitation energies for ionic bonded molecules calculated according to the local plasma approximation are compared to the Bragg rule. Adjustments of 15% are calculated for LiF in agreement with experiments while 6% adjustments are predicted for HF and 3% for LiH.

  5. The energy of the intramolecular hydrogen bond in chloro-substituted N-methyl-salicylidene imines

    NASA Astrophysics Data System (ADS)

    Koll, A.; Karpfen, A.; Wolschann, P.

    2007-11-01

    The energetic effects of the conformational rearrangement of eight Schiff bases, differently chloro-substituted, are discussed on the basis of the results of B3LYP/6-31+G(d,p) calculations. The proton transfer tautomers as well as "open"-non-hydrogen-bonded forms were considered. It was found, that the hydrogen-bonded forms have the lowest energy, but the second most stable were the proton transfer states with an O…H sbnd N intramolecular hydrogen bond. The proton transfer in Schiff bases dominates in comparison to other conformational rearrangements. This is important for the understanding of thermochromic and photochromic properties of these molecules. By using a thermodynamic cycle, the steric effects connected with chelate ring formation are estimated to be up to 5 kcal/mol, much higher than in related Mannich bases (˜1 kcal/mol) which do not form resonance assisted hydrogen bonds. Accounting these effects the "real" value of the energy of hydrogen bond formation was estimated to be 15 kcal/mol which increases with growing number of chlorine atoms up to 16.5 kcal/mol for 4,5,6-trichloro substitution.

  6. The Quadruple Bonding in C2 Reproduces the Properties of the Molecule.

    PubMed

    Shaik, Sason; Danovich, David; Braida, Benoit; Hiberty, Philippe C

    2016-03-14

    Ever since Lewis depicted the triple bond for acetylene, triple bonding has been considered as the highest limit of multiple bonding for main elements. Here we show that C2 is bonded by a quadruple bond that can be distinctly characterized by valence-bond (VB) calculations. We demonstrate that the quadruply-bonded structure determines the key observables of the molecule, and accounts by itself for about 90% of the molecule's bond dissociation energy, and for its bond lengths and its force constant. The quadruply-bonded structure is made of two strong π bonds, one strong σ bond and a weaker fourth σ-type bond, the bond strength of which is estimated as 17-21 kcal mol(-1). Alternative VB structures with double bonds; either two π bonds or one π bond and one σ bond lie at 129.5 and 106.1 kcal mol(-1), respectively, above the quadruply-bonded structure, and they collapse to the latter structure given freedom to improve their double bonding by dative σ bonding. The usefulness of the quadruply-bonded model is underscored by "predicting" the properties of the (3)Σ+u state. C2's very high reactivity is rooted in its fourth weak bond. Thus, carbon and first-row main elements are open to quadruple bonding!

  7. Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

    PubMed

    Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

    2017-03-14

    We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

  8. Dissociation dynamics of fluorinated ethene cations: from time bombs on a molecular level to double-regime dissociators.

    PubMed

    Harvey, Jonelle; Bodi, Andras; Tuckett, Richard P; Sztáray, Bálint

    2012-03-21

    The dissociative photoionization mechanism of internal energy selected C(2)H(3)F(+), 1,1-C(2)H(2)F(2)(+), C(2)HF(3)(+) and C(2)F(4)(+) cations has been studied in the 13-20 eV photon energy range using imaging photoelectron photoion coincidence spectroscopy. Five predominant channels have been found; HF loss, statistical and non-statistical F loss, cleavage of the C-C bond post H or F-atom migration, and cleavage of the C=C bond. By modelling the breakdown diagrams and ion time-of-flight distributions using statistical theory, experimental 0 K appearance energies, E(0), of the daughter ions have been determined. Both C(2)H(3)F(+) and 1,1-C(2)H(2)F(2)(+) are veritable time bombs with respect to dissociation via HF loss, where slow dissociation over a reverse barrier is followed by an explosion with large kinetic energy release. The first dissociative ionization pathway for C(2)HF(3) and C(2)F(4) involves an atom migration across the C=C bond, giving CF-CHF(2)(+) and CF-CF(3)(+), respectively, which then dissociate to form CHF(2)(+), CF(+) and CF(3)(+). The nature of the F-loss pathway has been found to be bimodal for C(2)H(3)F and 1,1-C(2)H(2)F(2), switching from statistical to non-statistical behaviour as the photon energy increases. The dissociative ionization of C(2)F(4) is found to be comprised of two regimes. At low internal energies, CF(+), CF(3)(+) and CF(2)(+) are formed in statistical processes. At high internal energies, a long-lived excited electronic state is formed, which loses an F atom in a non-statistical process and undergoes statistical redistribution of energy among the nuclear degrees of freedom. This is followed by a subsequent dissociation. In other words only the ground electronic state phase space stays inaccessible. The accurate E(0) of CF(3)(+) and CF(+) formation from C(2)F(4) together with the now well established Δ(f)H(o) of C(2)F(4) yield self-consistent enthalpies of formation for the CF(3), CF, CF(3)(+) and CF(+) species.

  9. Three-body dissociations: The photodissociation of dimethyl sulfoxide at 193 nm

    SciTech Connect

    Blank, D.A.; North, S.W.; Stranges, D.

    1997-04-01

    When a molecule with two equivalent chemical bonds is excited above the threshold for dissociation of both bonds, how the rupture of the two bonds is temporally coupled becomes a salient question. Following absorption at 193 nm dimethyl sulfoxide (CH{sub 3}SOCH{sub 3}) contains enough energy to rupture both C-S bonds. This can happen in a stepwise (reaction 1) or concerted (reaction 2) fashion where the authors use rotation of the SOCH{sub 3} intermediate prior to dissociation to define a stepwise dissociation: (1) CH{sub 3}SOCH{sub 3} {r_arrow} 2CH{sub 3} + SO; (2a) CH{sub 3}SOCH{sub 3} {r_arrow} CH{sub 3} + SOCH{sub 3}; and (2b) SOCH{sub 3} {r_arrow} SO + CH{sub 3}. Recently, the dissociation of dimethyl sulfoxide following absorption at 193 nm was suggested to involve simultaneous cleavage of both C-S bonds on an excited electronic surface. This conclusion was inferred from laser induced fluorescence (LIF) and resonant multiphoton ionization (2+1 REMPI) measurements of the internal energy content in the CH{sub 3} and SO photoproducts and a near unity quantum yield measured for SO. Since this type of concerted three body dissociation is very interesting and a rather rare event in photodissociation dynamics, the authors chose to investigate this system using the technique of photofragment translational spectroscopy at beamline 9.0.2.1. The soft photoionization provided by the VUV undulator radiation allowed the authors to probe the SOCH{sub 3} intermediate which had not been previously observed and provided good evidence that the dissociation of dimethyl sulfoxide primarily proceeds via a two step dissociation, reaction 2.

  10. Average bond energies between boron and elements of the fourth, fifth, sixth, and seventh groups of the periodic table

    NASA Technical Reports Server (NTRS)

    Altshuller, Aubrey P

    1955-01-01

    The average bond energies D(gm)(B-Z) for boron-containing molecules have been calculated by the Pauling geometric-mean equation. These calculated bond energies are compared with the average bond energies D(exp)(B-Z) obtained from experimental data. The higher values of D(exp)(B-Z) in comparison with D(gm)(B-Z) when Z is an element in the fifth, sixth, or seventh periodic group may be attributed to resonance stabilization or double-bond character.

  11. The peptide-chain size dependence of positive dissociation energy effect in metallized and protonated polydentate oligoglycine peptides

    NASA Astrophysics Data System (ADS)

    Ai, Hongqi; Bu, Yuxiang; Li, Ping; Yan, Shihai

    2005-10-01

    The dependence of the positive dissociation energy (PDE) on the size of both protonated and various metal cationized (M+/2+=Na+, K+, Mg2+, and Ca2+) oligoglycines GnHM (G =glycine; n =1-5, and including 6 for GnHK) in the gas phase has been first determined at the B3LYP level with different basis sets. Results show that these PDEs become negative ones when n ⩾5 for GnHNa, n ⩾6 for GnHK, n ⩾2 for GnHMg, and n ⩾3 for GnHCa. Moreover, the PDE effect decreases gradually along the increase of oligoglycine size for all these PDE systems. More charge transfer to the ambient ligand and large electrostatic effect of the two divalent cation (Mg2+ and Ca2+) involved systems make them lose the PDE effect more rapidly, and hold more compact and oblate shapes than the monovalent ones. Differently, polydentate GnHK prefers a spherical to oblate shape along with the increase of oligoglycine size.

  12. Rovibrational internal energy transfer and dissociation of N2(1Σg+)-N(4S(u)) system in hypersonic flows.

    PubMed

    Panesi, Marco; Jaffe, Richard L; Schwenke, David W; Magin, Thierry E

    2013-01-28

    A rovibrational collisional model is developed to study energy transfer and dissociation of N(2)((1)Σ(g)(+)) molecules interacting with N((4)S(u)) atoms in an ideal isochoric and isothermal chemical reactor. The system examined is a mixture of molecular nitrogen and a small amount of atomic nitrogen. This mixture, initially at room temperature, is heated by several thousands of degrees Kelvin, driving the system toward a strong non-equilibrium condition. The evolution of the population densities of each individual rovibrational level is explicitly determined via the numerical solution of the master equation for temperatures ranging from 5000 to 50,000 K. The reaction rate coefficients are taken from an ab initio database developed at NASA Ames Research Center. The macroscopic relaxation times, energy transfer rates, and dissociation rate coefficients are extracted from the solution of the master equation. The computed rotational-translational (RT) and vibrational-translational (VT) relaxation times are different at low heat bath temperatures (e.g., RT is about two orders of magnitude faster than VT at T = 5000 K), but they converge to a common limiting value at high temperature. This is contrary to the conventional interpretation of thermal relaxation in which translational and rotational relaxation timescales are assumed comparable with vibrational relaxation being considerable slower. Thus, this assumption is questionable under high temperature non-equilibrium conditions. The exchange reaction plays a very significant role in determining the dynamics of the population densities. The macroscopic energy transfer and dissociation rates are found to be slower when exchange processes are neglected. A macroscopic dissociation rate coefficient based on the quasi-stationary distribution, exhibits excellent agreement with experimental data of Appleton et al. [J. Chem. Phys. 48, 599-608 (1968)]. However, at higher temperatures, only about 50% of dissociation is found to

  13. Energy-resolved collision-induced dissociation of non-covalent ions: charge- and guest-dependence of decomplexation reaction efficiencies.

    PubMed

    Carroy, Glenn; Lemaur, Vincent; De Winter, Julien; Isaacs, Lyle; De Pauw, Edwin; Cornil, Jérôme; Gerbaux, Pascal

    2016-05-14

    Supramolecular chemistry, and especially host-guest chemistry, has been the subject of great interest in the past few decades leading to the synthesis of host cage molecules such as calixarenes, cyclodextrins and more recently cucurbiturils. Mass spectrometry methods are increasingly used to decipher at the molecular level the non-covalent interactions between the different associated molecules. The present article illustrates that the association between mass spectrometry and computational chemistry techniques proves very complementary to depict the gas-phase dissociation processes of ionic non-covalent complexes when subjected to collisional activation. The selected system associates a nor-seco-cucurbit[10]uril bitopic receptor with different amino compounds (adamantylamine, para-xylylenediamine, and para-phenylenediamine). When subjected to CID experiments, the ternary complexes undergo fragmentation via dissociation of non-covalently bound partners. Interestingly, depending on their charge state, the collisionally excited complexes can selectively expel either a neutral guest molecule or a protonated guest molecule. Moreover, based on energy-resolved CID experiments, it is possible to evaluate the guest molecule dependence on the gas phase dissociation efficiency. We observed that the relative order of gas phase dissociation is charge state dependent, with the adamantylamine-containing complexes being the weakest when triply charged and the strongest when doubly charged. The energetics of the gas-phase dissociation reactions have been estimated by density functional theory (DFT) calculations. We succeeded in theoretically rationalizing the experimental collision-induced dissociation results with a special emphasis on: (i) the charge state of the expelled guest molecule and (ii) the nature of the guest molecule.

  14. Adsorption, Dissociation, and Dehydrogenation of Water Monomer and Water Dimer on the Smallest 3D Aluminum Particle. The O-H Dissociation Barrier Disappears for the Dimer.

    PubMed

    Moc, Jerzy

    2016-11-03

    We present a detailed mechanistic study on the interaction and reaction of water monomer and water dimer with the smallest 3D aluminum particle (Al6) by employing density functional and explicitly correlated coupled cluster CCSD(T)-F12 theories. Water adsorption, dissociation, and dehydrogenation are considered. For the monomer reaction, where core-valence correlation and an extrapolation to the complete basis set limit is allowed for, our coupled cluster calculations predict the O-H dissociation barrier of about 2 kcal/mol. For the dimer reaction, two distinct reaction paths are identified, initiated by forming separate dimer complexes wherein (H2O)2 adsorbs mainly via the oxygen atom of the donor H2O molecule. The key O-H dissociation transition states of the dimer reaction involve a concerted migration of two H atoms resulting in the dissociation of the donor molecule and formation of the OH-water complex adsorbed on the metal cluster's surface. The most remarkable feature of both dimer reaction energy profiles is the lack of the overall energy barrier for the (rate-determining) O-H dissociation. The hydrogen bond acceptor molecule is suggested to have an extra catalytic effect on the O-H dissociation barrier of the hydrogen bond donor molecule by removing this barrier. A similar effect on the dehydrogenation step is indicated.

  15. Controlling the subtle energy balance in protic ionic liquids: dispersion forces compete with hydrogen bonds.

    PubMed

    Fumino, Koichi; Fossog, Verlaine; Stange, Peter; Paschek, Dietmar; Hempelmann, Rolf; Ludwig, Ralf

    2015-02-23

    The properties of ionic liquids are determined by the energy-balance between Coulomb-interaction, hydrogen-bonding, and dispersion forces. Out of a set of protic ionic liquids (PILs), including trialkylammonium cations and methylsulfonate and triflate anions we could detect the transfer from hydrogen-bonding to dispersion-dominated interaction between cation and anion in the PIL [(C6 H13 )3 NH][CF3 SO3 ]. The characteristic vibrational features for both ion-pair species can be detected and assigned in the far-infrared spectra. Our approach gives direct access to the relative strength of hydrogen-bonding and dispersion forces in a Coulomb-dominated system. Dispersion-corrected density functional theory (DFT) calculations support the experimental findings. The dispersion forces could be quantified to contribute about 2.3 kJ mol(-1) per additional methylene group in the alkyl chains of the ammonium cation.

  16. Competitive Hydrogen Atom Migrations Accompanying Cascade Dissociations of Peptide Cation-Radicals of the z(+•) Type.

    PubMed

    Ledvina, Aaron R; Coon, Joshua J; Tureček, František

    2015-02-01

    We report a combined experimental and computational study of energy-resolved collision-induced dissociation (ER-CID) and time-resolved infrared multiphoton dissociation (TR-IRMPD) of z4 ions prepared by electron transfer dissociation of peptide (Ala-Ala-Asn-Ala-Arg + 2H)(2+) ions. The z4 cation-radicals, (•)ANAR(+), undergo competitive dissociations by backbone cleavage and loss of a CONH2 radical from the Asn side chain. The backbone cleavage proceeds by radical-assisted dissociation of the Asn Cα-CO bond, forming an x2 ion intermediate which rapidly dissociates by HNCO elimination to yield a stable z2 fragment ion, (•)AR(+). The ER-CID and TR-IRMPD data were consistent with the consecutive nature of the backbone dissociation but showed different branching ratios for the two major fragmentations. The ER-CID data showed branching ratios 0.6-1.0 for the side-chain and backbone cleavages whereas the TR-IRMPD data showed an earlier onset for the latter dissociation. Computational analysis of the potential energy surface with density functional theory and ab initio calculations was carried out to provide structures and energies for the reactant ions as well as several intermediates, products, and transition states. Dissociation pathways for cis and trans amide conformers were distinguished and their energies were evaluated. The threshold dissociation energies for the backbone and side-chain dissociations were similar in accordance with the experimental ER-CID branching ratio. The TR-IRMPD data were interpreted by different absorbances of intermediates produced by hydrogen atom migrations along the dissociation pathways.

  17. Competitive Hydrogen Atom Migrations Accompanying Cascade Dissociations of Peptide Cation-Radicals of the z+• Type

    PubMed Central

    Ledvina, Aaron R.; Coon, Joshua J.

    2014-01-01

    We report a combined experimental and computational study of energy-resolved collision-induced dissociation (ER-CID) and time-resolved infrared multiphoton dissociation (TR-IRMPD) of z4 ions prepared by electron transfer dissociation of peptide (Ala-Ala-Asn-Ala-Arg + 2H)2+ ions. The z4 cation-radicals, •ANAR+, undergo competitive dissociations by backbone cleavage and loss of a CONH2 radical from the Asn side chain. The backbone cleavage proceeds by radical-assisted dissociation of the Asn Cα—CO bond, forming an x2 ion intermediate which rapidly dissociates by HNCO elimination to yield a stable z2 fragment ion, •AR+. The ER-CID and TR-IRMPD data were consistent with the consecutive nature of the backbone dissociation but showed different branching ratios for the two major fragmentations. The ER-CID data showed branching ratios 0.6-1.0 for the side-chain and backbone cleavages whereas the TR-IRMPD data showed an earlier onset for the latter dissociation. Computational analysis of the potential energy surface with density functional theory and ab initio calculations was carried out to provide structures and energies for the reactant ions as well as several intermediates, products, and transition states. Dissociation pathways for cis and trans amide conformers were distinguished and their energies were evaluated. The threshold dissociation energies for the backbone and side-chain dissociations were similar in accordance with the experimental ER-CID branching ratio. The TR-IRMPD data were interpreted by different absorbances of intermediates produced by hydrogen atom migrations along the dissociation pathways. PMID:25844055

  18. Detection and Characterization of Low Abundance Glycopeptides Via Higher-Energy C-Trap Dissociation and Orbitrap Mass Analysis

    NASA Astrophysics Data System (ADS)

    Hart-Smith, Gene; Raftery, Mark J.

    2012-01-01

    Broad-scale mass spectrometric analyses of glycopeptides are constrained by the considerable complexity inherent to glycoproteomics, and techniques are still being actively developed to address the associated analytical difficulties. Here we apply Orbitrap mass analysis and higher-energy C-trap dissociation (HCD) to facilitate detailed insights into the compositions and heterogeneity of complex mixtures of low abundance glycopeptides. By generating diagnostic oxonium product ions at mass measurement errors of <5 ppm, highly selective glycopeptide precursor ion detections are made at sub-fmol limits of detection: analyses of proteolytic digests of a hen egg glycoprotein mixture detect 88 previously uncharacterized glycopeptides from 666 precursor ions selected for MS/MS, with only one false positive due to co-fragmentation of a non-glycosylated peptide with a glycopeptide. We also demonstrate that by (1) identifying multiple series of glycoforms using high mass accuracy single stage MS spectra, and (2) performing product ion scans at optimized HCD collision energies, the identification of peptide + N-acetylhexosamine (HexNAc) ions (Y1 ions) can be readily achieved at <5 ppm mass measurement errors. These data allow base peptide sequences and glycan compositional information to be attained with high confidence, even for glycopeptides that produce weak precursor ion signals and/or low quality MS/MS spectra. The glycopeptides characterized from low fmol abundances using these methods allow two previously unreported glycosylation sites on the Gallus gallus protein ovoglycoprotein (amino acids 82 and 90) to be confirmed; considerable glycan heterogeneities at amino acid 90 of ovoglycoprotein, and amino acids 34 and 77 of Gallus gallus ovomucoid are also revealed.

  19. Serum lipidomics profiling using LC-MS and high-energy collisional dissociation fragmentation: focus on triglyceride detection and characterization.

    PubMed

    Bird, Susan S; Marur, Vasant R; Sniatynski, Matthew J; Greenberg, Heather K; Kristal, Bruce S

    2011-09-01

    There is a growing need both clinically and experimentally to improve the characterization of blood lipids. A liquid chromatography-mass spectrometry (LC-MS) method, developed for the qualitative and semiquantitative detection of lipids in biological samples and previously validated in mitochondrial samples, was now evaluated for the profiling of serum lipids. Data were acquired using high-resolution, full scan MS and high-energy, collisional dissociation (HCD), all ion fragmentation. The method was designed for efficient separation and detection in both positive and negative ionization mode and evaluated using standards spanning seven lipid classes. Platform performance, related to the identification and characterization of serum triglycerides (TGs), was assessed using extracted ion chromatograms with mass tolerance windows of 5 ppm or less from full scan exact mass measurements determined using SIEVE nondifferential LC-MS analysis software. The platform showed retention time coefficients of variation (CV) of <0.3%, mass accuracy values of <2 ppm error, and peak area CV of <13%, with the majority of that error coming from sample preparation and extraction rather than the LC-MS analysis, and linearity was shown to be over 4 orders of magnitude (r(2) = 0.999) for the standard TG (15:0)(3) spiked into serum. Instrument mass accuracy and precision were critical to the identification of unknown TG species, in part because these parameters enabled us to reduce false positives. In addition to detection and relative quantitation of TGs in serum, TG structures were characterized through the use of alternating HCD scans at different energies to produce diagnostic fragmentations on all ions in the analysis. The lipidomics method was applied to serum samples from 192 rats maintained on diets differing in macronutrient composition. The analysis identified 86 TG species with 81 unique masses that varied over 3.5 orders of magnitude and showed diet-dependency, consistent with

  20. Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time-and Energy-Resolved Surface-Induced Dissociation Studies

    SciTech Connect

    Laskin, Julia

    2006-07-13

    Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM based approach developed in our laboratory. The following threshold energies and activation entropies were determined in this study: E0=1.20 eV and ΔS‡=-20 e.u.1 (MH+→b5); E0=1.14 eV and ΔS‡=-14.7 e.u. (MH+→b4); E0=1.42 eV and ΔS‡=-2.5 e.u. (MH+→b3); E0=1.30 eV and ΔS‡=-4.1 e.u. (MH+→a4); E0=1.37 eV and ΔS‡=-5.2 e.u. (MH+→y ions); E0=1.50 eV and ΔS‡=1.6 e.u. (MH+→internal fragments); E0=1.62 eV and S‡=5.2 e.u. (MH+→F). Comparison with Arrhenius activation energies reported in the literature demonstrated for the first time the reversal of the order of activation energies as compared to threshold energies for dissociation.

  1. Physical and chemical transformations of highly compressed carbon dioxide at bond energies.

    PubMed

    Yoo, Choong-Shik

    2013-06-07

    Carbon dioxide exhibits a richness of high-pressure polymorphs with a great diversity in intermolecular interaction, chemical bonding, and crystal structures. It ranges from typical molecular solids to fully extended covalent solids with crystal structures similar to those of SiO2. These extended solids of carbon dioxide are fundamentally new materials exhibiting interesting optical nonlinearity, low compressibility and high energy density. Furthermore, the large disparity in chemical bonding between the extended network and molecular structures results in a broad metastability domain for these phases to room temperature and almost to ambient pressure and thereby offers enhanced opportunities for novel materials developments. Broadly speaking, these molecular-to-non-molecular transitions occur due to electron delocalization manifested as a rapid increase in electron kinetic energy at high density. The detailed mechanisms, however, are more complex with phase metastabilities, path-dependent phases and phase boundaries, and large lattice strains and structural distortions - all of which are controlled by well beyond thermodynamic constraints to chemical kinetics associated with the governing phases and transitions. As a result, the equilibrium phase boundary is difficult to locate precisely (experimentally or theoretically) and is often obscured by the presence of metastable phases (ordered or disordered). This paper will review the pressure-induced transformations observed in highly compressed carbon dioxide and present chemistry perspectives on those molecular-to-non-molecular transformations that can be applied to other low-Z molecular solids at Mbar pressures where the compression energy rivals the chemical bond energies.

  2. Water aggregation and dissociation on the ZnO(101[combining macron]0) surface.

    PubMed

    Kenmoe, Stephane; Biedermann, P Ulrich

    2017-01-04

    A comprehensive search for stable structures in the low coverage regime (0-1 ML) and at 2 ML and 3 ML using DFT revealed several new aggregation states of water on the non-polar ZnO(101[combining macron]0) surface. Ladder-like structures consisting of half-dissociated dimers, arranged side-by-side along the polar axis, constitute the most stable aggregate at low coverages (≤1 ML) with a binding energy exceeding that of the monolayer. At coverages beyond the monolayer - a regime that has hardly been studied previously - a novel type of structure with a continuous honeycomb-like 2D network of hydrogen bonds was discovered, where each surface oxygen atom is coordinated by additional H-bonding water molecules. This flat double-monolayer has a relatively high adsorption energy, every zinc and oxygen atom is 4-fold coordinated and every hydrogen atom is engaged in a hydrogen bond. Hence this honeycomb double monolayer offers no H-bond donor or acceptor sites for further growth of the water film. At 3 ML coverage, the interface restructures forming a contact layer of half-dissociated water dimers and a liquid-like overlayer of water attached by hydrogen bonds. The structures and their adsorption energies are analysed to understand the driving forces for aggregation and dissociation of water on the surface. We apply a decomposition scheme based on a Born-Haber cycle, discussing difficulties that may occur in applying such an analysis to the adsorption of dissociated molecules and point out alternatives to circumvent the bias against severely stretched bonds. Water aggregation on the ZnO surface is favoured by direct water-water interactions including H-bonds and dipole-dipole interactions and surface- or adsorption-mediated interactions including enhanced water-surface interactions and reduced relaxations of the water molecules and surface. While dissociation of isolated adsorbed molecules is unfavourable, partial or even full dissociation is preferred for aggregates

  3. Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics.

    PubMed

    Tsiatsiani, Liana; Giansanti, Piero; Scheltema, Richard A; van den Toorn, Henk; Overall, Christopher M; Altelaar, A F Maarten; Heck, Albert J R

    2017-02-03

    A key step in shotgun proteomics is the digestion of proteins into peptides amenable for mass spectrometry. Tryptic peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) because the fragmentation rules are well-understood. Here, we investigate LysargiNase, a perfect trypsin mirror protease, because it cleaves equally specific at arginine and lysine residues, albeit at the N-terminal end. LysargiNase peptides are therefore practically tryptic-like in length and sequence except that following ESI, the two protons are now both positioned at the N-terminus. Here, we compare side-by-side the chromatographic separation properties, gas-phase fragmentation characteristics, and (phospho)proteome sequence coverage of tryptic (i.e., (X)nK/R) and LysargiNase (i.e., K/R(X)n) peptides using primarily electron-transfer dissociation (ETD) and, for comparison, HCD. We find that tryptic and LysargiNase peptides fragment nearly as mirror images. For LysargiNase predominantly N-terminal peptide ions (c-ions (ETD) and b-ions (HCD)) are formed, whereas for trypsin, C-terminal fragment ions dominate (z-ions (ETD) and y-ions (HCD)) in a homologous mixture of complementary ions. Especially during ETD, LysargiNase peptides fragment into low-complexity but information-rich sequence ladders. Trypsin and LysargiNase chart distinct parts of the proteome, and therefore, the combined use of these enzymes will benefit a more in-depth and reliable analysis of (phospho)proteomes.

  4. A nearly exact MCSCF+CI calculation of the dissociation energy of OH. [Multiconfiguration, Self-Consistent Field plus Configuration Interaction

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.; Whiting, E. E.; Sharbaugh, L. F.

    1976-01-01

    The dissociation energy and dipole moment of the ground state of OH have been obtained with a newly developed multiconfiguration, self-consistent field plus configuration interaction CDC 7600 computer program. The computed value of the dissociation energy is 4.62 eV, which is within the uncertainty limits for the experimental value of 4.63 plus or minus 0.01 eV. The computed value of the dipole moment is 1.645 D, which is very close to the experimental result of 1.66 plus or minus 0.01 D. The present results are also compared to the data obtained from similar calculations with the BISON-MC computer program developed by Das and Wahl.

  5. A potential-energy surface study of the 2A1 and low-lying dissociative states of the methoxy radical

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Accurate, ab initio quantum chemical techniques are applied in the present study of low lying bound and dissociative states of the methoxy radical at C3nu conformations, using a double zeta quality basis set that is augmented with polarization and diffuse functions. Excitation energy estimates are obtained for vertical excitation, vertical deexcitation, and system origin. The rate of methoxy photolysis is estimated to be too small to warrant its inclusion in atmospheric models.

  6. Full Empirical Potential Curves and Improved Dissociation Energies for the X ^1Σ^+ and a ^1Π States of CH^+

    NASA Astrophysics Data System (ADS)

    Cho, Young-Sang; Le Roy, Robert

    2014-06-01

    CH^+ has been a species of interest since the dawn of molecular astrophysics,and it is an important intermediate in combustion processes. In the domain of `conventional' spectroscopy there have been a number of studies of low v' and v" portions of the A ^1Π-X ^1Σ^+ band system of various isotopologues, and Amano recently reported microwave measurements of the ground-state R(0) lines of 12CH^+, 13CH^+ and 12CD^+. used photodissociation spectroscopy to observe transitions to very high-J' tunneling-predissociation levels (shape resonances) involving v(A)=0-10, for many of which they also measured the photo-fragment kinetic energy release. More recently Hechtfischer et al. used photodissociation spectroscopy of `Feschbach resonance' levels at very high v'(A) and low J' to obtain the first direct measurement of the 12CH^+ dissociation energy with near-spectroscopic accuracy (± 1.1 cm-1). However, to date, all analyses of the data for this system had been performed using traditional band-constant or Dunham-expansion fits to data for the lowest vibrational levels, and there have been no attempts to combine the `conventional' low-v data with the high-J' and high-v' photodissociation data in a single treatment. The present work has addressed this problem by performing a Direct-Potential-Fit (DPF) analysis that obtains full analytic potential energy functions for the X ^1Σ^+ and A ^1Π states of CH^+ that are able to account for all of the available data (on average) within their uncertainties. A.E. Douglas and G. Herzberg, Astrophys. J. 94, 381 (1941). T. Amano, Astrophys. J. Lett. {716}, L1 (2010) H. Helm, P.C. Crosby, M.M. Graff and J.T. Mosley, Phys. Rev. A 25, 304 (1982) U. Hechtfischer and C. J. Williams, M. Lange, J. Linkemann, D. Schwalm, R. Wester, A. Wolf and D. Zajfman, J.Chem.Phys. 117, 8754 (2002). H.S.P. Müller, Astron. Astrophys. 514, L7 (2010)

  7. Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment.

    PubMed

    Liu, Wei; Tan, Zhenyu; Zhang, Liming; Champion, Christophe

    2017-03-01

    In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40-70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20-40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A-T.

  8. Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

    PubMed

    Uddin, M; Coombe, D

    2014-03-20

    Molecular dynamics simulations of gas hydrate dissociation comparing the behavior of CH4 and CO2 hydrates are presented. These simulations were based on a structurally correct theoretical gas hydrate crystal, coexisting with water. The MD system was first initialized and stabilized via a thorough energy minimization, constant volume-temperature ensemble and constant volume-energy ensemble simulations before proceeding to constant pressure-temperature simulations for targeted dissociation pressure and temperature responses. Gas bubble evolution mechanisms are demonstrated as well as key investigative properties such as system volume, density, energy, mean square displacements of the guest molecules, radial distribution functions, H2O order parameter, and statistics of hydrogen bonds. These simulations have established the essential similarities between CH4 and CO2 hydrate dissociation. The limiting behaviors at lower temperature (no dissociation) and higher temperature (complete melting and formation of a gas bubble) have been illustrated for both hydrates. Due to the shift in the known hydrate stability curves between guest molecules caused by the choice of water model as noted by other authors, the intermediate behavior (e.g., 260 K) showed distinct differences however. Also, because of the more hydrogen-bonding capability of CO2 in water, as reflected in its molecular parameters, higher solubility of dissociated CO2 in water was observed with a consequence of a smaller size of gas bubble formation. Additionally, a novel method for analyzing hydrate dissociation based on H-bond breakage has been proposed and used to quantify the dissociation behaviors of both CH4 and CO2 hydrates. Activation energies Ea values from our MD studies were obtained and evaluated against several other published laboratory and MD values. Intrinsic rate constants were estimated and upscaled. A kinetic reaction model consistent with macroscale fitted kinetic models has been proposed to

  9. Comparison of laser-induced dissociation and high-energy collision-induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification.

    PubMed

    Macht, Marcus; Asperger, Arndt; Deininger, Sören-Oliver

    2004-01-01

    The fragmentation of peptides under laser-induced dissociation (LID) as well as high-energy collision-induced dissociation (CID) conditions has been investigated. The effect of the different fragmentation mechanisms on the formation of specific fragment ion types and the usability of the resulting spectra, e.g. for high-throughput protein identification, has been evaluated. Also, basic investigations on the influence of the matrix, as well as laser fluence, on the fragment ion formation and the consequences in the spectral appearance are discussed. The preconditions for obtaining 'pure' CID spectra on matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) instruments are evaluated and discussed as well as the differences between LID and CID in the resulting fragment ion types. While containing a wealth of information due to additional fragment ions in comparison with LID, CID spectra are significantly more complex than LID spectra and, due to different fragmentation patterns, the CID spectra are of limited use for protein identification, even under optimized parameter settings, due to significantly lower scores for the individual spectra. Conditions for optimal results regarding protein identification using MALDI-TOF/TOF instruments have been evaluated. For database searches using tandem mass spectrometric data, the use of LID as fragmentation technique in combination with parameter settings supporting the use of internal fragment ions turned out to yield the optimal results.

  10. PREDICTION OF BOND DISSOCIATION ENERGIES AND TRANSITION STATE BARRIERS BY A MODIFIED COMPLETE BASIS SET MODEL CHEMISTRY. (R824970)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  11. Description of molecular dynamics in intense laser fields by the time-dependent adiabatic state approach: application to simultaneous two-bond dissociation of CO2 and its control.

    PubMed

    Sato, Yukio; Kono, Hirohiko; Koseki, Shiro; Fujimura, Yuichi

    2003-07-02

    We theoretically investigated the dynamics of structural deformations of CO(2) and its cations in near-infrared intense laser fields (approximately 10(15) W cm(-2)) by using the time-dependent adiabatic state approach. To obtain "field-following" adiabatic potentials for nuclear dynamics, the electronic Hamiltonian including the interaction with the instantaneous laser electric field is diagonalized by the multiconfiguration self-consistent-field molecular orbital method. In the CO(2) and CO(2+) stages, ionization occurs before the field intensity becomes high enough to deform the molecule. In the CO(2)(2+) stage, simultaneous symmetric two-bond stretching occurs as well as one-bond stretching. Two-bond stretching is induced by an intense field in the lowest time-dependent adiabatic state |1> of CO(2)(2+), and this two-bond stretching is followed by the occurrence of a large-amplitude bending motion mainly in the second-lowest adiabatic state |2> nonadiabatically created at large internuclear distances by the field from |1>. It is concluded that the experimentally observed stretched and bent structure of CO(2)(3+) just before Coulomb explosions originates from the structural deformation of CO(2)(2+). We also show in this report that the concept of "optical-cycle-averaged potential" is useful for designing schemes to control molecular (reaction) dynamics, such as dissociation dynamics of CO(2), in intense fields. The present approach is simple but has wide applicability for analysis and prediction of electronic and nuclear dynamics of polyatomic molecules in intense laser fields.

  12. Full-dimensional quantum calculations of the dissociation energy, zero-point, and 10 K properties of H7+/D7+ clusters using an ab initio potential energy surface.

    PubMed

    Barragán, Patricia; Pérez de Tudela, Ricardo; Qu, Chen; Prosmiti, Rita; Bowman, Joel M

    2013-07-14

    Diffusion Monte Carlo (DMC) and path-integral Monte Carlo computations of the vibrational ground state and 10 K equilibrium state properties of the H7 (+)/D7 (+) cations are presented, using an ab initio full-dimensional potential energy surface. The DMC zero-point energies of dissociated fragments H5 (+)(D5 (+))+H2(D2) are also calculated and from these results and the electronic dissociation energy, dissociation energies, D0, of 752 ± 15 and 980 ± 14 cm(-1) are reported for H7 (+) and D7 (+), respectively. Due to the known error in the electronic dissociation energy of the potential surface, these quantities are underestimated by roughly 65 cm(-1). These values are rigorously determined for first time, and compared with previous theoretical estimates from electronic structure calculations using standard harmonic analysis, and available experimental measurements. Probability density distributions are also computed for the ground vibrational and 10 K state of H7 (+) and D7 (+). These are qualitatively described as a central H3 (+)/D3 (+) core surrounded by "solvent" H2/D2 molecules that nearly freely rotate.

  13. Comparison of high- and low-energy collision-induced dissociation tandem mass spectrometry in the analysis of glycoalkaloids and their aglycons.

    PubMed

    Claeys, M; Van den Heuvel, H; Chen, S; Derrick, P J; Mellon, F A; Price, K R

    1996-02-01

    Four aglycons (tomatidine, demissidine, solanidine, and solasodine) and three glycoalkaloids (α-tomatine, α-chaconine, and α-solanine) have been analyzed by positive ion liquid secondary ion high-energy and low-energy collision-induced dissociation (CID) tandem mass Spectrometry, performed on a four-sector (EBEB) and a hybrid (EBQQ) instrument, respectively. Both high- and low-energy collision-induced dissociation mass spectra of [M+H](+) ions of these compounds provided structural information that aided the characterization of the different aglycons and of the carbohydrate sequence and linkage sites in the glycoalkaloids. Low-energy CID favors charge-driven fragmentation of the aglycon rings, whilst high-energy CID spectra are more complex and contain additional ions that appear to result from charge-remote fragmentations, multiple cleavages, or complex charge-driven rearrangements. With respect to the structural characterization of the carbohydrate part, low-energy CID fragmentations of sugar residues in the glycoalkaloids generate Y n (+) ions and some low intensity Z n (+) ions; the high-energy spectra also exhibit strong (1,5)X n (+) ions, formed by multiple cleavage of the sugar ring, and significant Z n (+) ions.

  14. Appropriate choice of collision-induced dissociation energy for qualitative analysis of notoginsenosides based on liquid chromatography hybrid ion trap time-of-flight mass spectrometry.

    PubMed

    Wang, Guang-Ji; Fu, Han-Xu; Xiao, Jing-Cheng; Ye, Wei; Rao, Tai; Shao, Yu-Hao; Kang, Dian; Xie, Lin; Liang, Yan

    2016-04-01

    Liquid chromatography hybrid ion trap/time-of-flight mass spectrometry possessesd both the MS(n) ability of ion trap and the excellent resolution of a time-of-flight, and has been widely used to identify drug metabolites and determine trace multi-components for in natural products. Collision energy, one of the most important factors in acquiring MS(n) information, could be set freely in the range of 10%-400%. Herein, notoginsenosides were chosen as model compounds to build a novel methodology for the collision energy optimization. Firstly, the fragmental patterns of the representatives for the authentic standards of protopanaxadiol-type and protopanaxatriol-type notoginsenosides authentic standards were obtained based on accurate MS(2) and MS(3) measurements via liquid chromatography hybrid ion trap/time-of-flight mass spectrometry. Then the extracted ion chromatograms of characteristic product ions of notoginsenosides in Panax Notoginseng Extract, which were produced under a series of collision energies and, were compared to screen out the optimum collision energies values for MS(2) and MS(3). The results demonstrated that the qualitative capability of liquid chromatography hybrid ion trap/time-of-flight mass spectrometry was greatly influenced by collision energies, and 50% of MS(2) collision energy was found to produce the highest collision-induced dissociation efficiency for notoginsenosides. BesidesAddtionally, the highest collision-induced dissociation efficiency appeared when the collision energy was set at 75% in the MS(3) stage.

  15. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  16. Dissociation of diatomic gases

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1991-01-01

    The Landau-Zener theory of reactive cross sections has been applied to diatomic molecules dissociating from a ladder of rotational and vibrational states. Although the preexponential factor of the Arrhenius rate expression is shown to be a complex function of the dimensionless activation energy, the average over all states in the ladder is well represented by a single factor that varies about as T exp (-n), where the coefficient n is the order of unity. This relation agrees very well with experimental data for dissociation of O2 and N2, for example. The results validate previous empirical assignment of a single preexponential factor in the Arrhenius expression and justify the extrapolation of the expression well beyond the range of data. The theory is then used to calculate the effect of vibrational nonequilibrium on dissociation rate. For Morse oscillators the results are about the same as for harmonic oscillators, and the dissociation from a ladder of equilibrium rotational and nonequilibrium vibrational states is close to an analytic approximation provided by Hammerling, Kivel, and Teare for harmonic oscillators all dissociating from the ground rotational state.

  17. Paramagnetic-diamagnetic phase transition accompanied by coordination bond formation-dissociation in the dithiolate complex Na[Ni(pdt)2]·2H2O.

    PubMed

    Takaishi, Shinya; Ishihara, Nozomi; Kubo, Kazuya; Katoh, Keiichi; Breedlove, Brian K; Miyasaka, Hitoshi; Yamashita, Masahiro

    2011-07-18

    Bis(2,3-pyrazinedithiolate)nickel complex Na[Ni(pdt)(2)]·2H(2)O formed one-dimensional stacks of the Ni(pdt)(2) units and showed strong antiferromagnetic interactions along the stacking direction. A first-order phase transition between the paramagnetic and diamagnetic states, which was driven by dimerization of the Ni(pdt)(2) units, accompanied by coordination bond formation, was observed.

  18. Dissociative electron attachment studies on acetone

    NASA Astrophysics Data System (ADS)

    Prabhudesai, Vaibhav S.; Tadsare, Vishvesh; Ghosh, Sanat; Gope, Krishnendu; Davis, Daly; Krishnakumar, E.

    2014-10-01

    Dissociative electron attachment (DEA) to acetone is studied in terms of the absolute cross section for various fragment channels in the electron energy range of 0-20 eV. H- is found to be the most dominant fragment followed by O- and OH- with only one resonance peak between 8 and 9 eV. The DEA dynamics is studied by measuring the angular distribution and kinetic energy distribution of fragment anions using Velocity Slice Imaging technique. The kinetic energy and angular distribution of H- and O- fragments suggest a many body break-up for the lone resonance observed. The ab initio calculations show that electron is captured in the multi-centered anti-bonding molecular orbital which would lead to a many body break-up of the resonance.

  19. Dissociative electron attachment studies on acetone

    SciTech Connect

    Prabhudesai, Vaibhav S. Tadsare, Vishvesh; Ghosh, Sanat; Gope, Krishnendu; Davis, Daly; Krishnakumar, E.

    2014-10-28

    Dissociative electron attachment (DEA) to acetone is studied in terms of the absolute cross section for various fragment channels in the electron energy range of 0–20 eV. H{sup −} is found to be the most dominant fragment followed by O{sup −} and OH{sup −} with only one resonance peak between 8 and 9 eV. The DEA dynamics is studied by measuring the angular distribution and kinetic energy distribution of fragment anions using Velocity Slice Imaging technique. The kinetic energy and angular distribution of H{sup −} and O{sup −} fragments suggest a many body break-up for the lone resonance observed. The ab initio calculations show that electron is captured in the multi-centered anti-bonding molecular orbital which would lead to a many body break-up of the resonance.

  20. Generation of peptide radical dications via low-energy collision-induced dissociation of [CuII(terpy)(M + H)].3+ .

    PubMed

    Chu, Ivan K; Lam, Corey N W

    2005-11-01

    The first example of the formation of hydrogen-deficient radical cations of the type [M + H](.2+) is demonstrated to occur through a one-electron-transfer mechanism upon low-energy collision-induced dissociation (CID) of gas-phase triply charged [Cu(II)(terpy)(M + H)](.3+) complex ions (where M is an angiotensin III or enkephalin derivative; terpy = 2,2':6',2''-terpyridine). The collision-induced dissociation of doubly charged [M + H](.2+) radical cations generates similar product ions to those prepared through hot electron capture dissociation (HECD). Isomeric isoleucine and leucine residues were distinguished by observing the mass differences between [z(n) + H](.+) and w(n)(+) ions (having the same residue number, n) of the Xle residues. The product ion spectrum of [z(n) + H](.+) reveals that the w(n)(+) ions are formed possibly from consecutive fragmentations of [z(n) + H](.+) ions. Although only the first few [M + H](.2+) species have been observed using this approach, these hydrogen-deficient radical cations produce fragment ions that have more structure-informative patterns and are very different from those formed during the low-energy tandem mass spectrometry of protonated peptides.

  1. Low-energy electron-induced dissociation in condensed-phase L-cysteine II: a comparative study on anion desorption from chemisorbed and physisorbed films

    NASA Astrophysics Data System (ADS)

    Alizadeh, Elahe; Massey, Sylvain; Sanche, Léon; Rowntree, Paul A.

    2016-04-01

    Due to its multifunctional structure, cysteine is becoming an ideal model molecule for investigating the complex interactions of proteins with metallic surfaces such as gold nanoparticles. We report herein the results of low-energy electron induced degradation of L-cysteine films, chemisorbed on a gold substrate via the thiol group or physisorbed into a clean gold surface. The data were recorded under ultra-high vacuum conditions at room temperature. Anion yields desorbed from these films by the impact of 0.5 to 19 eV electrons provide clear evidence of the efficient decomposition of this amino acid via dissociative electron attachment (i.e., from dissociation of intermediate transient anions located between 5 and 14 eV). The peaks in the desorbed-anion yield functions, associated with DEA, are superimposed on a continuously rising signal attributed to dipolar dissociation. Similar to the results previously observed from physisorbed films, light anionic species, with masses lower than 35 amu, have been detected. In addition, we measured for first time fragments at 14 amu (CH2-) and 15 amu (CH3-) desorbing from physisorbed films, as well as heavier fragments of mass 45 and 46 amu desorbing from chemisorbed films. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic, B. Sivaraman.

  2. Low-energy dissociative electron attachment to CH2Br2, CHClBr2, and CCl3Br: Intermediate lifetimes and decay energetics

    NASA Astrophysics Data System (ADS)

    Parthasarathy, R.; Finch, C. D.; Wolfgang, J.; Nordlander, P.; Dunning, F. B.

    1998-11-01

    Dissociative electron attachment to the brominated methanes CH2Br2, CHClBr2, and CCl3Br is investigated by measuring the velocity and angular distributions of negative ions produced through electron transfer in collisions with velocity selected K(np) Rydberg atoms. The data are analyzed with the aid of a Monte Carlo collision code that models the detailed kinematics of the reactions. Measurements with CH2Br2 show that essentially all the excess energy of reaction appears in translation, indicating that the electron is captured directly into an antibonding orbital. Data for CHClBr2 show that reaction proceeds by two channels: in the first, essentially all the excess energy appears in translation; in the second, limited conversion of the excess energy to internal motions occurs, pointing to a CHClBr2-* intermediate lifetime of ˜0.1 to 1 ps. In the case of CCl3Br, electron transfer leads to the formation of both Br- and Cl- ions. Br- production is again associated with two channels: in one, essentially all the excess energy appears in translation; in the other, near statistical redistribution of the excess energy occurs prior to dissociation, pointing to a relatively long-lived (τ˜several ps) CCl3Br-* intermediate. Data for Cl- production suggest only limited energy transfer to internal motions. Possible reaction mechanisms for the various channels are discussed with the aid of ab initio calculations.

  3. Calculation of rate constants for dissociative attachment of low-energy electrons to hydrogen halides HCl, HBr, and HI and their deuterated analogs

    SciTech Connect

    Houfek, Karel; Cizek, Martin; Horacek, Jiri

    2002-12-01

    Calculations of rate constants for the process of dissociative attachment of low-energy electrons to hydrogen halides HCl, HBr, and HI and for the reverse process of associative detachment based on the nonlocal resonance model are reported. The calculated data are of importance for the modeling of plasma processes, environmental chemistry, etc. The calculated dissociative attachment rate constants are found to be in good agreement with existing experimental data. It is shown that at low temperatures the rate constants are very sensitive to small changes of the parameters of the nonlocal resonance model used for the calculation of the rate constants and represent a severe test of the theory. The isotopic effect and its dependence on the temperature is also discussed. The calculations of rate constants for the reverse process of associative detachment are also reported and discussed.

  4. Dissociation of {sup 10}C nuclei in a track nuclear emulsion at an energy of 1.2 GeV per nucleon

    SciTech Connect

    Mamatkulov, K. Z.; Kattabekov, R. R.; Alikulov, S. S.; Artemenkov, D. A.; Bekmirzaev, R. N.; Bradnova, V.; Zarubin, P. I. Zarubina, I. G.; Kondratieva, N. V.; Kornegrutsa, N. K.; Krivenkov, D. O.; Malakhov, A. I.; Olimov, K.; Peresadko, N. G.; Polukhina, N. G.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.; Kharlamov, S. P.

    2013-10-15

    The charge topology in the fragmentation of {sup 10}C nuclei in a track nuclear emulsion at an energy of 1.2 GeV per nucleon is studied. In the coherent dissociation of {sup 10}C nuclei, about 82% of events are associated with the channel {sup 10}C {yields} 2{alpha}+ 2p. The angular distributions and correlations of product fragments are presented for this channel. It is found that among {sup 10}C {yields} 2{alpha}+ 2p events, about 30% are associated with the process in which dissociation through the ground state of the unstable {sup 9}Be{sub g.s.} nucleus is followed by {sup 8}Be{sub g.s.} + p decays.

  5. Photofragment translational spectroscopy of three body dissociations and free radicals

    SciTech Connect

    North, Simon William

    1995-04-01

    This dissertation describes several three-body dissociations and the photodissociation of methyl radicals studied using photofragment translational spectroscopy. The first chapter provides an introduction to three body dissociation, examines current experimental methodology, and includes a discussion on the treatment of photofragment translational spectroscopy data arising from three-body fragmentation. The ultraviolet photodissociation of azomethane into two methyl radicals and nitrogen is discussed in chapter 2. Chapter 3 describes the photodissociation of acetone at 248 nm and 193 nm. At 248 nm the translational energy release from the initial C-C bond cleavage matches the exit barrier height and a comparison with results at 266 nm suggests that T> is invariant to the available energy. A fraction of the nascent CH3CO radicals spontaneously dissociate following rotational averaging. The T> for the second C-C bond cleavage also matches the exit barrier height. At 193 nm the experimental data can be successfully fit assuming that the dynamics are analogous to those at 248 nm. A simplified model of energy partitioning which adequately describes the experimental results is discussed. Experiments on acetyl halides provide additional evidence to support the proposed acetone dissociation mechanism. A value of 17.0±1.0 kcal/mole for the barrier height, CH3CO decomposition has been determined. The photodissociation of methyl radical at 193 nm and 212.8 nm is discussed in the chapter 5. The formation of CH2(1Al) and H (2S) was the only single photon dissociation pathway observed at both wavelengths.

  6. Energy and density analysis of the H2 molecule from the united atom to dissociation: The 3Σg+ and 3Σu+ states

    NASA Astrophysics Data System (ADS)

    Corongiu, Giorgina; Clementi, Enrico

    2009-11-01

    The first 14 Σ3g+ and the first 15 Σ3u+ states of the H2 molecule are computed with full configuration interaction both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals within the Born-Oppenheimer approximation, following recent studies for the Σ1g+ and Σ1u+ manifolds [Corongiu and Clementi, J. Chem. Phys. 131, 034301 (2009) and J. Phys. Chem. (in press)]. The basis sets utilized are extended and optimized Slater-type functions and spherical Gaussian functions. The states considered correspond to the configurations (1s1nl1) with n from 1 to 5; the internuclear separations sample the distances from 0.01 to 10 000 bohrs. For the first three Σ3g+ and Σ3u+ states and for the fourth and fifth Σ3g+ states, our computed energies at the equilibrium internuclear separation, when compared to the accurate values by Staszewska and Wolniewicz and by Kołos and Rychlewski, show deviations of about 0.006 kcal/mol, a test on the quality of our computations. Motivation for this work comes not only from obtaining potential energy curves for the high excited states of H2 but also from characterizing the electronic density evolution from the united atom to dissociation to provide a detailed analysis of the energy contributions from selected basis subsets and to quantitatively decompose the state energies into covalent and ionic components. Furthermore, we discuss the origin of the seemingly irregular patterns in potential energy curves in the two manifolds, between 4 and 6-9 bohrs—there are two systems of states: the first, from the united atom to about 4 bohrs, is represented by functions with principal quantum number higher than the one needed at dissociation; this system interacts at around 4 bohrs with the second system, which is represented by functions with principal quantum number corresponding to one of the dissociation products.

  7. Influence of buried hydrogen-bonding groups within monolayer films on gas-surface energy exchange and accommodation.

    PubMed

    Ferguson, M K; Lohr, J R; Day, B S; Morris, J R

    2004-02-20

    Self-assembled monolayers (SAMs) of carbonyl-containing alkanethiols on gold are employed to explore the influence of hydrogen-bonding interactions on gas-surface energy exchange and accommodation. H-bonding, COOH-terminated SAMs are found to produce more impulsive scattering and less thermal accommodation than non-H-bonding, COOCH3-terminated monolayers. For carbamate-functionalized SAMs of the form Au/S(CH2)16OCONH(CH2)(n-1)CH3, impulsive scattering decreases and accommodation increases as the H-bonding group is positioned farther below the terminal CH3.

  8. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  9. Prediction of Reliable Metal-PH₃ Bond Energies for Ni, Pd, and Pt in the 0 and +2 Oxidation States

    SciTech Connect

    Craciun, Raluca; Vincent, Andrew J.; Shaughnessy, Kevin H.; Dixon, David A.

    2010-06-21

    Phosphine-based catalysts play an important role in many metal-catalyzed carbon-carbon bond formation reactions yet reliable values of their bond energies are not available. We have been studying homogeneous catalysts consisting of a phosphine bonded to a Pt, Pd, or Ni. High level electronic structure calculations at the CCSD(T)/complete basis set level were used to predict the M-PH₃ bond energy (BE) for the 0 and +2 oxidation states for M=Ni, Pd, and Pt. The calculated bond energies can then be used, for example, in the design of new catalyst systems. A wide range of exchange-correlation functionals were also evaluated to assess the performance of density functional theory (DFT) for these important bond energies. None of the DFT functionals were able to predict all of the M-PH3 bond energies to within 5 kcal/mol, and the best functionals were generalized gradient approximation functionals in contrast to the usual hybrid functionals often employed for main group thermochemistry.

  10. Syntheses, photophysical properties, and application of through-bond energy-transfer cassettes for biotechnology.

    PubMed

    Jiao, Guan-Sheng; Thoresen, Lars H; Kim, Taeg Gyum; Haaland, Wade C; Gao, Feng; Topp, Michael R; Hochstrasser, Robin M; Metzker, Michael L; Burgess, Kevin

    2006-10-16

    We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.

  11. Dissociative ionization of the 1-propanol dimer in a supersonic expansion under tunable synchrotron VUV radiation.

    PubMed

    Tao, Yanmin; Hu, Yongjun; Xiao, Weizhan; Guan, Jiwen; Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi

    2016-05-11

    Photoionization and dissociation of the 1-propanol dimer and subsequent fragmentations have been investigated by synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry and theoretical calculations. Besides the protonated monomer cation (C3H7OH)·H(+) (m/z = 61) and Cα-Cβ bond cleavage fragment CH2O·(C3H7OH)H(+) (m/z = 91), the measured mass spectrum at an incident photon energy of 13 eV suggests a new dissociation channel resulting in the formation of the (C3H7OH)·H(+)·(C2H5OH) (m/z = 107) fragment. The appearance energies of the fragments (C3H7OH)·H(+), CH2O·(C3H7OH)H(+) and (C3H7OH)·H(+)·(C2H5OH) are measured at 10.05 ± 0.05 eV, 9.48 ± 0.05 eV, and 12.8 ± 0.1 eV, respectively, by scanning photoionization efficiency (PIE) spectra. The 1-propanol ion fragments as a function of VUV photon energy were interpreted with the aid of theoretical calculations. In addition to O-H and Cα-Cβ bond cleavage, a new dissociation channel related to Cβ-Cγ bond cleavage opens. In this channel, molecular rearrangement (proton transfer and hydrogen transfer after surmounting an energy barrier) gives rise to the generated complex, which then dissociates to produce the mixed propanol/ethanol proton bound cation (C3H7OH)·H(+)·(C2H5OH). This new dissociation channel has not been reported in previous studies of ethanol and acetic acid dimers. The photoionization and dissociation processes of the 1-propanol dimer are described in the photon energy range of 9-15 eV.

  12. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations

    PubMed Central

    König, Gerhard; Brooks, Bernard R.

    2014-01-01

    Background Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. Methods The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. Results We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007 kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04 kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. Conclusions The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. General Significance The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics

  13. Contribution of π-bonds to effective charges, cohesive energy, and force constants of graphene-like compounds

    NASA Astrophysics Data System (ADS)

    Davydov, S. Yu.

    2016-02-01

    For 14 two-dimensional hexagonal compounds IV-IV and III-V, analytical expressions have been obtained using the Harrison bond-orbital method for the contribution from the π-interaction to the polarity of interatomic bonds, the effective atomic and transverse dynamical charges and their dependences on the deformation, as well as to the binding energy, the cohesive energy, and the central and non-central force constants.

  14. A fusion of the closed-shell coupled cluster singles and doubles method and valence-bond theory for bond breaking.

    PubMed

    Small, David W; Head-Gordon, Martin

    2012-09-21

    Closed-shell coupled cluster singles and doubles (CCSD) is among the most important of electronic-structure methods. However, it fails qualitatively when applied to molecular systems with more than two strongly correlated electrons, such as those with stretched or broken covalent bonds. We show that it is possible to modify the doubles amplitudes to obtain a closed-shell CCSD method that retains the computational cost and desirable features of standard closed-shell CCSD, e.g., correct spin symmetry, size extensivity, orbital invariance, etc., but produces greatly improved energies upon bond dissociation of multiple electron pairs; indeed, under certain conditions the dissociation energies are exact.

  15. Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV)

    SciTech Connect

    Francés-Monerris, Antonio; Segarra-Martí, Javier; Merchán, Manuela; Roca-Sanjuán, Daniel

    2015-12-07

    Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N–H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N–H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π{sub 1}{sup −} and π{sub 2}{sup −} states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

  16. Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV)

    NASA Astrophysics Data System (ADS)

    Francés-Monerris, Antonio; Segarra-Martí, Javier; Merchán, Manuela; Roca-Sanjuán, Daniel

    2015-12-01

    Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1- and π2- states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

  17. Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV).

    PubMed

    Francés-Monerris, Antonio; Segarra-Martí, Javier; Merchán, Manuela; Roca-Sanjuán, Daniel

    2015-12-07

    Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1 (-) and π2 (-) states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.

  18. Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding.

    PubMed

    Brinck, Tore; Carlqvist, Peter; Stenlid, Joakim H

    2016-12-22

    A new local property, the local electron attachment energy [E(r)], is introduced and is demonstrated to be a useful guide to predict intermolecular interactions and chemical reactivity. The E(r) is analogous to the average local ionization energy but indicates susceptibility toward interactions with nucleophiles rather than electrophiles. The functional form E(r) is motivated based on Janak's theorem and the piecewise linear energy dependence of electron addition to atomic and molecular systems. Within the generalized Kohn-Sham method (GKS-DFT), only the virtual orbitals with negative eigenvalues contribute to E(r). In the present study, E(r) has been computed from orbitals obtained from GKS-DFT computations with a hybrid exchange-correlation functional. It is shown that E(r) computed on a molecular isodensity surface, ES(r), reflects the regioselectivity and relative reactivity for nucleophilic aromatic substitution, nucleophilic addition to activated double bonds, and formation of halogen bonds. Good to excellent correlations between experimental or theoretical measures of interaction strengths and minima in ES(r) (ES,min) are demonstrated.

  19. Ab initio studies of isomerization and dissociation reactions of peroxyacetyl nitrate (PAN)

    NASA Astrophysics Data System (ADS)

    Wei, Wen-Mei; Tan, Wei; Zheng, Ren-Hui; He, Tian-Jing; Chen, Dong-Ming; Liu, Fan-Chen

    2005-06-01

    The complex potential energy surface for the unimolecular isomerization and decomposition of peroxyacetyl nitrate (PAN, CH3C(O)OONO2), including 11 isomers, 45 interconversion transition states and 18 major dissociation products, is probed theoretically at the G2MP2//B3LYP/6-311G(2d,2p) level of theory. The geometries and relative energies for various stationary points are determined. Based on the calculated G2MP2 potential energy surface, the possible unimolecular decomposition mechanism of PAN is proposed. It is shown that the most feasible decomposition channels of PAN are those leading to 2CH3C(O)OO + NO2, 2CH3C(O)O + 2NO3, and 2CH3 + CO2 + 2NO3, respectively. Among them, the formations of the products of the first two channels are produced by the homolytic O-N and O-O bond ruptures of PAN with the bond dissociation energies of 32.3 and 33.9 kcal/mol, respectively, while the last one is initiated by the concerted C-C and O-O bond fissions via a barrier of 36.5 kcal/mol. Our results suggest that besides the first two decomposition pathways which have been reported by the literature, the last concerted bond fission dissociation channel via a well-defined transition state is also feasible, which has been confirmed by using CBS-Q and CBS-QB3 methods. Therefore, PAN dissociation occurs mainly via the homolytic O-N or O-O bond ruptures or via the concerted C-C and O-O bond fissions while the first channel is more favorable than the last two channels.

  20. Quasiclassical trajectory study of the collision-induced dissociation dynamics of Ar + CH3SH+ using an ab initio interpolated potential energy surface.

    PubMed

    Martínez-Núñez, Emilio; Vázquez, Saulo A; Aoiz, F Javier; Castillo, Jesús F

    2006-02-02

    Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential energy surface includes seven accessible dissociation channels of the cation. The present QCT calculations show that migration of hydrogen atoms, leading to the rearrangement CH(3)SH(+) <--> CH(2)SH(2)(+), is significant at the collision energies considered (6.5-34.7 eV) and that the formation of CH(3)(+), CH(3)S(+), and CH(2)(+) cations takes place primarily by a "shattering" mechanism in which the products are formed just after the collision. The theoretical product abundances are found to be in qualitative agreement with the experimental data. However, at high collision energies, the calculated total cross sections for the formation of CH(3)(+) and CH(2)SH(+) cations are noticeably larger than the experimental determinations. Several features of the dynamics of the CID processes are discussed.

  1. Comparison of DFT with Traditional Methods for the Calculation of Vibrational Frequencies and Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Arnold, James O. (Technical Monitor)

    1997-01-01

    The vibrational frequencies of MO2 are computed at many levels of theory, including HF, B3LYP, BP86, CASSCF, MP2, and CCSD(T). The computed results are compared with the available experimental results. Most of the methods fail for at least one state of the systems considered. The accuracy of the results and the origin of the observed failures are discussed. The B3LYP bond energies are compared with traditional methods for a variety of systems, ranging from FeCOn+ to SiCln and its positive ions. The cases where B3LYP differs from the traditional methods are discussed.

  2. Scapholunate Dissociation.

    PubMed

    Ramponi, Denise; McSwigan, Tara

    2016-01-01

    Wrist injuries are a common complaint in the emergency setting. Any disruption of the anatomy of the carpal bones can impair hand function, leading to pain, weakness, and complications. One of the most common forms of carpal bone instability is scapholunate dissociation. This injury can lead to significant morbidity including avascular necrosis, impaired healing, limited function, and arthritis. These diagnostic findings may be subtle, thus identifying high-risk mechanisms of injury, and clinical manifestations will assist the emergency practitioner with early diagnosis and treatment of this high-risk injury.

  3. Evaluating interaction energies of weakly bonded systems using the Buckingham-Hirshfeld method

    SciTech Connect

    Krishtal, A.; Van Alsenoy, C.; Geerlings, P.

    2014-05-14

    We present the finalized Buckingham-Hirshfeld method (BHD-DFT) for the evaluation of interaction energies of non-bonded dimers with Density Functional Theory (DFT). In the method, dispersion energies are evaluated from static multipole polarizabilities, obtained on-the-fly from Coupled Perturbed Kohn-Sham calculations and partitioned into diatomic contributions using the iterative Hirshfeld partitioning method. The dispersion energy expression is distributed over four atoms and has therefore a higher delocalized character compared to the standard pairwise expressions. Additionally, full multipolar polarizability tensors are used as opposed to effective polarizabilities, allowing to retain the anisotropic character at no additional computational cost. A density dependent damping function for the BLYP, PBE, BP86, B3LYP, and PBE0 functionals has been implemented, containing two global parameters which were fitted to interaction energies and geometries of a selected number of dimers using a bi-variate RMS fit. The method is benchmarked against the S22 and S66 data sets for equilibrium geometries and the S22x5 and S66x8 data sets for interaction energies around the equilibrium geometry. Best results are achieved using the B3LYP functional with mean average deviation values of 0.30 and 0.24 kcal/mol for the S22 and S66 data sets, respectively. This situates the BHD-DFT method among the best performing dispersion inclusive DFT methods. Effect of counterpoise correction on DFT energies is discussed.

  4. Dissociation of gaseous zwitterion glycine-betaine by slow electrons

    NASA Astrophysics Data System (ADS)

    Kopyra, J.; Abdoul-Carime, H.

    2010-05-01

    In this work, we investigate dissociation processes induced by low-energy electrons to gas phase N,N,N-trimethylglycine [glycine-betaine, (CH3)3N+CH2COO-] molecules. Glycine-betaine represents a model system for zwitterions. All negative fragments are observed to be produced only at subelectronic excitation energies (<4 eV). With the exception of the loss of a neutral H atom that could arise from any CH bond breaking, we tentatively suggest that the zwitterion dissociates exclusively from the fragmentation of the cation site of the molecule, subsequent to the attachment of the excess electron. Within the context of radiation induced damage to biological systems, the present findings contribute to a more complete description of the fragmentation mechanism occurring to amino acids, peptides, and proteins since they adopt usually a zwitterion structure.

  5. A shock-tube determination of the CN ground state dissociation energy and electronic transition moments for the CN violet and red band systems

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.; Nicholls, R. W.

    1973-01-01

    The CN ground state dissociation energy and the sum of squares of the electronic transition moments of the CN violet bands have been simultaneously determined from spectral emission measurements behind incident shock waves. The unshocked test gases were composed of various CO2-CO-N2-Ar mixtures, and the temperatures behind the incident shocks ranged from 3500 to 8000 K. The variation of the electronic transition moment with internuclear separation was found to be small for both the CN violet and red band systems.

  6. AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes.

    PubMed

    Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

    2008-07-01

    In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

  7. Energy and density analyses of the 1Sigma(u)+ states in the H2 molecule from the united atom to dissociation.

    PubMed

    Corongiu, Giorgina; Clementi, Enrico

    2009-12-31

    The 1Sigma(u)+ excited states of the H2 molecule are computed following a recent study by Corongiu and Clementi (J. Chem. Phys. 2009, 131, 034301) on the 1Sigma(g)+ states. Full configuration interaction computations both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals are presented and correlated with a comprehensive analysis. The basis sets utilized are either extended and optimized Slater type functions, STO, or spherical Gaussian functions, GTO. Computations and analyses are presented for states 1 to 14, covering the internuclear distances from 0.01 to 10000 bohr. The accurate data by L. Wolniewicz and collaborators, available for the first six excited states, verify the good quality of our computations. We focus on the characterization of the orbitals in the excited state wave functions, on the electronic density evolution from the united atom to dissociation, on quantitative decomposition of the total energy into covalent and ionic components and on detailed analyses of energy contributions to the total state energy from selected STO subsets. Each manifold has one state, specifically the states 1, 3 and 6, where the second minimum has strong ionic character. State 10 dissociates into the ion pair H+H-.

  8. Energy and Density Analyses of the 1Σu+ States in the H2 Molecule from the United Atom to Dissociation

    NASA Astrophysics Data System (ADS)

    Corongiu, Giorgina; Clementi, Enrico

    2009-07-01

    The 1Σu+ excited states of the H2 molecule are computed following a recent study by Corongiu and Clementi (J. Chem. Phys. 2009, 131, 034301) on the 1Σg+ states. Full configuration interaction computations both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals are presented and correlated with a comprehensive analysis. The basis sets utilized are either extended and optimized Slater type functions, STO, or spherical Gaussian functions, GTO. Computations and analyses are presented for states 1 to 14, covering the internuclear distances from 0.01 to 10000 bohr. The accurate data by L. Wolniewicz and collaborators, available for the first six excited states, verify the good quality of our computations. We focus on the characterization of the orbitals in the excited state wave functions, on the electronic density evolution from the united atom to dissociation, on quantitative decomposition of the total energy into covalent and ionic components and on detailed analyses of energy contributions to the total state energy from selected STO subsets. Each manifold has one state, specifically the states 1, 3 and 6, where the second minimum has strong ionic character. State 10 dissociates into the ion pair H+H-.

  9. Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

    PubMed

    Bellucci, Michael A; Coker, David F

    2011-07-28

    We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent.

  10. Dynamics of chemical bonding mapped by energy-resolved 4D electron microscopy.

    PubMed

    Carbone, Fabrizio; Kwon, Oh-Hoon; Zewail, Ahmed H

    2009-07-10

    Chemical bonding dynamics are fundamental to the understanding of properties and behavior of materials and molecules. Here, we demonstrate the potential of time-resolved, femtosecond electron energy loss spectroscopy (EELS) for mapping electronic structural changes in the course of nuclear motions. For graphite, it is found that changes of milli-electron volts in the energy range of up to 50 electron volts reveal the compression and expansion of layers on the subpicometer scale (for surface and bulk atoms). These nonequilibrium structural features are correlated with the direction of change from sp2 [two-dimensional (2D) graphene] to sp3 (3D-diamond) electronic hybridization, and the results are compared with theoretical charge-density calculations. The reported femtosecond time resolution of four-dimensional (4D) electron microscopy represents an advance of 10 orders of magnitude over that of conventional EELS methods.

  11. Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

    PubMed

    Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

    2016-11-29

    Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.

  12. Towards simple orbital-dependent density functionals for molecular dissociation

    NASA Astrophysics Data System (ADS)

    Zhang, Igor Ying; Richter, Patrick; Scheffler, Matthias

    2015-03-01

    Density functional theory (DFT) is one of the leading first-principles electronic-structure theories. However, molecular dissociation remains a challenge, because it requires a well-balanced description of the drastically different electronic structure at different bond lengths. One typical and well-documented case is the dissociation of both H2+ and H2, for which all popular DFT functionals fail. We start from the Bethe-Goldstone equation to propose a simple orbital-dependent correlation functional which generalizes the linear adiabatic connection approach. The resulting scheme is based on second-order perturbation theory (PT2), but includes the self-consistent coupling of electron-hole pairs, which ensures the correct H2 dissociation limit and gives a finite correlation energy for systems with a (near)-degenerate energy gap. This coupling PT2-like (CPT2) approximation delivers a significant improvement over all existing functionals for both H2 and H2+ dissociation. We will demonstrate the reason for this improvement analytically for H2 in a minimal basis.

  13. Seniority number description of potential energy surfaces: Symmetric dissociation of water, N{sub 2}, C{sub 2}, and Be{sub 2}

    SciTech Connect

    Bytautas, Laimutis; Scuseria, Gustavo E.; Ruedenberg, Klaus

    2015-09-07

    The present study further explores the concept of the seniority number (Ω) by examining different configuration interaction (CI) truncation strategies in generating compact wave functions in a systematic way. While the role of Ω in addressing static (strong) correlation problem has been addressed in numerous previous studies, the usefulness of seniority number in describing weak (dynamic) correlation has not been investigated in a systematic way. Thus, the overall objective in the present work is to investigate the role of Ω in addressing also dynamic electron correlation in addition to the static correlation. Two systematic CI truncation strategies are compared beyond minimal basis sets and full valence active spaces. One approach is based on the seniority number (defined as the total number of singly occupied orbitals in a determinant) and another is based on an excitation-level limitation. In addition, molecular orbitals are energy-optimized using multiconfigurational-self-consistent-field procedure for all these wave functions. The test cases include the symmetric dissociation of water (6-31G), N{sub 2} (6-31G), C{sub 2} (6-31G), and Be{sub 2} (cc-pVTZ). We find that the potential energy profile for H{sub 2}O dissociation can be reasonably well described using only the Ω = 0 sector of the CI wave function. For the Be{sub 2} case, we show that the full CI potential energy curve (cc-pVTZ) is almost exactly reproduced using either Ω-based (including configurations having up to Ω = 2 in the virtual-orbital-space) or excitation-based (up to single-plus-double-substitutions) selection methods, both out of a full-valence-reference function. Finally, in dissociation cases of N{sub 2} and C{sub 2}, we shall also consider novel hybrid wave functions obtained by a union of a set of CI configurations representing the full valence space and a set of CI configurations where seniority-number restriction is imposed for a complete set (full-valence-space and virtual) of

  14. TiCl, TiH and TiH+ Bond Energies, a Test of a Correlation Consistent Ti Basis Set

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1999-01-01

    Correlation consistent basis sets are developed for Ti atom. The polarization functions are optimized for the average of the 3F and 5F states. One series of correlation consistent basis sets is for 3d and 4s correlation, while the second series includes 3s and 3p correlation as well as 3d and 4s correlation. These basis sets are tested using the Ti 3F-5F separation and the dissociation energies of TiCl X4Phi, TiH X4Phi, and TiH(+) X3Phi. The CCSD(T) complete basis set limit values are determined by extrapolation. The Douglas Kroll approach is used to compute the scalar relativistic effect. Spin-orbit effects are taken from experiment and/or computed at the CASSCF level. The Ti 3F-5F separation is in excellent agreement with experiment, while the TiCl, TiH, and TiH(+) bond energies are in good agreement with experiment. Extrapolation with the valence basis set is consistent with other atoms, while including 3s and 3p correlation appears to make extrapolation.

  15. Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds.

    PubMed

    Madan, B; Lee, B

    1994-08-01

    The free energies of cavity formation in water with and without hydrogen bonding potential were computed from the results of a set of Monte Carlo simulation calculations on pure liquid TIP4P water model and on the same model but with the electrostatic charges turned off (Lennard-Jones liquid). The free energies of cavity formation in the Lennard-Jones liquids are higher than or approximately equal to those in TIP4P water, depending, respectively, on whether the Lennard-Jones size parameter sigma is set equal to 3.15 A, which is the value of sigma for TIP4P water, or to 2.8 A, which is the commonly assumed value for the oxygen-oxygen distance between two hydrogen-bonded water molecules. This result indicates that changes in the hydrogen-bonded structure of water and/or in the orientational degree of freedom of water are not essential features in the production of the large free energy change upon cavity formation.

  16. Dissociation Rates of Diatomic Molecules

    DTIC Science & Technology

    1992-12-01

    relatively simple design that we have used extensively in earlier research; its characteristics were recently described in detail. 10 This source is by...the dominant dissociation background when observing electron- impact dissociation products. This background constitutes the single greatest impediment...a3aF) + o(3P) at 11.385 eV. Photoexcitation studies indeed find that O(1S) and CO(a) are the dominant photodissociation products. 32,33 If the energy

  17. Energy dependent sticking coefficients of trimethylamine on Si(001)-Influence of the datively bonded intermediate state on the adsorption dynamics

    NASA Astrophysics Data System (ADS)

    Lipponer, M. A.; Reutzel, M.; Dürr, M.; Höfer, U.

    2016-11-01

    The adsorption dynamics of the datively bonded trimethylamine (TMA) on Si(001) was investigated by means of molecular beam techniques. The initial sticking probability s0 of TMA on Si(001) was measured as a function of kinetic energy at two different surface temperatures (230 and 550 K). At given surface temperature, s0 was found to decrease with increasing kinetic energy (0.1 to 0.6 eV) indicating a non-activated reaction channel. At increased surface temperature, s0 is reduced due to the onset of desorption into the gas phase. The energy dependence of s0 is compared to the results for the adsorption of tetrahydrofuran (THF) on Si(001), which reacts via a datively bonded intermediate into a covalently bound final state. As s0 follows the same energy dependence both for TMA and THF, the datively bonded intermediate state is concluded to dominate the reaction dynamics in the latter case as well.

  18. Benchmark, DFT assessments, cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes.

    PubMed

    de Oliveira, Paulo McMiller C; Silva, Juliana A B; Longo, Ricardo L

    2017-02-01

    Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields. Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexesᅟ.

  19. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    SciTech Connect

    Finkelstein, Y.; Moreh, R.; Shang, S. L.; Wang, Y.; Liu, Z. K.; Shchur, Ya.

    2016-02-07

    The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH{sub 2}PO{sub 4}, X = K, Cs, Rb, Tl), the DKDP (XD{sub 2}PO{sub 4}, X = K, Cs, Rb) type, and the X{sub 3}H(SO{sub 4}){sub 2} superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M{sub 3}H(SO{sub 4}){sub 2} compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance R{sub OO}, being a measure of the HB strength.

  20. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    NASA Astrophysics Data System (ADS)

    Finkelstein, Y.; Moreh, R.; Shang, S. L.; Shchur, Ya.; Wang, Y.; Liu, Z. K.

    2016-02-01

    The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH2PO4, X = K, Cs, Rb, Tl), the DKDP (XD2PO4, X = K, Cs, Rb) type, and the X3H(SO4)2 superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M3H(SO4)2 compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance ROO, being a measure of the HB strength.

  1. Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors.

    PubMed

    Nguyen, Thanh Ha; Hibbs, David E; Howard, Siân T

    2005-09-01

    The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.

  2. Energy and density analysis of the H2 molecule from the united atom to dissociation: the 3Sigma(g)+ and 3Sigma(u)+ states.

    PubMed

    Corongiu, Giorgina; Clementi, Enrico

    2009-11-14

    The first 14 (3)Sigma(g)(+) and the first 15 (3)Sigma(u)(+) states of the H(2) molecule are computed with full configuration interaction both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals within the Born-Oppenheimer approximation, following recent studies for the (1)Sigma(g)(+) and (1)Sigma(u)(+) manifolds [Corongiu and Clementi, J. Chem. Phys. 131, 034301 (2009) and J. Phys. Chem. (in press)]. The basis sets utilized are extended and optimized Slater-type functions and spherical Gaussian functions. The states considered correspond to the configurations (1s(1)nl(1)) with n from 1 to 5; the internuclear separations sample the distances from 0.01 to 10,000 bohrs. For the first three (3)Sigma(g)(+) and (3)Sigma(u)(+) states and for the fourth and fifth (3)Sigma(g)(+) states, our computed energies at the equilibrium internuclear separation, when compared to the accurate values by Staszewska and Wolniewicz and by Kołos and Rychlewski, show deviations of about 0.006 kcal/mol, a test on the quality of our computations. Motivation for this work comes not only from obtaining potential energy curves for the high excited states of H(2) but also from characterizing the electronic density evolution from the united atom to dissociation to provide a detailed analysis of the energy contributions from selected basis subsets and to quantitatively decompose the state energies into covalent and ionic components. Furthermore, we discuss the origin of the seemingly irregular patterns in potential energy curves in the two manifolds, between 4 and 6-9 bohrs--there are two systems of states: the first, from the united atom to about 4 bohrs, is represented by functions with principal quantum number higher than the one needed at dissociation; this system interacts at around 4 bohrs with the second system, which is represented by functions with principal quantum number corresponding to one of the dissociation products.

  3. Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: first-principles free energy and entropy calculations.

    PubMed

    Maurer, Patrick; Iftimie, Radu

    2010-02-21

    We introduce a novel approach to compute dissociation free energy and entropy values in simulations that employ a density functional theory description of the acidic moiety and of the solvent. The approach consists of utilizing an alchemical transformation of a weak acid A-COOH into the strong acid B-COOH, which makes it practical to employ alchemical free energy perturbation methods in the context of ab initio molecular dynamics simulations. The present alchemical transformation circumvents the need to tackle changes in the total number of electrons and atoms by replacing the chemical residue responsible for the change in acidity with an easily tunable external effective potential. Our investigation demonstrates that (1) a simple but effective class of external potentials that control acidity changes in the acetic/trifluoroacetic acid series can be achieved by replacing the methyl and trifluoromethyl substituents by screened dipoles. Using this dipole-field/quantum-mechanics (DF/QM) approach one can predict gas-phase geometries, proton dissociation energies, total dipole moments, and water binding energies in good agreement with full-QM values. (2) The resulting alchemical perturbation calculations are stable and well converged and allow one to compute absolute pK(a) values whose accuracy is limited primarily by the exchange-correlation functional employed: H-COOH=2.5+/-0.6 (full-QM calculation), 3.7 (exp); F(3)C-COOH=0.4+/-0.6 (DF/QM calculation), 0.5 (exp); H(3)C-COOH=3.1+/-0.7 (DF/QM calculation), 4.7 (exp); 3) Our DF/QM model predicts that the difference in acidity between H-COOH and H(3)C-COOH is dominated by solvent entropy effects, in excellent agreement with experimental observations. The calculated difference between the dissociation energies of these acids is DeltaDelta(d)U=0.0+/-0.26 kcal/mol while the experimental value is 0.0+/-0.1 kcal/mol.

  4. Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation.

    PubMed

    Guan, Ziqiang; Yates, Nathan A; Bakhtiar, Ray

    2003-06-01

    Electron capture dissociation (ECD) and collision-induced dissociation (CID), the two complementary fragmentation techniques, are demonstrated to be effective in the detection and localization of the methionine sulfoxide [Met(O)] residues in peptides using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The presence of Met(O) can be easily recognized in the low-energy CID spectrum showing the characteristic loss of methanesulfenic acid (CH(3)SOH, 64 Da) from the side chain of Met(O). The position of Met(O) can then be localized by ECD which is capable of providing extensive peptide backbone fragmentation without detaching the labile Met(O) side chain. We studied CID and ECD of several Met(O)-containing peptides that included the 44-residue human growth hormone-releasing factor (GRF) and the human atrial natriuretic peptide (ANP). The distinction and complementarity of the two fragmentation techniques were particularly remarkable in their effects on ANP, a disulfide bond-containing peptide. While the predominant fragmentation pathway in CID of ANP was the loss of CH(3)SOH (64 Da) from the molecular ion, ECD of ANP resulted in many sequence-informative products, including those from cleavages within the disulfide-bonded cyclic structure, to allow for the direct localization of Met(O) without the typical procedures for disulfide bond reduction followed by [bond]SH alkylation.

  5. Excited-State N2 Dissociation Pathway on Fe-Functionalized Au.

    PubMed

    Martirez, John Mark P; Carter, Emily A

    2017-03-20

    Localized surface plasmon resonances (LSPRs) offer the possibility of light-activated chemical catalysis on surfaces of strongly plasmonic metal nanoparticles. This technology relies on lower-barrier bond formation and/or dissociation routes made available through energy transfer following the eventual decay of LSPRs. The coupling between these decay processes and a chemical trajectory (nuclear motion, charge-transfer, intersystem crossing, etc.) dictates the availability of these alternative (possibly lower barrier) excited-state channels. The Haber-Bosch method of NH3 synthesis from N2 and H2 is notoriously energy intensive. This is due to the difficulty of N2 dissociation despite the overall reaction being thermodynamically favorable at ambient temperatures and pressures. LSPRs may provide means to improve the kinetics of N2 dissociation via induced resonance electronic excitation. In this work, we calculate, via embedded n-electron valence second-order perturbation theory within the density functional embedding theory, the excited-state potential energy surfaces for dissociation of N2 on an Fe-doped Au(111) surface. This metal alloy may take advantage simultaneously of the strong LSPR of Au and the catalytic activity of Fe toward N2 dissociation. We find the ground-state dissociation activation energy to be 4.74 eV/N2, with Fe as the active site on the surface. Consecutive resonance energy transfers (RETs) may be accessed due to the availability of many electronically excited states with intermediate energies arising from the metal surface that may couple to states induced by the Fe-dopant and the adsorbate molecule, and crossing between excited states may effectively lower the dissociation barrier to 1.33 eV. Our work illustrates that large energetic barriers, prohibitive toward chemical reaction, may be overcome through multiple RETs facilitating an otherwise difficult chemical process.

  6. Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces.

    PubMed

    Pratihar, Subha; Barnes, George L; Hase, William L

    2016-07-07

    There are two components to the review presented here regarding simulations of collisions of protonated peptide ions peptide-H(+) with organic surfaces. One is a detailed description of the classical trajectory chemical dynamics simulation methodology. Different simulation approaches are used, and identified as MM, QM + MM, and QM/MM dependent on the potential energy surface used to represent the peptide-H(+) + surface collision. The second are representative examples of the information that may be obtained from the simulations regarding energy transfer and peptide-H(+) surface-induced dissociation, soft-landing, and reactive-landing for the peptide-H(+) + surface collisions. Good agreement with experiment is obtained for each of these four collision properties. The simulations provide atomistic interpretations of the peptide-H(+) + surface collision dynamics.

  7. High-energy collision induced dissociation fragmentation pathways of peptides, probed using a multiturn tandem time-of-flight mass spectrometer 'MULTUM-TOF/TOF'

    SciTech Connect

    Toyoda, Michisato; Giannakopulos, Anastassios E.; Colburn, Alex W.; Derrick, Peter J.

    2007-07-15

    A new multiturn tandem time-of-flight (TOF) mass spectrometer 'MULTUM-TOF/TOF' has been designed and constructed. It consists of a matrix-assisted laser desorption/ionization ion source, a multiturn TOF mass spectrometer, a collision cell, and a quadratic-field ion mirror. The multiturn TOF mass spectrometer can overcome the problem of precursor ion selection in TOF, due to insufficient time separation between two adjacent TOF peaks, by increasing the number of cycles. As a result, the total TOF increases with the increase in resolving power. The quadratic-field ion mirror allows temporal focusing for fragment ions with different kinetic energies. Product ion spectra from monoisotopically selected precursor ions of angiotensin I, substance P, and bradykinin have been obtained. The fragment ions observed are mainly the result of high-energy collision induced dissociation.

  8. Financing Public Sector Projects with Clean Renewable Energy Bonds; Fact Sheet Series on Financing Renewable Energy Projects, National Renewable Energy Laboratory (NREL)

    SciTech Connect

    Kreycik, C.; Couglin, J.

    2009-12-01

    Clean renewable energy bonds (CREBs) present a low-cost opportunity for public entities to issue bonds to finance renewable energy projects. The federal government lowers the cost of debt by providing a tax credit to the bondholder in lieu of interest payments from the issuer. Because CREBs are theoretically interest free, they may be more attractive than traditional tax-exempt municipal bonds. In February 2009, Congress appropriated a total of $2.4 billion for the "New CREBs" program. No more than one-third of the budget may be allocated to each of the eligible entities: governmental bodies, electric cooperatives, and public power providers. Applications for this round of "New CREBs" were due to the Internal Revenue Service (IRS) on August 4, 2009. There is no indication Congress will extend the CREBs program; thus going forward, only projects that are approved under the 2009 round will be able to issue CREBs. This factsheet explains the CREBs mechanism and provides guidance on procedures related to issuing CREBs.

  9. Threshold collision induced dissociation experiment for azobenzene and its derivatives

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    In this study we investigated protonated azobenzene cation and properties of trans 2,2',6,6'-tetrafluoroazobenzene anion using the collision induced dissociation method and the results are compared with the results from ab initio electronic structure calculations. We measured the bond dissociation energies experimentally and found which theoretical quantum chemistry methods yield best results. Several high accuracy multi-level calculations such as CBS-QB3, G3 and G4 had been carried out to obtain reliable thermochemical information for azobenzene and several of its derivatives and their anion or cation. We also performed other experiments such as Raman spectroscopy to study these light sensitive molecules with promising applications such as photo-switching.

  10. Monte Carlo configuration interaction with perturbation corrections for dissociation energies of first row diatomic molecules: C{sub 2}, N{sub 2}, O{sub 2}, CO, and NO

    SciTech Connect

    Kelly, Thomas P.; Greer, James C.; Perera, Ajith; Bartlett, Rodney J.

    2014-02-28

    Dissociation energies for the diatomic molecules C{sub 2}, N{sub 2}, O{sub 2}, CO, and NO are estimated using the Monte Carlo configuration interaction (MCCI) and augmented by a second order perturbation theory correction. The calculations are performed using the correlation consistent polarized valence “triple zeta” atomic orbital basis and resulting dissociation energies are compared to coupled cluster calculations including up to triple excitations (CCSDT) and Full Configuration Interaction Quantum Monte Carlo (FCIQMC) estimates. It is found that the MCCI method readily describes the correct behavior for dissociation for the diatomics even when capturing only a relatively small fraction (∼80%) of the correlation energy. At this level only a small number of configurations, typically O(10{sup 3}) from a FCI space of dimension O(10{sup 14}), are required to describe dissociation. Including the perturbation correction to the MCCI estimates, the difference in dissociation energies with respect to CCSDT ranges between 1.2 and 3.1 kcal/mol, and the difference when comparing to FCIQMC estimates narrows to between 0.5 and 1.9 kcal/mol. Discussions on MCCI's ability to recover static and dynamic correlations and on the form of correlations in the electronic configuration space are presented.

  11. Bond breaking in a Morse chain under tension: Fragmentation patterns, higher index saddles, and bond healing

    NASA Astrophysics Data System (ADS)

    Mauguière, F. A. L.; Collins, P.; Ezra, G. S.; Wiggins, S.

    2013-04-01

    We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices), and energy of all equilibria for the general n-particle chain, and have highlighted the importance of saddle points with index >1. We show that for an n = 2-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectories passing through a neighborhood of the saddle point using the values of the integrals associated with the normal form. We also generalize our definition of the dividing surface and define an extended dividing surface (EDS), which is used to sample and classify all trajectories that pass through a phase space neighborhood of the index 2 saddle at total energies less than that of the saddle. Classical trajectory simulations are used to study fragmentation patterns for the n = 2 chain under tension. That is, we investigate the relative probability for breaking one bond versus concerted fission of several (two, in this case) bonds. Initial conditions for trajectories are obtained by sampling the EDS at constant energy. We sample trajectories at fixed energies both above and below the energy of the saddle. The fate of trajectories (single versus multiple bond breakage) is explored as a function of the location of the initial condition on the EDS, and a connection made to the work of Chesnavich on collision-induced dissociation. A significant finding is that we can readily identify trajectories that exhibit bond healing. Such trajectories pass outside the nominal (index 1) transition state for single bond dissociation, but return to the potential well region, possibly several times, before ultimately dissociating.

  12. Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides.

    PubMed

    Ledvina, Aaron R; Chung, Thomas W; Hui, Renjie; Coon, Joshua J; Tureček, Frantisek

    2012-08-01

    Dissociations of z(4) ions from pentapeptides AAXAR where X=H, Y, F, W, and V produce dominant z(2) ions that account for >50 % of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z(4) ions proceed by amide trans→cis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable C(β) radical intermediates. These undergo rate-determining cleavage of the C(α)-CO bond at the X residue followed by loss of the neutral AX fragment, forming x(2) intermediates. The latter were detected by energy-resolved resonant excitation collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments. The x(2) intermediates undergo facile loss of HNCO to form z(2) fragment ions, as also confirmed by energy-resolved CID and IRMPD MS(4) experiments. The loss of HNCO from the x(2) ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate.

  13. Cascade Dissociations of Peptide Cation-Radicals. Part2. Infrared Multiphoton Dissociation and Mechanistic Studies of z-Ions from Pentapeptides

    PubMed Central

    Ledvina, Aaron R.; Chung, Thomas W.; Hui, Renjie; Coon, Joshua J.

    2013-01-01

    Dissociations of z4 ions from pentapeptides AAXAR, where X = H, Y, F, W, and V, produce dominant z2 ions that account for >50% of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z4 ions proceed by amide transcis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable Cβ radical intermediates. These undergo rate-determining cleavage of the Cα—CO bond at the X residue followed by loss of the neutral AX fragment, forming x2 intermediates. The latter were detected by energy-resolved resonant excitation collision-activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) experiments. The x2 intermediates undergo facile loss of HNCO to form z2 fragment ions, as also confirmed by energy-resolved CAD and IRMPD MS4 experiments. The loss of HNCO from the x2 ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate. PMID:22669762

  14. Influence of warm air-drying on enamel bond strength and surface free-energy of self-etch adhesives.

    PubMed

    Shiratsuchi, Koji; Tsujimoto, Akimasa; Takamizawa, Toshiki; Furuichi, Tetsuya; Tsubota, Keishi; Kurokawa, Hiroyasu; Miyazaki, Masashi

    2013-08-01

    We examined the effect of warm air-drying on the enamel bond strengths and the surface free-energy of three single-step self-etch adhesives. Bovine mandibular incisors were mounted in self-curing resin and then wet ground with #600 silicon carbide (SiC) paper. The adhesives were applied according to the instructions of the respective manufacturers and then dried in a stream of normal (23°C) or warm (37°C) air for 5, 10, and 20 s. After visible-light irradiation of the adhesives, resin composites were condensed into a mold and polymerized. Ten samples per test group were stored in distilled water at 37°C for 24 h and then the bond strengths were measured. The surface free-energies were determined by measuring the contact angles of three test liquids placed on the cured adhesives. The enamel bond strengths varied according to the air-drying time and ranged from 15.8 to 19.1 MPa. The trends for the bond strengths were different among the materials. The value of the γS⁺ component increased slightly when drying was performed with a stream of warm air, whereas that of the γS⁻ component decreased significantly. These data suggest that warm air-drying is essential to obtain adequate enamel bond strengths, although increasing the drying time did not significantly influence the bond strength.

  15. Dissociative Recombination without a Curve Crossing

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1994-01-01

    Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

  16. Catalytic Behavior Study of Bifunctional Hydrogen-Bonding Catalysts Guided by Free Energy Relationship Analyses of Steric Parameters.

    PubMed

    Li, Xin; Yang, Chen; Wang, Jie; Liu, Yang; Ni, Xiang; Cheng, JinPei

    2017-02-28

    Free energy relationship (FER) studies to correlate steric parameters against enantiocatalytic performance of bifunctional tertiary-amine hydrogen-bonding type catalysts, including (S, S)-cyclohexane-1, 2-diamine derived thioureas, Cinchona alkaloid derived thioureas and (S, S)-cyclohexane-1, 2-diamine derived squaramides, for Michael reactions revealed that the Michael reactions are much favored by catalysts with less bulky N-substituents. The observed FERs are independent of chiral scaffold and hydrogen-bond donors, deepening the understanding of current bifunctional hydrogen-bonding catalysts. Moreover, DFT calculations were performed to interpret the observed high reactivities of thioureas with less bulky substituents. Especially, the computations demonstrated the advantage of benzyl thiourea catalyst, in which extra CH-π interaction of hydrogen bond between catalyst and substrate should be the key point.

  17. Tripartite efflux pumps: energy is required for dissociation, but not assembly or opening of the outer membrane channel of the pump.

    PubMed

    Janganan, Thamarai K; Bavro, Vassiliy N; Zhang, Li; Borges-Walmsley, Maria Inês; Walmsley, Adrian R

    2013-05-01

    The MtrCDE multidrug pump, from Neisseria gonorrhoeae, is assembled from the inner and outer membrane proteins MtrD and MtrE, which are connected by the periplasmic membrane fusion protein MtrC. Although it is clear that MtrD delivers drugs to the channel of MtrE, it remains unclear how drug delivery and channel opening are connected. We used a vancomycin sensitivity assay to test for opening of the MtrE channel. Cells expressing MtrE or MtrE-E434K were insensitive to vancomycin; but became moderately and highly sensitive to vancomycin respectively, when coexpressed with MtrC, suggesting that the MtrE channel opening requires MtrC binding and is energy-independent. Cells expressing wild-type MtrD, in an MtrCE background, were vancomycin-insensitive, but moderately sensitive in an MtrCE-E434K background. The mutation of residues involved in proton translocation inactivated MtrD and abolished drug efflux, rendered both MtrE and MtrE-E434K vancomycin-insensitive; imply that the pump-component interactions are preserved, and that the complex is stable in the absence of proton flux, thus sealing the open end of MtrE. Following the energy-dependent dissociation of the tripartite complex, the MtrE channel is able to reseal, while MtrE-E434K is unable to do so, resulting in the vancomycin-sensitive phenotype. Thus, our findings suggest that opening of the OMP via interaction with the MFP is energy-independent, while both drug export and complex dissociation require active proton flux.

  18. Chemical bonding in excited states: Energy transfer and charge redistribution from a real space perspective.

    PubMed

    Jara-Cortés, Jesús; Guevara-Vela, José Manuel; Martín Pendás, Ángel; Hernández-Trujillo, Jesús

    2017-05-15

    This work provides a novel interpretation of elementary processes of photophysical relevance from the standpoint of the electron density using simple model reactions. These include excited states of H2 taken as a prototype for a covalent bond, excimer formation of He2 to analyze non-covalent interactions, charge transfer by an avoided crossing of electronic states in LiF and conical interesections involved in the intramolecular scrambling in C2 H4 . The changes of the atomic and interaction energy components along the potential energy profiles are described by the interacting quantum atoms approach and the quantum theory of atoms in molecules. Additionally, the topological analysis of one- and two-electron density functions is used to explore basic reaction mechanisms involving excited and degenerate states in connection with the virial theorem. This real space approach allows to describe these processes in a unified way, showing its versatility and utility in the study of chemical systems in excited states. © 2017 Wiley Periodicals, Inc.

  19. Geometries and bond energies of PHn and PHn + (n=1-3)

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Chung, Young, Sir; Glaunsinger, William S.

    1993-06-01

    All-electron complete active space self-consistent field (CASSCF) followed by full second-order configuration interaction (SOCI) calculations which included up to 1.7 million configurations have been made on several electronic states of PHn and PHn+ (n=1-3). A comparison is made of the results of several basis sets up to the largest set, namely, the (13s10p3d2 f1g/7s6p3d2 f1g) basis set for P and a (10s5p1d/8s4p1d) basis set for the hydrogen atom. Relativistic effective core potentials/CASSCF/multireference configuration interaction computations have also been carried out. The properties of three new excited states for PH3 have been computed as well as the experimentally observed X 1A1, 3A'2, and 1A'2 states. The calculated inversion barrier of PH3 is 34.6 kcal/mol whereas the corresponding inversion barrier of PH3+ is only 2.5 kcal/mol. The bond energies of PHn and PHn+ as well as adiabatic ionization energies of PHn are computed and compared with experimental results. The core-valence and core-external correlation effects are also computed for the diatomic PH molecule.

  20. Microsolvation of methylmercury: structures, energies, bonding and NMR constants ((199)Hg, (13)C and (17)O).

    PubMed

    Flórez, Edison; Maldonado, Alejandro F; Aucar, Gustavo A; David, Jorge; Restrepo, Albeiro

    2016-01-21

    Hartree-Fock (HF) and second order perturbation theory (MP2) calculations within the scalar and full relativistic frames were carried out in order to determine the equilibrium geometries and interaction energies between cationic methylmercury (CH3Hg(+)) and up to three water molecules. A total of nine structures were obtained. Bonding properties were analyzed using the Quantum Theory of Atoms In Molecules (QTAIM). The analyses of the topology of electron densities reveal that all structures exhibit a partially covalent HgO interaction between methylmercury and one water molecule. Consideration of additional water molecules suggests that they solvate the (CH3HgOH2)(+) unit. Nuclear magnetic shielding constants σ((199)Hg), σ((13)C) and σ((17)O), as well as indirect spin-spin coupling constants J((199)Hg-(13)C), J((199)Hg-(17)O) and J((13)C-(17)O), were calculated for each one of the geometries. Thermodynamic stability and the values of NMR constants correlate with the ability of the system to directly coordinate oxygen atoms of water molecules to the mercury atom in methylmercury and with the formation of hydrogen bonds among solvating water molecules. Relativistic effects account for 11% on σ((13)C) and 14% on σ((17)O), which is due to the presence of Hg (heavy atom on light atom, HALA effect), while the relativistic effects on σ((199)Hg) are close to 50% (heavy atom on heavy atom itself, HAHA effect). J-coupling constants are highly influenced by relativity when mercury is involved as in J((199)Hg-(13)C) and J((199)Hg-(17)O). On the other hand, our results show that the values of NMR constants for carbon and oxygen, atoms which are connected through mercury (C-HgO), are highly correlated and are greatly influenced by the presence of water molecules. Water molecules introduce additional electronic effects to the relativistic effects due to the mercury atom.

  1. Quantum enhancement of vibrational predissociation near the dissociation threshold

    SciTech Connect

    Cote, R.; Dashevskaya, E.I.; Nikitin, E.E.; Troe, J.

    2004-01-01

    We discuss quantum enhancement of the quasiclassical vibrational predissociation (VP) rate of an atom (A)-diatom (BC) van der Waals (vdW) complex A-BC from a state lying close to the dissociation threshold. The enhancement is due to the accumulation of a noticeable fraction of the state population near the outer turning point of the A-BC bond. For potentials behaving as power-laws at large separations, the enhancement manifests itself in the variation of the energy dependence of the VP frequency factor from the classical frequency to its quantum counterpart. We show that it is related to the complex scattering length associated with the vibrational relaxation of BC in collisions with A. We also discuss the corrected quasiclassical quantization condition for energy levels of a diatom lying very close to the dissociation threshold. Our results generalize those of J. Trost, C. Eltshka, and H. Friedrich [J. Phys. B 31, 361 (1998)] and C. Boisseau et al. [Eur. Phys. J. D 12, 199 (2000)] for the calculation of complex energy levels of an anharmonic oscillator that dissociates from highly excited states under the action of a weak high-frequency perturbation.

  2. Electric and magnetic properties computed for valence bond structures: is there a link between pauling resonance energy and ring current?

    PubMed

    Havenith, Remco W A

    2006-04-28

    To establish the link between the aromaticity descriptors based on the Pauling resonance energy and the molecular properties, the electric (polarizability) and magnetic (magnetizability) field response properties have been calculated using the valence bond approach for various molecules and their individual Kekulé resonance structures. The results show that there is no direct relationship between the Pauling resonance energy and the properties; the response properties are weighted averages of the properties of the individual structures. According to the aromaticity criteria based on molecular properties, one-structure benzene would be aromatic; thus, concerning molecular properties, spin-coupled bonds do not behave like localized bonds in Lewis structures, with which they are usually associated.

  3. Dissociative recombination of protonated dimer ions H+·(HCOH)2 and H+·(CH3COH)2 with electrons at near thermal energies

    NASA Astrophysics Data System (ADS)

    Glosík, J.; Plasil, R.; Zakouril, P.; Poterya, V.

    2001-07-01

    Formation of the protonated formaldehyde and acetaldehyde dimer ions, H+·(HCOH)2 and H+·(CH3COH)2, respectively, and their subsequent dissociative recombination with electrons was studied in a high-pressure flowing afterglow (HPFA) using the axially movable Langmuir probe. The obtained recombination rate coefficients are (3.3±1)×10-6 cm3 s-1 for H+·(HCOH)2 and (1.4±0.5)×10-6 cm3 s-1 for H+·(CH3COH)2, at 450 and 500 K, respectively. The evolution of the electron energy distribution function and the electron temperature in the recombination-dominated flowing afterglow plasma were also measured.

  4. Dissociative phenomenology of dissociative identity disorder.

    PubMed

    Dell, Paul F

    2002-01-01

    The goal of this study was to investigate the dissociative phenomenology of dissociative identity disorder (DID). The Multidimensional Inventory of Dissociation (MID) was administered to 34 patients with DID, 23 patients with dissociative disorder not otherwise specified (DDNOS), 52 patients with mixed psychiatric disorders, and 58 normal individuals. DID patients obtained significantly higher scores than the other three groups on 27 dissociation-related variables. DDNOS patients had significantly higher scores than normals and mixed psychiatric patients on 17 and 15 dissociation-related variables, respectively. The findings of the present study are virtually identical to a large body of replicated findings about the dissociative phenomenology of DID. This broad range of dissociation-related phenomena, which routinely occurs in individuals with DID, is largely absent from the DSM-IV-TR account of DID. Factor analysis of the 11 dimensions of dissociation that are measured by the MID extracted only one factor that accounted for 85% of the variance. It was concluded that dissociation is a unifactorial taxon or natural type that has different aspects or epiphenomena (i.e., amnesia, depersonalization, voices, trance, etc.).

  5. Molecular resonant dissociation of surface-adsorbed molecules by plasmonic nanoscissors

    NASA Astrophysics Data System (ADS)

    Zhang, Zhenglong; Sheng, Shaoxiang; Zheng, Hairong; Xu, Hongxing; Sun, Mengtao

    2014-04-01

    The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis, photosynthesis and the degradation of plastic, it is hard to break individual molecular bonds for those molecules adsorbed on the surface because of the weak light-absorption in molecules and the redistribution of the resulting vibrational energy both inside the molecule and to its surrounding environment. Here we show how to overcome these obstacles with a plasmonic hot-electron mediated process and demonstrate a new method that allows the sensitive control of resonant dissociation of surface-adsorbed molecules by `plasmonic' scissors. To that end, we used a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) setup to dissociate resonantly excited NC2H6 fragments from Malachite green. The surface plasmons (SPs) excited at the sharp metal tip not only enhance the local electric field to harvest the light incident from the laser, but crucially supply `hot electrons' whose energy can be transferred to individual bonds. These processes are resonant Raman, which result in some active chemical bonds and then weaken these bonds, followed by dumping in lots of indiscriminant energy and breaking the weakest bond. The method allows for sensitive control of both the rate and probability of dissociation through their dependence on the density of hot electrons, which can be manipulated by tuning the laser intensity or tunneling current/bias voltage in the HV-TERS setup, respectively. The concepts of plasmonic scissors open up new versatile avenues for the deep understanding of in situ surface-catalyzed chemistry.The ability to break individual bonds or specific modes in chemical reactions is an ardently sought goal by chemists and physicists. While photochemistry based methodologies are very successful in controlling e.g. photocatalysis

  6. Chemical Bonds II

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

    The continuation of a paper discussing chemical bonding from a bond energy viewpoint, with a number of examples of single and multiple bonds. (Part I appeared in volume 1 number 3, pages 16-23, February 1972.) (AL)

  7. Probing royal demolition explosive (1,3,5-trinitro-1,3,5-triazocyclohexane) by low-energy electrons: Strong dissociative electron attachment near 0 eV.

    PubMed

    Sulzer, P; Mauracher, A; Ferreira da Silva, F; Denifl, S; Märk, T D; Probst, M; Limão-Vieira, P; Scheier, P

    2009-10-14

    Low energy electron attachment to gas phase royal demolition explosive (RDX) (and RDX-A3) has been performed by means of a crossed electron-molecular beam experiment in an electron energy range from 0 to 14 eV with an energy resolution of approximately 70 meV. The most intense signals are observed at 102 and 46 amu and assigned to C(2)H(4)N(3)O(2) (-) and NO(2) (-), respectively. Anion efficiency curves of 16 anions have been measured. Product ions are observed mainly in the low energy region, near 0 eV arising from surprisingly complex reactions associated with multiple bond cleavages and structural and electronic rearrangement. The remarkable instability of RDX to electron attachment with virtually thermal electrons reflects the highly explosive nature of this compound. The present results are compared to other explosive aromatic nitrocompounds studied in our laboratory recently.

  8. Mediatorless solar energy conversion by covalently bonded thylakoid monolayer on the glassy carbon electrode.

    PubMed

    Lee, Jinhwan; Im, Jaekyun; Kim, Sunghyun

    2016-04-01

    Light reactions of photosynthesis that take place in thylakoid membranes found in plants or cyanobacteria are among the most effective ways of utilizing light. Unlike most researches that use photosystem I or photosystem II as conversion units for converting light to electricity, we have developed a simple method in which the thylakoid monolayer was covalently immobilized on the glassy carbon electrode surface. The activity of isolated thylakoid membrane was confirmed by measuring evolving oxygen under illumination. Glassy carbon surfaces were first modified with partial or full monolayers of carboxyphenyl groups by reductive C-C coupling using 4-aminobenzoic acid and aniline and then thylakoid membrane was bioconjugated through the peptide bond between amine residues of thylakoid and carboxyl groups on the surface. Surface properties of modified surfaces were characterized by cyclic voltammetry, contact angle measurements, and electrochemical impedance spectroscopy. Photocurrent of 230 nA cm(-2) was observed when the thylakoid monolayer was formed on the mixed monolayer of 4-carboxylpheny and benzene at applied potential of 0.4V vs. Ag/AgCl. A small photocurrent resulted when the 4-carboxyphenyl full monolayer was used. This work shows the possibility of solar energy conversion by directly employing the whole thylakoid membrane through simple surface modification.

  9. Bond ionicity of alkaline-earth oxides studied by low-energy D+ scattering

    NASA Astrophysics Data System (ADS)

    Souda, R.; Yamamoto, K.; Hayami, W.; Aizawa, T.; Ishizawa, Y.

    1994-08-01

    Low-energy D+ scattering is employed to explore the nature of the bonding of polycrystalline alkaline-earth oxides MgO, CaO, SrO, and BaO, with particular emphasis on the investigation of the ionicity of the topmost-layer atoms. Increasing ionicity as one goes to the heavier cations is concluded from the probability of the resonance neutraliztion of the D+ ions, which is consistent with the conventional chemical arguments based on electronegativity scales but is in apparent contradiction to the results of recent ab initio cluster-model calculations. It is also concluded that the metallic Ba layer is formed rather patchily on the BaO surface after the heat treatment up to 1000 °C. This is probably because free Ba atoms, being supplied by the reaction of BaO with the Ta substrate, are precipitated at the BaO surface. Another example is concerned with the interactions of the Ba adatoms with Si(001) and Pt(111) surfaces; Ba is found to have marked covalency with the substrate atoms.

  10. Low temperature pollutant trapping and dissociation over two-dimensional tin.

    PubMed

    Takahashi, Lauren; Takahashi, Keisuke

    2015-09-07

    Newly discovered two-dimensional tin, named stanene, has been theoretically predicted and found to have unique electronic properties. Stanene is found to have a buckled structure which could be a key structure against chemical reactivity. Hence, the reactivity of stanene against key air pollutants NO, NO2, SO, SO2, CO, and CO2 is investigated within first principles calculations. The results showed that stanene is reactive against those air pollutants. Furthermore, the dissociation activation energies of those pollutants over stanene are lower than previously reported catalysts. The physical origin of low dissociation barriers rests in the charge transfer from stanene to those pollutants, resulting in bond weakening. Hence, one can predict that unique reactivities of stanene offer low temperature trapping and dissociation of air pollutants.

  11. Electron-hole pair effects in methane dissociative chemisorption on Ni(111).

    PubMed

    Luo, Xuan; Jiang, Bin; Juaristi, J Iñaki; Alducin, Maite; Guo, Hua

    2016-07-28

    The dissociative chemisorption of methane on metal surfaces has attracted much attention in recent years as a prototype of gas-surface reactions in understanding the mode specific and bond selective chemistry. In this work, we systematically investigate the influence of electron-hole pair excitations on the dissociative chemisorption of CH4/CH3D/CHD3 on Ni(111). The energy dissipation induced by surface electron-hole pair excitations is modeled as a friction force introduced in the generalized Langevin equation, in which the independent atomic friction coefficients are determined within the local-density friction approximation. Quasi-classical trajectory calculations for CH4/CH3D/CHD3 have been carried out on a recently developed twelve-dimensional potential energy surface. Comparing the dissociation probabilities obtained with and without friction, our results clearly indicate that the electron-hole pair effects are generally small, both on absolute reactivity of each vibrational state and on the mode specificity and bond selectivity. Given similar observations in both water and methane dissociation processes, we conclude that electron-hole pair excitations would not play an important role as long as the reaction is direct and the interaction time between the molecule and metal electrons is relatively short.

  12. Thermochemical benchmarking of hydrocarbon bond separation reaction energies: Jacob's ladder is not reversed!

    NASA Astrophysics Data System (ADS)

    Krieg, Helge; Grimme, Stefan

    2010-10-01

    We reinvestigate the performance of Kohn-Sham density functional (DF) methods for a thermochemical test set of bond separation reactions of alkanes (BSR36) published recently by Steinmann et al. [J. Chem. Theory Comput. 5, 2950 (2009)]. According to our results, the tested approximations perform for this rather special benchmark as usual. We show that the choice of reference enthalpies plays a crucial role in the assessment. Due to the large stoichiometric factors involved, errors of various origin are strongly amplified. Inconsistent reference data are avoided by computing reference energies at the CCSD(T)/CBS level. These are compared to results for a variety of standard DFs. Two different versions of London dispersion corrections (DFT-D2 and DFT-D3) are applied and found to be very significant. The most accurate results are obtained with B2GPPLYP-D2 (MAD = 0.4 kcal mol-1) B2PLYP-D2 (MAD = 0.5 kcal mol-1) and B97-D2 (MAD = 0.9 kcal mol-1 methods. Dispersion corrections not only improve the computed BSR energies but also diminish the accuracy differences between the DFs. The previous DFT-D2 version performs better due to error compensation of medium-range correlation effects between the semi-classical and the density-based description. We strongly recommend not to overinterpret results regarding DF accuracy when based on a single set of chemical reactions and to use high-level theoretical data for benchmarking purposes.

  13. Adhesive-Bonded Composite Joint Analysis with Delaminated Surface Ply Using Strain-Energy Release Rate

    NASA Technical Reports Server (NTRS)

    Chadegani, Alireza; Yang, Chihdar; Smeltzer, Stanley S. III

    2012-01-01

    This paper presents an analytical model to determine the strain energy release rate due to an interlaminar crack of the surface ply in adhesively bonded composite joints subjected to axial tension. Single-lap shear-joint standard test specimen geometry with thick bondline is followed for model development. The field equations are formulated by using the first-order shear-deformation theory in laminated plates together with kinematics relations and force equilibrium conditions. The stress distributions for the adherends and adhesive are determined after the appropriate boundary and loading conditions are applied and the equations for the field displacements are solved. The system of second-order differential equations is solved to using the symbolic computation tool Maple 9.52 to provide displacements fields. The equivalent forces at the tip of the prescribed interlaminar crack are obtained based on interlaminar stress distributions. The strain energy release rate of the crack is then determined by using the crack closure method. Finite element analyses using the J integral as well as the crack closure method are performed to verify the developed analytical model. It has been shown that the results using the analytical method correlate well with the results from the finite element analyses. An attempt is made to predict the failure loads of the joints based on limited test data from the literature. The effectiveness of the inclusion of bondline thickness is justified when compared with the results obtained from the previous model in which a thin bondline and uniform adhesive stresses through the bondline thickness are assumed.

  14. Dissociative Electron Attachment

    NASA Astrophysics Data System (ADS)

    Arreola, Esmeralda; Esmeralda Arreola Collaboration; Leigh Hargreaves Collaboration

    Since the pioneering work of Boudiaffa et al., it has been understood that electrons, even with energies near or below the ionization threshold, are capable of initiating strand-breaks in human DNA. This discovery raised important questions for cancer treatments, since sub-ionizing electrons are known to be the most copiously produced secondary product of radiation therapy. But even to date these factors are largely excluded from dosimetry calculations. This lack of inclusion is, at least in part, certainly due to the dearth of fundamental data describing low-energy electron interactions with nucleotide molecules that form the basis of DNA. Understanding of how such slow electrons are able to damage DNA remains incomplete, but the strongly peaked nature of Boudiaffa et al.'s data gives strong hints at resonantly driven collision processes. DNA damage is therefore most likely driven by ``dissociative electron attachment'' (DEA). DEA is a rather complicated process to model due to the coupling of electronic and nuclear degrees of freedom in the molecule. At the California State University Fullerton, we are currently commissioning a new spectrometer to study dissociation channels, reaction rates and orientation effects in DEA collisions between slow electrons and nucleotide molecules. At the meeting we will present design parameters and commissioning data for this new apparatus.

  15. Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study

    SciTech Connect

    Wang, Xu-Dong; Xuan, Chuan-Jin; Feng, Wen-Ling; Tian, Shan Xi

    2015-02-14

    Dissociation dynamics of the temporary negative ions of ethanol and acetaldehyde formed by the low-energy electron attachments is investigated by using the anion velocity map imaging technique and ab initio molecular dynamics simulations. The momentum images of the dominant fragments O{sup −}/OH{sup −} and CH{sub 3}{sup −} are recorded, indicating the low kinetic energies of O{sup −}/OH{sup −} for ethanol while the low and high kinetic energy distributions of O{sup −} ions for acetaldehyde. The CH{sub 3}{sup −} image for acetaldehyde also shows the low kinetic energy. With help of the dynamics simulations, the fragmentation processes are qualitatively clarified. A new cascade dissociation pathway to produce the slow O{sup −} ion via the dehydrogenated intermediate, CH{sub 3}CHO{sup −} (acetaldehyde anion), is proposed for the dissociative electron attachment to ethanol. After the electron attachment to acetaldehyde molecule, the slow CH{sub 3}{sup −} is produced quickly in the two-body dissociation with the internal energy redistributions in different aspects before bond cleavages.

  16. Full-dimensional diabatic potential energy surfaces including dissociation: The {sup 2}E{sup ″} state of NO{sub 3}

    SciTech Connect

    Eisfeld, Wolfgang; Vieuxmaire, Olivier; Viel, Alexandra

    2014-06-14

    A scheme to produce accurate full-dimensional coupled diabatic potential energy surfaces including dissociative regions and suitable for dynamical calculations is proposed. The scheme is successfully applied to model the two-sheeted surface of the {sup 2}E{sup ″} state of the NO{sub 3} radical. An accurate potential energy surface for the NO{sub 3}{sup −} anion ground state is developed as well. Both surfaces are based on high-level ab initio calculations. The model consists of a diabatic potential matrix, which is expanded to higher order in terms of symmetry polynomials of symmetry coordinates. The choice of coordinates is key for the accuracy of the obtained potential energy surfaces and is discussed in detail. A second central aspect is the generation of reference data to fit the expansion coefficients of the model for which a stochastic approach is proposed. A third ingredient is a new and simple scheme to handle problematic regions of the potential energy surfaces, resulting from the massive undersampling by the reference data unavoidable for high-dimensional problems. The final analytical diabatic surfaces are used to compute the lowest vibrational levels of NO{sub 3}{sup −} and the photo-electron detachment spectrum of NO{sub 3}{sup −} leading to the neutral radical in the {sup 2}E{sup ″} state by full dimensional multi-surface wave-packet propagation for NO{sub 3} performed using the Multi-Configuration Time Dependent Hartree method. The achieved agreement of the simulations with available experimental data demonstrates the power of the proposed scheme and the high quality of the obtained potential energy surfaces.

  17. The key role of dislocation dissociation in the plastic behaviour of single crystal nickel-based superalloy with low stacking fault energy: Three-dimensional discrete dislocation dynamics modelling

    NASA Astrophysics Data System (ADS)

    Huang, Minsheng; Li, Zhenhuan

    2013-12-01

    To model the deformation of single crystal nickel based superalloys (SCNBS) with low stacking fault energy (SFE), three-dimensional discrete dislocation dynamics (3D-DDD) is extended by incorporating dislocation dissociation mechanism. The present 3D-DDD simulations show that, consistent with the existing TEM observation, the leading partial can enter the matrix channel efficiently while the trailing partial can hardly glide into it when the dislocation dissociation is taken into account. To determine whether the dislocation dissociation can occur or not, a critical percolation stress (CPS) based criterion is suggested. According to this CPS criterion, for SCNBS there exists a critical matrix channel width. When the channel width is lower than this critical value, the dislocation tends to dissociate into an extended configuration and vice versa. To clarify the influence of dislocation dissociation on CPS, the classical Orowan formula is improved by incorporating the SFE. Moreover, the present 3D-DDD simulations also show that the yielding stress of SCNBSs with low SFE may be overestimated up to 30% if the dislocation dissociation is ignored. With dislocation dissociation being considered, the size effect due to the width of γ matrix channel and the length of γ‧ precipitates on the stress-strain responses of SCNBS can be enhanced remarkably. In addition, due to the strong constraint effect by the two-phase microstructure in SCNBS, the configuration of formed junctions is quite different from that in single phase crystals such as Cu. The present results not only provide clear understanding of the two-phase microstructure levelled microplastic mechanisms in SCNBSs with low SFE, but also help to develop new continuum-levelled constitutive laws for SCNBSs.

  18. A theoretical study on the strength of the C-NO2 bond and ring strain upon the formation of the intermolecular H-bonding interaction between HF and nitro group in nitrocyclopropane, nitrocyclobutane, nitrocyclopentane or nitrocyclohexane.

    PubMed

    Qiu, Wei; Ren, Fu-de; Shi, Wen-jing; Wang, Yan-hong

    2015-05-01

    As a follow-up to our investigation into the influence of H-bond on the C-NO2 trigger bond, a comparison of the effect of the H-bond on the ring strain energy with the C-NO2 bond dissociation energy was carried out in the HF complex with nitrocyclopropane, nitrocyclobutane, nitrocyclopentane, and nitrocyclohexane by using the DFT-B3LYP and MP2 (full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The C-NO2 bond length decreases with strengthening of trigger-bond while the ring perimeter increases companied by weakening of ring strain upon the complex formation. The H-bonding energy correlates well with the increment of ring perimeter and the change of ring bond angle. For nitrocyclopropane∙∙∙HF, the effect of H-bond on the ring strain energy is notable, while for the other complex, it is negligible. Therefore, for nitrocyclopropane∙∙∙HF, the origin of the change of explosive sensitivity might be due to the increment of the C-NO2 bond dissociation energy and decrease of the ring strain energy, while for the other complex, it might be only due to the strengthening of C-NO2 bond. The analysis of electron density shifts shows that the C-C bond in ring loses density while the C-NO2 bond gains density, leading to the weakened ring strain and strengthened C-NO2 bond, and thus the possibly reduced explosive sensitivity.

  19. Using Qualified Energy Conservation Bonds (QECBs) to Fund a Residential Energy Efficiency Loan Program: Case Study on Saint Louis County, MO

    SciTech Connect

    Zimring, Mark

    2011-06-23

    Qualified Energy Conservation Bonds (QECBs) are federally-subsidized debt instruments that enable state, tribal, and local government issuers to borrow money to fund a range of qualified energy conservation projects. QECBs offer issuers very attractive borrowing rates and long terms, and can fund low-interest energy efficiency loans for home and commercial property owners. Saint Louis County, MO recently issued over $10 million of QECBs to finance the Saint Louis County SAVES residential energy efficiency loan program. The county's experience negotiating QECB regulations and restrictions can inform future issuers.

  20. Formulating the bonding contribution equation in heterogeneous catalysis: a quantitative description between the surface structure and adsorption energy.

    PubMed

    Wang, Ziyun; Hu, P

    2017-02-15

    The relation between the surface structure and adsorption energy of adsorbates is of great importance in heterogeneous catalysis. Based on density functional theory calculations, we propose an explicit equation with three chemically meaningful terms, namely the bonding contribution equation, to quantitatively account for the surface structures and the adsorption energies. Successful predictions of oxygen adsorption energies on complex alloy surfaces containing up to 4 components are demonstrated, and the generality of this equation is also tested using different surface sizes and other adsorbates. This work may not only offer a powerful tool to understand the structure-adsorption relation, but may also be used to inversely design novel catalysts.

  1. The stabilization energies of polyenyl radicals

    NASA Astrophysics Data System (ADS)

    Luo, Yu-Ran; Holmes, John L.

    1994-10-01

    The resonance stabilization energies, Es, of polyenyl radicals can be estimated by the equation Es( N)=-13.2+[3.95-15.8(2) -2/ n] kcal mol -1, where N is the number of C, C-π bonds in the polyenyl radicals. This correlation has been extended for predicting the weakest HC, CC and COH bond dissociation energies in vitamin A and similar compounds.

  2. Diffraction dissociation at the LHC

    SciTech Connect

    Jenkovszky, Laszlo; Orava, Risto; Salii, Andrii

    2013-04-15

    We report on recent calculations of low missing mass single (SD) and double (DD) diffractive dissociation at LHC energies. The calculations are based on a dual-Regge model, dominated by a single Pomeron exchange. The diffractively excited states lie on the nucleon trajectory N*, appended by the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing mass dependence of the differential and integrated single-and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

  3. Dissociated expression of mitochondrial and cytosolic creatine kinases in the human brain: a new perspective on the role of creatine in brain energy metabolism

    PubMed Central

    Lowe, Matthew TJ; Kim, Eric H; Faull, Richard LM; Christie, David L; Waldvogel, Henry J

    2013-01-01

    The phosphocreatine/creatine kinase (PCr/CK) system in the brain is defined by the expression of two CK isozymes: the cytosolic brain-type CK (BCK) and the ubiquitous mitochondrial CK (uMtCK). The system plays an important role in supporting cellular energy metabolism by buffering adenosine triphosphate (ATP) consumption and improving the flux of high-energy phosphoryls around the cell. This system is well defined in muscle tissue, but there have been few detailed studies of this system in the brain, especially in humans. Creatine is known to be important for neurologic function, and its loss from the brain during development can lead to mental retardation. This study provides the first detailed immunohistochemical study of the expression pattern of BCK and uMtCK in the human brain. A strikingly dissociated pattern of expression was found: uMtCK was found to be ubiquitously and exclusively expressed in neuronal populations, whereas BCK was dominantly expressed in astrocytes, with a low and selective expression in neurons. This pattern indicates that the two CK isozymes are not widely coexpressed in the human brain, but rather are selectively expressed depending on the cell type. These results suggest that the brain cells may use only certain properties of the PCr/CK system depending on their energetic requirements. PMID:23715059

  4. Lipidomics profiling by high-resolution LC-MS and high-energy collisional dissociation fragmentation: focus on characterization of mitochondrial cardiolipins and monolysocardiolipins.

    PubMed

    Bird, Susan S; Marur, Vasant R; Sniatynski, Matthew J; Greenberg, Heather K; Kristal, Bruce S

    2011-02-01

    A liquid chromatography-mass spectrometry (LC-MS) method was used for separation of lipid classes as well as both qualitative and semiquantitative detection of individual lipids in biological samples. Data were acquired using high-resolution full-scan MS and high-energy collisional dissociation (HCD) all ion fragmentation. The method was evaluated for efficient separation and detection in both positive and negative ionization mode using standards spanning six lipid classes. Platform linearity and robustness, related to the mitochondrial lipid cardiolipin (CL), were assessed using extracted ion chromatograms with mass tolerance windows of 5 ppm or less from full scan exact mass measurements. The platform CL limit of detection was determined to be 5 pmol (0.9 μM) on the column, with mass accuracy <1.5 ppm, retention time coefficients of variation (CV) < 0.5%, and area CV < 13%. This mass accuracy was critical to the identification of unknown CL species in mitochondria samples, through the elimination of false positives. In addition to detection and relative quantitation of CL species in mitochondria, CL structures were characterized through the use of alternating HCD scans at different energies to produce diagnostic fragmentations on all ions in the analysis. The developed lipid profiling method was applied to mitochondrial samples from an animal study related to the linkages between diet, mitochondrial function, and disease. The analysis identified 28 unique CL species and two monolysocardiolipin species that are often associated with mitochondrial stress and dysfunction.

  5. Validity of the site-averaging approximation for modeling the dissociative chemisorption of H{sub 2} on Cu(111) surface: A quantum dynamics study on two potential energy surfaces

    SciTech Connect

    Liu, Tianhui; Fu, Bina E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H. E-mail: zhangdh@dicp.ac.cn

    2014-11-21

    A new finding of the site-averaging approximation was recently reported on the dissociative chemisorption of the HCl/DCl+Au(111) surface reaction [T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 139, 184705 (2013); T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 140, 144701 (2014)]. Here, in order to investigate the dependence of new site-averaging approximation on the initial vibrational state of H{sub 2} as well as the PES for the dissociative chemisorption of H{sub 2} on Cu(111) surface at normal incidence, we carried out six-dimensional quantum dynamics calculations using the initial state-selected time-dependent wave packet approach, with H{sub 2} initially in its ground vibrational state and the first vibrational excited state. The corresponding four-dimensional site-specific dissociation probabilities are also calculated with H{sub 2} fixed at bridge, center, and top sites. These calculations are all performed based on two different potential energy surfaces (PESs). It is found that the site-averaging dissociation probability over 15 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability for H{sub 2} (v = 0) and (v = 1) on the two PESs.

  6. Inferring modules of functionally interacting proteins using the Bond Energy Algorithm

    PubMed Central

    Watanabe, Ryosuke LA; Morett, Enrique; Vallejo, Edgar E

    2008-01-01

    Background Non-homology based methods such as phylogenetic profiles are effective for predicting functional relationships between proteins with no considerable sequence or structure similarity. Those methods rely heavily on traditional similarity metrics defined on pairs of phylogenetic patterns. Proteins do not exclusively interact in pairs as the final biological function of a protein in the cellular context is often hold by a group of proteins. In order to accurately infer modules of functionally interacting proteins, the consideration of not only direct but also indirect relationships is required. In this paper, we used the Bond Energy Algorithm (BEA) to predict functionally related groups of proteins. With BEA we create clusters of phylogenetic profiles based on the associations of the surrounding elements of the analyzed data using a metric that considers linked relationships among elements in the data set. Results Using phylogenetic profiles obtained from the Cluster of Orthologous Groups of Proteins (COG) database, we conducted a series of clustering experiments using BEA to predict (upper level) relationships between profiles. We evaluated our results by comparing with COG's functional categories, And even more, with the experimentally determined functional relationships between proteins provided by the DIP and ECOCYC databases. Our results demonstrate that BEA is capable of predicting meaningful modules of functionally related proteins. BEA outperforms traditionally used clustering methods, such as k-means and hierarchical clustering by predicting functional relationships between proteins with higher accuracy. Conclusion This study shows that the linked relationships of phylogenetic profiles obtained by BEA is useful for detecting functional associations between profiles and extending functional modules not found by traditional methods. BEA is capable of detecting relationship among phylogenetic patterns by linking them through a common element shared in

  7. Reactions of fourth-period metal ions (Ca + - Zn + ) with O2: Metal-oxide ion bond energies

    NASA Astrophysics Data System (ADS)

    Fisher, Ellen R.; Elkind, J. L.; Clemmer, D. E.; Georgiadis, R.; Loh, S. K.; Aristov, N.; Sunderlin, L. S.; Armentrout, P. B.

    1990-08-01

    Reactions of Ca+, Zn+ and all first-row atomic transition metal ions with O2 are studied using guided ion beam techniques. While reactions of the ground states of Sc+, Ti+, and V+ are exothermic, the remaining metal ions react with O2 in endothermic processes. Analyses of these endothermic reactions provide new determinations of the M+-O bond energies for these eight elements. Source conditions are varied such that the contributions of excited states of the metal ions can be explicitly considered for Mn+, Co+, Ni+, and Cu+. Results (in eV) at 0 K are D0(Ca+-O)= 3.57±0.05, D0(Cr+-O)=3.72±0.12, D0(Mn+-O)=2.95±0.13, D0(Fe+-O)=3.53±0.06 (reported previously), D0(Co+-O)=3.32±0.06, D0(Ni+-O) =2.74±0.07, D0(Cu+-O)=1.62±0.15, and D0(Zn+-O)=1.65±0.12. These values along with literature data for neutral metal oxide bond energies and ionization energies are critically evaluated. Periodic trends in the ionic metal oxide bond energies are compared with those of the neutral metal oxides and those of other related molecules.

  8. ION PAIR DISSOCIATION: Spectroscopy and Dynamics

    NASA Astrophysics Data System (ADS)

    Suits, Arthur G.; Hepburn, John W.

    2006-05-01

    Ion pair dissociation processes may be studied using coherent vacuum ultraviolet laser sources in a manner entirely analogous to photoelectron spectroscopy, albeit with the anion playing the role of a heavy electron. If the excitation energy is above the dissociation energy and the kinetic energy of the fragment is measured using ion imaging, this approach is termed ion pair imaging spectroscopy (IPIS) and is related to conventional photoelectron spectroscopy. If the excitation energy is just below the dissociation energy and pulsed-field dissociation is employed, this approach is analogous to mass analyzed threshold ionization (MATI) spectroscopy and is termed threshold ion pair production spectroscopy (TIPPS). These approaches provide a novel means of investigating ion thermochemistry and spectroscopy and superexcited state decay dynamics at high resolution.

  9. Low energy (0-4 eV) electron impact to N{sub 2}O clusters: Dissociative electron attachment, ion-molecule reactions, and vibrational Feshbach resonances

    SciTech Connect

    Vizcaino, Violaine; Denifl, Stephan; Maerk, Tilmann D.; Scheier, Paul; Illenberger, Eugen

    2010-10-21

    Electron attachment to clusters of N{sub 2}O in the energy range of 0-4 eV yields the ionic complexes [(N{sub 2}O){sub n}O]{sup -}, [(N{sub 2}O){sub n}NO]{sup -}, and (N{sub 2}O){sub n}{sup -} . The shape of the ion yields of the three homologous series differs substantially reflecting the different formation mechanisms. While the generation of [(N{sub 2}O){sub n}O]{sup -} can be assigned to dissociative electron attachment (DEA) of an individual N{sub 2}O molecule in the target cluster, the formation of [(N{sub 2}O){sub n}NO]{sup -} is interpreted via a sequence of ion molecule reactions involving the formation of O{sup -} via DEA in the first step. The nondecomposed complexes (N{sub 2}O){sub n}{sup -} are preferentially formed at very low energies (below 0.5 eV) as a result of intramolecular stabilization of a diffuse molecular anion at low energy. The ion yields of [(N{sub 2}O){sub n}O]{sup -} and (N{sub 2}O){sub n}{sup -} versus electron energy show sharp peaks at the threshold region, which can be assigned to vibrational Feshbach resonances mediated by the diffuse anion state as already observed in an ultrahigh resolution electron attachment study of N{sub 2}O clusters [E. Leber, S. Barsotti, J. Boemmels, J. M. Weber, I. I. Fabrikant, M.-W. Ruf, and H. Hotop, Chem. Phys. Lett. 325, 345 (2000)].

  10. Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

    PubMed Central

    Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

    2014-01-01

    An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

  11. Is the decrease of the total electron energy density a covalence indicator in hydrogen and halogen bonds?

    PubMed

    Angelina, Emilio L; Duarte, Darío J R; Peruchena, Nélida M

    2013-05-01

    In this work, halogen bonding (XB) and hydrogen bonding (HB) complexes were studied with the aim of analyzing the variation of the total electronic energy density H(r b ) with the interaction strengthening. The calculations were performed at the MP2/6-311++G(2d,2p) level of approximation. To explain the nature of such interactions, the atoms in molecules theory (AIM) in conjunction with reduced variational space self-consistent field (RVS) energy decomposition analysis were carried out. Based on the local virial theorem, an equation to decompose the total electronic energy density H(r b ) in two energy densities, (-G(r b )) and 1/4∇(2)ρ(r b ), was derived. These energy densities were linked with the RVS interaction energy components. Through the connection between both decomposition schemes, it was possible to conclude that the decrease in H(r b ) with the interaction strengthening observed in the HB as well as the XB complexes, is mainly due to the increase in the attractive electrostatic part of the interaction energy and in lesser extent to the increase in its covalent character, as is commonly considered.

  12. Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

    PubMed

    Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

    2014-05-28

    An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.