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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. 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.

  3. Determination of bond dissociation energies via energy-resolved collision induced dissociation in a fourier transform ion cyclotron resonance spectrometer

    NASA Astrophysics Data System (ADS)

    Hop, C. E. C. A.; McMahon, T. B.; Willett, G. D.

    1990-12-01

    A Fourier transform ion cyclotron resonance (ICR) spectrometer has been used to determine bond dissociation energies via translation energy controlled collisions between mass-selected ions and a stationary target gas. The ions examined were the proton-bound dimers of diethyl ether, acetone and water, which were generated in a high pressure external ion source. A comparison between bond dissociation energies obtained with this technique and literature values showed that the r.f. excitation of ions in the ICR cell produced ions with a well-defined translation energy. Moreover, the translational energy distribution of the ions was narrow, as indicated by the fact that experimentally obtained threshold curves for dissociation were close to computed curves corrected for Doppler broadening.

  4. 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.

  5. Bond dissociation energies from the topology of the charge density using gradient bundle analysis

    NASA Astrophysics Data System (ADS)

    Morgenstern, Amanda; Eberhart, Mark

    2016-02-01

    New and more robust models of chemical bonding are necessary to further our understanding of chemical phenomena. Among these are bond bundle and gradient bundle methods, which analyze bonding interactions in terms of property distributions over geometrically defined volumes. These methods have been shown to provide a systematic framework from which to search for structure-property relationships. In addition to providing a brief review of some of the relationships found using this framework, we present new findings that relate the lowering of kinetic energy in bonding regions to bond dissociation energy.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Kaur, Damanjit; Sharma, Punita; Bharatam, Prasad V.; Kaur, Mondeep

    Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6-31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6-311++G*//B3LYP/6-31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine.0

  8. 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.

  9. 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.

  10. Bond energies on the cesium halides determined by collision-induced dissociation

    SciTech Connect

    Parks, E.K.; Wexler, S.

    1984-09-27

    The bond energies of the four cesium halides are determined from the threshold for collision-induced dissociation to ion pairs by rare gas atoms. The bond energies (to neutral atoms) are 5.32 +/- 0.08, 4.58 +/- 0.08, 4.00 +/- 0.08, and 3.47 +/- 0.15 eV for CsF, CsCl, CsBr, and CsI, respectively. Except for CsI the ion thresholds are obtained from the sharply peaked cross section vs. energy curves for CsM/sup +/ + X/sup -/ formation (M = rare gas atom; X/sup -/ = halide ion) and for CsI the ion threshold is obtained from the onset of the channel M + Cs/sup +/ + I/sup -/. Comparison is made with bond energies determined by other techniques as well as that derived from the T-Rittner model potential.

  11. 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.

  12. 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.

  13. 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.

  14. Assessment of experimental bond dissociation energies using composite ab initio methods and evaluation of the performances of density functional methods in the calculation of bond dissociation energies.

    PubMed

    Feng, Yong; Liu, Lei; Wang, Jin-Ti; Huang, Hao; Guo, Qing-Xiang

    2003-01-01

    Composite ab initio CBS-Q and G3 methods were used to calculate the bond dissociation energies (BDEs) of over 200 compounds listed in CRC Handbook of Chemistry and Physics (2002 ed.). It was found that these two methods agree with each other excellently in the calculation of BDEs, and they can predict BDEs within 10 kJ/mol of the experimental values. Using these two methods, it was found that among the examined compounds 161 experimental BDEs are valid because the standard deviation between the experimental and theoretical values for them is only 8.6 kJ/mol. Nevertheless, 40 BDEs listed in the Handbook may be highly inaccurate as the experimental and theoretical values for them differ by over 20 kJ/mol. Furthermore, 11 BDEs listed in the Handbook may be seriously flawed as the experimental and theoretical values for them differ by over 40 kJ/mol. Using the 161 cautiously validated experimental BDEs, we then assessed the performances of the standard density functional (DFT) methods including B3LYP, B3P86, B3PW91, and BH&HLYP in the calculation of BDEs. It was found that the BH&HLYP method performed poorly for the BDE calculations. B3LYP, B3P86, and B3PW91, however, performed reasonably well for the calculation of BDEs with standard deviations of about 12.1-18.0 kJ/mol. Nonetheless, all the DFT methods underestimated the BDEs by 4-17 kJ/mol in average. Sometimes, the underestimation by the DFT methods could be as high as 40-60 kJ/mol. Therefore, the DFT methods were more reliable for relative BDE calculations than for absolute BDE calculations. Finally, it was observed that the basis set effects on the BDEs calculated by the DFT methods were usually small except for the heteroatom-hydrogen BDEs. PMID:14632451

  15. A QSPR study of O-H bond dissociation energy in phenols.

    PubMed

    Bosque, Ramón; Sales, Joaquim

    2003-01-01

    A Quantitative Structure-Property Relationship (QSPR) is developed for the O-H bond dissociation energy (BDE) of a set of 78 phenols. The data set was composed of monosubstituted, disubstituted, and polysubstituted phenolic derivatives containing substituents with different steric and electronic effects in the ortho-, meta-, and para-positions of the aromatic ring. The proposed model, derived from multiple linear regression, contains seven descriptors calculated solely from the molecular structure of compounds. The average absolute relative errors are 1.37% (R(2) = 0.8978; SD: 6.67) and 1.13% (R(2) = 0.9076; SD: 4.26) for the working set (62 compounds) and the prediction set (16 compounds), respectively. These results are better than those obtained from DFT calculations, QSAR approach, and correlations with Hammet parameters. PMID:12653532

  16. Equilibrium Acidities and Homolytic Bond Dissociation Energies of Acidic C H Bonds in Alpha-Arylacetophenones and Related Compounds

    SciTech Connect

    Alnajjar, Mikhail S.); Zhang, Xian-Man; Gleicher, Gerald J.; Truksa, Scott V.; Franz, James A.)

    2002-12-13

    The equilibrium acidities (pKAHs) and the oxidation potentials of the conjugate anions (Eox(A?{approx})s) were determined in dimethyl sulfoxide (DMSO) for eight ketones of the structure GCOCH3 and twenty of the structure RCOCH2G, (where R= alkyl, phenyl and G= alkyl, aryl). The homolytic bond dissociation energies (BDEs) for the acidic C H bonds of the ketones were estimated using the equation, BDEAH= 1.37pKAH+ 23.1Eox(A?{approx})+ 73.3. While the equilibrium acidities of GCOCH3 were found to be dependent on the remote substituent G, the BDE values for the C H bonds remained essentially invariant (93.5+ 0.5 kcal/mol). A linear correlation between pKAH values and (Eox(A?{approx})s) was found for the ketones. For RCOCH2G ketones, both pKAH and BDE values for the adjacent C-H bonds are sensitive to the nature of the substituent G. However, the steric bulk of the aryl group tends to exert a leveling effect on BDE's. The BDE of?p-9-anthracenylacetophenone is higher than that of??-2-anthracenylacetophenone by 3 kcal/mole, reflecting significant steric inhibition of resonance in the 9-substituted system. A range of 80.7 - 84.4 kcal/mole is observed for RCOCH2G ketones. The results are discussed in terms of solvation, steric, and resonance effects. Ab initio density functional theory (DFT) calculations are employed to illustrate the effect of steric interactions on radical and anion geometries. The DFT results parallel the trends in the experimental BDEs of??-arylacetophenones.

  17. Equilibrium acidities and homolytic bond dissociation energies of acidic C-H bonds in alpha-arylacetophenones and related compounds.

    PubMed

    Alnajjar, Mikhail S; Zhang, Xian-Man; Gleicher, Gerald J; Truksa, Scott V; Franz, James A

    2002-12-13

    The equilibrium acidities (pK(AH)s) and the oxidation potentials of the congugate anions [E(ox)(A(-))s] were determined in dimethyl sulfoxide (DMSO) for eight ketones of the structure GCOCH(3) and 20 of the structure RCOCH(2)G, (where R = alkyl, phenyl and G = alkyl, aryl). The homolytic bond dissociation energies (BDEs) for the acidic C-H bonds of the ketones were estimated using the equation BDE(AH) = 1.37pK(AH) + 23.1E(ox)(A(-)) + 73.3. While the equilibrium acidities of GCOCH(3) were found to be dependent on the remote substituent G, the BDE values for the C-H bonds remained essentially invariant (93.5 +/- 0.5 kcal/mol). A linear correlation between pK(AH) values and [E(ox)(A(-))s] was found for the ketones. For RCOCH(2)G ketones, both pK(AH) and BDE values for the adjacent C-H bonds are sensitive to the nature of the substituent G. However, the steric bulk of the aryl group tends to exert a leveling effect on BDEs. The BDE of alpha-9-anthracenylacetophenone is higher than that of alpha-2-anthracenylacetophenone by 3 kcal/mol, reflecting significant steric inhibition of resonance in the 9-substituted system. A range of 80.7-84.4 kcal/mol is observed for RCOCH(2)G ketones. The results are discussed in terms of solvation, steric, and resonance effects. Ab initio density functional theory (DFT) calculations are employed to illustrate the effect of steric interactions on radical and anion geometries. The DFT results parallel the trends in the experimental BDEs of alpha-arylacetophenones. PMID:12467424

  18. 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.

  19. 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.

  20. Benchmark Database for Ylidic Bond Dissociation Energies and Its Use for Assessments of Electronic Structure Methods.

    PubMed

    Zhao, Yan; Ng, Hou T; Peverati, Roberto; Truhlar, Donald G

    2012-08-14

    We report a database of 18 ylidic bond dissociation energies obtained by using highly accurate quantum mechanical methods, and we use it to test approximate electronic structure methods. The new benchmark database is called YBDE18 and is used to test a large number of electronic structure methods, including eight wave function methods and 98 density functional exchange-correlation functionals. Among them, we include some very recent density functionals, including the SOGGA11 GGA functional, the SOGGA11-X hybrid GGA functional, the M11-L local meta-GGA functional, and the M11 range-separated hybrid meta-GGA functional. We also consider other functionals of these classes plus a local spin density approximation, global-hybrid meta-GGAs, range-separated hybrid GGAs, doubly hybrid GGAs, and doubly hybrid meta-GGAs. We found M05-2X-D3, MPWB1K-D3, M05-2X, LC-BLYP, PBE0-D3, and MC3MPWB to be the best DFT methods for this database. Although they do not place in the top four overall, our new-generation functionals show overall competitive performances; each of the new functionals provides the smallest mean signed error within its class, while in terms of mean unsigned errors, SOGGA11 is the best GGA, and SOGGA11-X and M11-L are among the first three best functionals in their categories, global-hybrid GGA and local meta-GGA. The best local functionals are VSXC and M06-L, the best global-hybrids are M05-2X, M08-HX, M06-2X, and MPWB1K, and the best range-separated hybrids are LC-BLYP, ωB97, ωB97X, and M11. PMID:26592123

  1. Isolation, Characterization of an Intermediate in an Oxygen Atom-Transfer Reaction, and the Determination of the Bond Dissociation Energy

    SciTech Connect

    Nemykin, Victor N.; Laskin, Julia; Basu, Partha

    2004-07-19

    Redox reactions coupled with the formal loss or gain of an oxygen atom are ubiquitous in chemical processes. Such reactions proceed through the reduction of the donor center (XO) and the oxidation of the acceptor (Y) molecule. Among many examples of the metal centered oxygen atom transfer (OAT) reactivity, those involving molybdenum complexes have been widely investigated due to their involvement in mononuclear molybdenum enzymes. The heat of reaction of the overall atom transfer process can be expressed as a difference between the bond dissociation energies (BDEs) of the oxygen-donor(X) and oxygen-acceptor(Y) bond, i.e., H=DX=o-DY=O.

  2. 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.

  3. Renewable energy liberation by nonthermal intermolecular bond dissociation in water and ethanol

    NASA Astrophysics Data System (ADS)

    Graneau, N.; Verdoold, S.; Oudakker, G.; Yurteri, C. U.; Marijnissen, J. C. M.

    2011-02-01

    Prior indication that renewable energy can be extracted from hydrogen bonds in water has led to several investigations of the energy balance when bulk liquid is converted into micron scale droplets by directional (nonthermal) forces. The demonstration of this effect has previously involved pulsed high current arcs in water which produce large electrodynamic forces. Here, we show that renewable energy is also liberated during the creation of droplets by electrostatic forces in electrohydrodynamic atomization (electrospray) experiments. Using both ethanol and water, the energy outputs, primarily the droplet kinetic energy, were always greater than the energy inputs, implying that stored energy was liberated from the liquid. The energetics of generic chemical bonding are investigated to demonstrate that although this discovery was not publicly anticipated, it is consistent with conventional theory. This experimental breakthrough should have a major impact on the quest for renewable energy sources, capable of powering electricity generators.

  4. Thermal chemiluminescence from ?-irradiated polytetrafluoroethylene and its emission mechanism: Kinetic analysis and bond dissociation energy of fluoroperoxide group

    NASA Astrophysics Data System (ADS)

    Yamada, Emi; Noguchi, Tsuyoshi; Akai, Nobuyuki; Ishii, Hiroshi; Satoh, Chikahiro; Hironiwa, Takayuki; Millington, Keith R.; Nakata, Munetaka

    2014-11-01

    Temperature dependence of the time evolution of chemiluminescence intensity from ?-irradiated polytetrafluoroethylene was examined by heating isothermally in the range of 150 and 200 C. Kinetic analysis was carried out to estimate the rate constants, from which the dissociation energy of the Osbnd O bond in the fluoroperoxide group was determined to be 97 4 kJ mol-1, being consistent with the corresponding value for small fluorocarbon model systems obtained by quantum chemical calculations. This strongly supports the emission mechanism [sbnd CF(OOF)sbnd CF2sbnd ? sbnd COsbnd CF2sbnd + OF2 + h?] proposed in our previous paper to explain chemiluminescence from the ?-irradiated polytetrafluoroethylene.

  5. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    PubMed

    Ge, Chuanqi; Shen, Yuneng; Deng, Gang-Hua; Tian, Yuhuan; Yu, Dongqi; Yang, Xueming; Yuan, Kaijun; Zheng, Junrong

    2016-03-31

    Isotopic effects on the formation and dissociation kinetics of hydrogen bonds are studied in real time with ultrafast chemical exchange spectroscopy. The dissociation time of hydrogen bond between phenol-OH and p-xylene (or mesitylene) is found to be identical to that between phenol-OD and p-xylene (or mesitylene) in the same solvents. The experimental results demonstrate that the isotope substitution (D for H) has negligible effects on the hydrogen bond kinetics. DFT calculations show that the isotope substitution does not significantly change the frequencies of vibrational modes that may be along the hydrogen bond formation and dissociation coordinate. The zero point energy differences of these modes between hydrogen bonds with OH and OD are too small to affect the activation energy of the hydrogen bond dissociation in a detectible way at room temperature. PMID:26967376

  6. Theoretical study of the C-H bond dissociation energies of CH4, C2H2, C2H4, and H2C2O

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    The successive C-H bond dissociation energies of CH4, C2H2, C2H4, and H2C2O (ketene) are determined using large-basis sets and a high level of correlation treatment. For CH4, C2H2, and C2H4 the computed values are in excellent agreement with experiment. Using these results, the values 107.9 + or - 2.0 and 96.7 + or - 2.0 kcal/mol are recommended for the C-H bond dissociation energies of H2C2O and HC2O, respectively.

  7. Metal-cyclopentadienyl bond energies in metallocene cations measured using threshold collision-induced dissociation mass spectrometry.

    PubMed

    Rowland, Tyson G; Sztáray, Bálint; Armentrout, Peter B

    2013-02-14

    Metal-cyclopentadienyl bond dissociation energies (BDEs) were measured for seven metallocene ions (Cp(2)M(+), Cp = η(5)-cyclopentadienyl = c-C(5)H(5), M = Ti, V, Cr, Mn, Fe, Co, Ni) using threshold collision-induced dissociation (TCID) performed in a guided ion beam tandem mass spectrometer. For all seven room temperature metallocene ions, the dominant dissociation pathway is simple Cp loss from the metal. Traces of other fragment ions were also detected, such as C(10)H(10)(+), C(10)H(8)(+), C(8)H(8)(+), C(3)H(3)(+), H(2)M(+), C(3)H(3)M(+), C(6)H(6)M(+), and C(7)H(6)M(+), depending on the metal center. Statistical modeling of the Cp-loss TCID experimental data, including consideration of energy distributions, multiple collisions, and kinetic shifts, allow the extraction of 0 K [CpM(+)- Cp] BDEs. These are found to be 4.85 ± 0.15, 4.02 ± 0.14, 4.22 ± 0.13, 3.51 ± 0.12, 4.26 ± 0.15, 4.57 ± 0.15, and 3.37 ± 0.12 eV for Cp(2)Ti(+), Cp(2)V(+), Cp(2)Cr(+), Cp(2)Mn(+), Cp(2)Fe(+), Cp(2)Co(+), and Cp(2)Ni(+), respectively. The measured BDE trend is largely in line with arguments based on a simple molecular orbital picture, with the exception of the anomalous case of titanocene, most likely attributable to its bent structure. The new results presented here are compared to previous literature values and are found to provide a more complete and accurate set of thermochemistry. PMID:23215634

  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. Photodissociation measurements of bond dissociation energies: Ti[sup +][sub 2], V[sup +][sub 2], Co[sup +][sub 2], and Co[sup +][sub 3

    SciTech Connect

    Russon, L.M.; Heidecke, S.A.; Birke, M.K.; Conceicao, J.; Morse, M.D.; Armentrout, P.B. )

    1994-04-01

    The bond dissociation energies of Ti[sup +][sub 2], V[sup +][sub 2], Co[sup +][sub 2], and Co[sup +][sub 3] have been measured from the sudden onset of predissociation in the photodissociation spectra of these molecules, yielding values of [ital D][sup [circ

  10. Effect of an external electric field on the dissociation energy and the electron density properties: The case of the hydrogen bonded dimer HF...HF.

    PubMed

    Mata, Ignasi; Molins, Elies; Alkorta, Ibon; Espinosa, Enrique

    2009-01-28

    The effect of a homogeneous external electric field parallel to the hydrogen bond in the FH...FH dimer has been studied by theoretical methods. The quantum theory of atoms in molecules methodology has been used for analyzing the electron distribution of the dimer, calculated with different hydrogen bond distances and external field magnitudes. It is shown that an electric field in the opposite direction to the dipole moment of the system strengthens the interaction due to a larger mutual polarization between both molecules and increases the covalent character of the hydrogen bond, while an external field in the opposite direction has the inverse effect. The properties of the complex at its equilibrium geometry with applied field have been calculated, showing that dependencies between hydrogen bond distance, dissociation energy, and properties derived from the topological analysis of the electron distribution are analogous to those observed in families of XDH...AY complexes. The application of an external field appears as a useful tool for studying the effect of the atomic environment on the hydrogen bond interaction. In the case of FH...FH, both the kinetic energy density and the curvature of the electron density along the hydrogen bond at the bond critical point present a surprisingly good linear dependence on the dissociation energy. The interaction energy can be modeled by the sum of two exponential terms that depend on both the hydrogen bond distance and the applied electric field. Moreover, as indicated by the resulting interaction energy observed upon application of different external fields, the equilibrium distance varies linearly with the external field, and the dependence of the dissociation energy on either the hydrogen bond distance or the external electric field is demonstrated to be exponential. PMID:19191374

  11. 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.

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

    PubMed

    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. PMID:25669533

  13. 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.

  14. Copper Complexes with NH-Imidazolyl and NH-Pyrazolyl Units and Determination of Their Bond Dissociation Gibbs Energies.

    PubMed

    Wilting, Alexander; Kügler, Merle; Siewert, Inke

    2016-02-01

    We synthesized two dinuclear copper complexes, which have ionizable N imidazole and N pyrazole protons in the ligand, respectively, and determined the BDFE of the hypothetical H atom transfer reactions Cu(II)(LH-1) + H(•) ↔ Cu(I)(L) in MeOH/H2O (BDFE: bond dissociation Gibbs (free) energy). The ligands have two adjacent N,N',O-binding pockets, which differ in one N-heterocycle: L(a) has an imidazole unit and L(c), a pyrazole unit. The copper(II) complexes of L(a) and L(c) have been characterized, and the substitution pattern has only little influence on the structural properties. The BDFEs of the hypothetical PCET reactions have been determined by means of the species distribution and the redox potentials of the involved species in MeOH/H2O (80/20 by weight). The pyrazole copper complex 3 exhibits a lower BDFE than the isoelectronic imidazole copper complex 1 (1, 292(3) kJ mol(-1); 3, 279(1) kJ mol(-1)). The difference is mainly caused by the higher acidity of the N pyrazole proton of 3 compared to the N imidazole proton of 1. The redox potentials of 1 and 3 are very similar. PMID:26788812

  15. 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.

  16. Mechanistic Investigation of Phosphate Ester Bond Cleavages of Glycylphosphoserinyltryptophan Radical Cations under Low-Energy Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Quan, Quan; Hao, Qiang; Song, Tao; Siu, Chi-Kit; Chu, Ivan K.

    2013-04-01

    Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G p SW]•+) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G• p SW]+). The dissociation of [G• p SW]+ is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H]•+/y1 + pair as the minor products. In contrast, for [G p SW]•+, competitive cleavages along the peptide backbone, such as the formation of [G p SW - CO2]•+ and the [c2 + 2H]+/[z1 - H]•+ pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G• p SW]+ and [G p SW]•+ and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G• p SW]+ results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G p SW]•+.

  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. Linear free energy relationships in C-N bond dissociations in molecular ions of 4-substituted N-(2-furylmethyl)anilines in the gas phase.

    PubMed

    Solano Espinoza, Eduardo A; Stashenko, Elena; Martínez, Jairo; Mora, Uriel; Kouznetsov, Vladimir

    2007-11-01

    The substituent effect on the reactivity of the C-N bond of molecular ions of 4-substituted N-(2-furylmethyl)anilines toward two dissociation pathways was studied. With this aim, six of these compounds were analyzed by mass spectrometry using electron ionization with energies between 7.8 and 69.9 eV. Also, the UB3LYP/6-31G (d,p) and UHF/6-31G (d, p) levels of theory were used to calculate the critical energies (reaction enthalpies at 0 K) of the processes that lead to the complementary ions [C(5)H(5)O](+) and [M - C(5)H(5)O](+), assuming structures that result from the heterolytic and homolytic C-N bond cleavages of the molecular ions, respectively. A kinetic approach proposed in the 1960s was applied to the mass spectral data to obtain the relative rate coefficients for both dissociation channels from ratios of the peak intensities of these ions. Linear relationships were obtained between the logarithms of the relative rate coefficients and the calculated critical energies and other thermochemical properties, whose slopes showed to be conditioned by the energy provided to the compounds within the ion source. Moreover, it was found that the dissociation that leads to [C(5)H(5)O](+) is a process strongly dependent upon the electron withdrawing or donating properties of the substituent, favored by those factors that destabilize the molecular ion. On the contrary, the dissociation that leads to [M - C(5)H(5)O](+) is indifferent to the polar electronic effects of the substituent. The abundance of both products was governed by the rule of Stevenson-Audier, according to which the major ion is the one of less negative electronic affinity. PMID:17687763

  19. 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.

  20. 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.

  1. Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory

    SciTech Connect

    DiLabio, Gino A.; Koleini, Mohammad; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4

    2014-05-14

    Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the “S66” set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the “D3” pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.

  2. Effect of the Hydrogen Bond in Photoinduced Water Dissociation: A Double-Edged Sword.

    PubMed

    Yang, Wenshao; Wei, Dong; Jin, Xianchi; Xu, Chenbiao; Geng, Zhenhua; Guo, Qing; Ma, Zhibo; Dai, Dongxu; Fan, Hongjun; Yang, Xueming

    2016-02-18

    Photoinduced water dissociation on rutile-TiO2 was investigated using various methods. Experimental results reveal that the water dissociation occurs via transferring an H atom to a bridge bonded oxygen site and ejecting an OH radical to the gas phase during irradiation. The reaction is strongly suppressed as the water coverage increases. Further scanning tunneling microscopy study demonstrates that hydrogen bonds between water molecules have a dramatic effect on the reaction. Interestingly, a single hydrogen bond in water dimer enhances the water dissociation reaction, while one-dimensional hydrogen bonds in water chains inhibit the reaction. Density functional theory calculations indicate that the effect of hydrogen bonds on the OH dissociation energy is likely the origin of this remarkable behavior. The results suggest that avoiding a strong hydrogen bond network between water molecules is crucial for water splitting. PMID:26810945

  3. 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.

  4. Highly Selective Dissociation of a Peptide Bond Following Excitation of Core Electrons.

    PubMed

    Lin, Yi-Shiue; Tsai, Cheng-Cheng; Lin, Huei-Ru; Hsieh, Tsung-Lin; Chen, Jien-Lian; Hu, Wei-Ping; Ni, Chi-Kung; Liu, Chen-Lin

    2015-06-18

    The controlled breaking of a specific chemical bond with photons in complex molecules remains a major challenge in chemistry. In principle, using the K-edge absorption of a particular atomic element, one might excite selectively a specific atomic entity in a molecule. We report here highly selective dissociation of the peptide bonds in N-methylformamide and N-methylacetamide on tuning the X-ray wavelength to the K-edge absorption of the atoms connected to (or near) the peptide bond. The high selectivity (56-71%) of this cleavage arises from the large energy shift of X-ray absorption, a large overlap of the 1s orbital and the valence π* orbital that is highly localized on a peptide bond with antibonding character, and the relatively low bond energy of the peptide bonds. These characteristics indicate that the high selectivity on bond dissociation following core excitation could be a general feature for molecules containing peptide bonds. PMID:25988354

  5. Does Electron Capture Dissociation Cleave Protein Disulfide Bonds?

    PubMed Central

    Ganisl, Barbara; Breuker, Kathrin

    2012-01-01

    Peptide and protein characterization by mass spectrometry (MS) relies on their dissociation in the gas phase into specific fragments whose mass values can be aligned as ‘mass ladders’ to provide sequence information and to localize possible posttranslational modifications. The most common dissociation method involves slow heating of even-electron (M+n H)n+ ions from electrospray ionization by energetic collisions with inert gas, and cleavage of amide backbone bonds. More recently, dissociation methods based on electron capture or transfer were found to provide far more extensive sequence coverage through unselective cleavage of backbone N–Cα bonds. As another important feature of electron capture dissociation (ECD) and electron transfer dissociation (ETD), their unique unimolecular radical ion chemistry generally preserves labile posttranslational modifications such as glycosylation and phosphorylation. Moreover, it was postulated that disulfide bond cleavage is preferred over backbone cleavage, and that capture of a single electron can break both a backbone and a disulfide bond, or even two disulfide bonds between two peptide chains. However, the proposal of preferential disulfide bond cleavage in ECD or ETD has recently been debated. The experimental data presented here reveal that the mechanism of protein disulfide bond cleavage is much more intricate than previously anticipated. PMID:24363980

  6. C-C and C-Heteroatom Bond Dissociation Energies in CH3R′C(OH)2: Energetics for Photocatalytic Processes of Organic Diolates on TiO2 Surfaces

    SciTech Connect

    Wang, Tsang-Hsiu; Dixon, David A.; Henderson, Michael A.

    2010-08-26

    The bond energies of a range of gem-diols, CH3R′C(OH)2 (R′ = H, F, Cl, Br, CN, NO2, CF3, CH3CH2, CH3CH2CH2, CH3CH2CH2CH2, ((CH3)2)CH, (CH3)3C, ((CH3)2CH)CH2, (CH3CH2)(CH3)CH, C6H5 (CH3CH2)(CH3)CH) which serve as models for binding to a surface have been studied with density functional theory (DFT) and the molecular orbital G3(MP2) methods to provide thermodynamic data for the analysis of the photochemistry of ketones on TiO2. The ultraviolet (UV) photon-induced photodecomposition of adsorbed acetone and 3,3-dimethylbutanone on the rutile TiO2 (110) surface have been investigated with photon stimulated desorption (PSD) and temperature programmed desorption (TPD). The C-CH3 and C-C(R′) bond dissociation energies in CH3R′C(OH)2 were predicted, and our calculated bond dissociation energies are in excellent agreement with the available experimental values. We used a series of isodemic reactions to provide small corrections to the various bond dissociation energies. The calculated bond dissociation energies are in agreement with the observed photodissociation processes except for R′ = CF3, suggesting that these processes are under thermodynamic control. For R′ = CF3, reaction dynamics also play a role in determining the photodissociation mechanism. The gas phase Brönsted acidities of the gem-diols were calculated. For three molecules, R′ = Cl, Br, and NO2, loss of a proton leads to the formation of a complex of acetic acid with the anion Cl-, Br-, and NO2-. The acidities of these three species are very high with the former two having acidities comparable to CF3SO3H. The ketones (R′RC(=O)) are weak Lewis acids except where addition of OH- leads to the dissociation of the complex to form an anion bonded to acetic acid, R' = NO2, Cl, and Br. The X-C bond dissociation energies for a number of X-CO2- species were calculated and these should be useful in correlating with photochemical reactivity studies.

  7. Exploring the energy disposal immediately after bond-breaking in solution: the wavelength-dependent excited state dissociation pathways of para-methylthiophenol.

    PubMed

    Zhang, Yuyuan; Oliver, Thomas A A; Das, Saptaparna; Roy, Anirban; Ashfold, Michael N R; Bradforth, Stephen E

    2013-11-21

    A wavelength-resolved (?pump = 295, 285, 270, and 267 nm) photodissociation study of para-methylthiophenol (p-MePhSH) in ethanol solution has been performed using femtosecond transient absorption (TA) spectroscopy, and the results compared with those from studies of the corresponding photodissociation in cyclohexane solution at 270 nm. Anisotropy spectra are used to identify the electronic character of the initially populated excited state(s). S-H bond fission is found to occur via the dissociative S2(1(1)??*) state, which can be populated directly, or by ultrafast nonradiative transitions from the S3(2(1)??*) state, or by very efficient tunneling from the S1(1(1)??*) state, depending on the excitation wavelength, in line with conclusions from previous gas-phase studies of this same molecular photodissociation (Oliver, T. A. A.; King, G. A.; Tew, D. P.; Dixon R. N.; Ashfold, M. N. R. J. Phys. Chem. A 2012, 116, 12444). p-MePhS radicals are observed on a time scale faster than the instrument response at all wavelengths, but the available time resolution affords a rare opportunity to explore the branching between different electronic states of a product (the and X? states of the p-MePhS radical in this case). The present study provides estimates of this branching in the products formed immediately after the first pass through the conical intersection (CI) between the S2 and S0 states. At 270 nm, for example, we identify a marked population inversion in the radical products, in contrast to the reported gas phase behavior. The finding that the contrast in branching ratio is largest between cyclohexane solution and the gas phase, with ethanol being intermediate, can be rationalized by recognizing the differing distributions of the S-H torsion angle (relative to the ring plane) in a room temperature solution compared with those in a jet-cooled molecular beam. The available time resolution also allows exploration of the electronic quenching of nascent state radicals as solvent motion encourages recrossing of the S2/S0 CI. The average separation distance, , between the H + p-MePhS products arising in successful dissociation events is seen to increase with decreasing photolysis wavelength. This finding accords with the previous gas phase results, which determined that most of the excess energy following population of the dissociative S2 state (directly, or by ultrafast coupling from the S3 state) is released as product translation, and the expectation that should scale with the total kinetic energy release. The present work also confirms that geminate recombination of the H + p-MePhS products leads not just to reformation of parent p-MePhSH molecules but also to alternative adducts wherein the H atom bonds to the benzene ring. Analysis of the present data and results of high level ab initio calculations together with recent UV-IR pump-probe measurements (Murdock, D.; Harris, S. J.; Karsili, T. N. V.; Greetham, G. M.; Clark, I. P.; Towrie, M.; Orr-Ewing, A. J.; Ashfold, M. N. R. J. Phys. Chem. Lett. 2012, 3, 3715) allows identification of the likely adduct structures. PMID:24047130

  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

    2014-10-01

    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. PMID:25180943

  9. 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.

  10. On the dissociation energy of Mg2

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    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.

  11. Competition between covalent and noncovalent bond cleavages in dissociation of phosphopeptide-amine complexes.

    PubMed

    Laskin, Julia; Yang, Zhibo; Woods, Amina S

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel. PMID:21387029

  12. Hydrogen-bond symmetrization and molecular dissociation in hydrogen halids

    NASA Astrophysics Data System (ADS)

    Aoki, K.; Katoh, E.; Yamawaki, H.; Sakashita, M.; Fujihisa, H.

    1999-04-01

    Hydrogen chloride is a simple diatomic molecule forming a planar zig-zag chain of molecules connected by hydrogen bonds in the solid phase. Raman spectra were measured for solid HCl to 60 GPa at room temperature. The molecular stretching frequency falls toward zero at about 51 GPa, where the molecular vibrational peaks disappear and the lattice peaks remain. The spectral changes are very similar to those observed for HBr at about 42 GPa and interpreted as hydrogen bond symmetrization. Molecular dissociation into diatomic halogen molecules, which has been observed for HBr, does not occur in HCl.

  13. Collisions induced dissociation and Ab initio study of azobenzene derivatives bond structure and electronic configuration

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    2015-05-01

    Collision induced dissociation (CID) and ab initio calculations were utilized to study a few derivatives of azobenzene molecule and their product ions. High level computational methods along with large basis set size yield values in close agreement with the experimental results. Mller-Plesset and coupled-cluster theory including perturbative triple excitations, CCSD(T), method were performed to obtain a high accuracy estimation of the bond dissociation energy value. The electron affinities have been studied experimentally using the photoelectron spectroscopy method as well as theoretically using ab inito calculations. For the trans-2,2',6,6' tetra-fluoro azobenzene the bond dissociation has been experimentally determined to be 1.88 eV and the vertical detachment energy is 1.78 eV.

  14. Competition between Covalent and Noncovalent Bond Cleavages in Dissociation of Phosphopeptide-Amine Complexes

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Woods, Amina S.

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A3pXA3-NH2 (X=S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. We demonstrate that covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel

  15. Dissociation Energies of Deoxyribose Nucleotide Dimer Anions Measured Using Blackbody Infrared Radiative Dissociation

    PubMed Central

    Strittmatter, Eric F.; Schnier, Paul D.; Klassen, John S.; Williams, Evan R.

    2005-01-01

    The dissociation kinetics of deprotonated deoxyribose nucleotide dimers were measured using blackbody infrared radiative dissociation. Experiments were performed with noncovalently bound dimers of phosphate, adenosine (dAMP), cytosine (dCMP), guanosine (dGMP), thymidine (dTMP), and the mixed dimers dAMP · dTMP and dGMP · dCMP. The nucleotide dimers fragment through two parallel pathways, resulting in formation of the individual nucleotide or nucleotide + HPO3 ion. Master equation modeling of this kinetic data was used to determine threshold dissociation energies. The dissociation energy of (dGMP · dCMP − H)− is much higher than that for the other nucleotide dimers. This indicates that there is a strong interaction between the nucleobases in this dimer, consistent with the existence of Watson–Crick hydrogen bonding between the base pairs. Molecular mechanics simulations indicate that Watson–Crick hydrogen bonding occurs in the lowest energy structures of (dGMP · dCMP − H)−, but not in (dAMP · dTMP − H)−. The trend in gas phase dissociation energies is similar to the trend in binding energies measured in nonaqueous solutions within experimental error. Finally, the acidity ordering of the nucleotides is determined to be dTMP < GMP < CMP < AMP, where dAMP has the highest acidity (largest ΔGacid). PMID:10536816

  16. 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.

  17. 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. PMID:25760799

  18. Ab initio characterization of the HCO{sup x} (x = {minus}1, 0, +1) species: Structures, vibrational frequencies, CH bond dissociation energies, and HCO ionization potential and electron affinity

    SciTech Connect

    Mourik, T. van; Dunning, T.H. Jr.; Peterson, K.A.

    2000-03-23

    The potential energy surfaces of the HCO{sup x} (x = +1, 0, -1) species near their equilibrium geometries have been calculated employing coupled cluster methods with augmented correlation consistent basis sets. The equilibrium structures, vibrational frequencies, zero point energies, and dissociation energies were computed for all three species. Valence-electron CCSD(T) calculations with the aug-cc-pV5Z basis set predict CH bond dissociation energies, D{sub 0}, of 140.3 kcal/mol for HCO{sup +}, 14.0 kcal/mol for HCO, and 4.5 kcal/mol for HCO{sup {minus}}, in good agreement with experiment (140.1 {+-} 1, 13.9--14.3, and 5.2 {+-} 0.2 kcal/mol, respectively). The same calculations predict the electron affinity, EA{sub 0}, and ionization potential, IP{sub 0}, of HCO to be 7.7 and 187.3 kcal/mol; these values are within 0.5 kcal/mol of the measured values. Inclusion of core-valence correlation corrections has only a minor effect on the calculated energetics.

  19. 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. PMID:26574366

  20. Threshold collision-induced dissociation of hydrogen-bonded dimers of carboxylic acids.

    PubMed

    Jia, Beike; Angel, Laurence A; Ervin, Kent M

    2008-02-28

    Energy-resolved competitive collision-induced dissociation is used to investigate the proton-bound heterodimer anions of a series of carboxylic acids (formic, acetic, and benzoic acid) and nitrous acid with their conjugate bases. The dissociation reactions of the complexes [CH3COO.H.OOCH]-, [CH3COO.H.ONO]-, [HCOO.H. ONO]-, [C6H5COO.H.OOCH]-, and [C6H5COO.H.ONO]- are investigated using a guided ion beam tandem mass spectrometer. Cross sections of the two dissociation channels are measured as a function of the collision energy between the complex ions and xenon target gas. Apparent relative gas-phase acidities are found by modeling the cross sections near the dissociation thresholds using statistical rate theory. Internal inconsistencies are found in the resulting relative acidities. These deviations apparently result from the formation of higher-energy conformers of the acids within the complex ions induced by double hydrogen bonding, which impedes the kinetics of dissociation to ground-state product acid conformations. PMID:18232677

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

    PubMed Central

    Hutchins, Patrick M.; Murphy, Robert C.

    2013-01-01

    The oxidative modification of polyunsaturated fatty acids which occurs through enzymatic and non-enzymatic 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 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. PMID:21472521

  2. The Effect of Hydrogen on the Bonding and Dissociation of Carbon Monoxide on AN IRON(100) Surface

    NASA Astrophysics Data System (ADS)

    Nassir, Mohamed Husain

    1993-01-01

    Adsorption and coadsorption of CO and H _2 on Fe(100) was studied using the following six methods: Temperature programmed desorption (TPD), x -ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), single reflection Fourier transform infrared spectroscopy (FTIR) and low-energy electron diffraction (LEED). The binding and dissociation of CO on a clean and hydrogen presaturated Fe(100) surface were investigated to provide better understanding of the first step in the Fischer-Tropsch synthesis, an important industrial catalytic reaction for converting CO and hydrogen to hydrocarbon. CO adsorbs molecularly on the clean surface in three states alpha_1, alpha_2 and alpha_3 . At temperatures above 350 K but below 440 K, CO is bound to the surface only in the highly perturbed alpha_3 state (pi -bonded geometry). The CO alpha_3 molecules are believed to occupy the 4-fold hollow sites. When the surface temperature is raised above 440 K, a fraction of the alpha_3 desorbs and the remainder dissociates. The dissociation fragments replace the CO alpha_3 molecules in the 4-fold hollow sites. These fragments recombine at higher temperatures and appear as beta CO. The bonding and dissociation of CO in the alpha_3 received more attention because it is believed that this state is a precursor to dissociation. A model describing the partitioning between desorption and dissociation is proposed in which the dissociation fragments displace the strongly bound CO in the beta -bonded state. The stoichiometry of this reaction at saturation requires that only half the original CO adsorbed in the beta-bonded CO state can dissociate. Presaturating the surface with hydrogen affects the bonding and dissociation of CO on the iron surface. One effect is to weaken CO-Fe bonds which results in a very weakly bound state (alpha^' _1). In addition to the alpha ^'_1 state, presaturating the surface with hydrogen results in isolating the alpha^'_2 state. Another effect of preadsorbed hydrogen appears in the alpha_3 state. The ratio of dissociation to desorption changes and suggests that hydrogen may induce island formation in the CO adlayer. Both factors, weakening CO-Fe bonds and influencing the dissociation/desorption ratio, might play an important role in the Fischer-Tropsch synthesis.

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

    PubMed

    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. PMID:26297186

  4. Formation, structure and bond dissociation thresholds of gas-phase vanadium oxide cluster ions

    NASA Astrophysics Data System (ADS)

    Bell, R. C.; Zemski, K. A.; Justes, D. R.; Castleman, A. W.

    2001-01-01

    The formation and structure of gas-phase vanadium oxide cluster anions are examined using a guided ion beam mass spectrometer coupled with a laser vaporization source. The dominant peaks in the anion total mass distribution correspond to clusters having stoichiometries of the form (VO2)n(VO3)m(O2)q-. Collision-induced dissociation studies of the vanadium oxide species V2O4-6-, V3O6-9-, V4O8-10-, V5O11-13-, V6O13-15-, and V7O16-18- indicate that VO2, VO3, and V2O5 units are the main building blocks of these clusters. There are many similarities between the anion mass distribution and that of the cation distribution studied previously. The principal difference is a shift to higher oxygen content by one additional oxygen atom for the stoichiometric anions (VxOy-) as compared to the cations with the same number of vanadium atoms, which is attributed to the extra pair of electrons of the anionic species. The oxygen-rich clusters, VxOy(O2)-, are shown to more tightly adsorb molecular oxygen than those of the corresponding cationic clusters. In addition, the bond dissociation thresholds for the vanadium oxide clusters ΔE(V+-O)=6.09±0.28 eV, ΔE(OV+-O)=3.51±0.36 eV, and ΔE(O2V--O)=5.43±0.31 eV are determined from the energy-dependent collision-induced dissociation cross sections with Xe as the collision partner. To the best of our knowledge, this is the first bond dissociation energy reported for the breaking of the V-O bond of a vanadium oxide anion.

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

    NASA Astrophysics Data System (ADS)

    Farjamnia, Azar; Jackson, Bret

    2015-06-01

    A fully quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of H2O, HOD, and D2O 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 D2O 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.

  6. Bond dissociation mechanism of ethanol during carbon nanotube synthesis via alcohol catalytic CVD technique: Ab initio molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Oguri, Tomoya; Shimamura, Kohei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu

    2014-03-01

    Dissociation of ethanol on a nickel cluster is investigated by ab initio molecular dynamics simulation to reveal the bond dissociation mechanism of carbon source molecules during carbon nanotube synthesis. C-C bonds in only CHxCO fragments are dissociated on the nickel cluster, whereas there is no preferential structure among the fragments for C-O bond dissociation. The dissociation preference is uncorrelated with the bond dissociation energy of corresponding bonds in freestanding molecules but is correlated with the energy difference between fragment molecules before and after dissociation on the nickel surface. Moreover, carbon-chain formation occurs after C-C bond dissociation in a continuous simulation. What determines the chirality of CNTs? What happens at the dissociation stage of carbon source molecules? Regarding the former question, many researchers have pointed out the good epitaxial relationship between a graphite network and a close-packed facet (i.e., fcc(1 1 1) or hcp(0 0 0 1)) of transition metals [17-19]. Therefore, the correlation between the chirality of CNTs and the angle of the step edge on metal (or metal carbide) surfaces has been closely investigated [20-22]. In association with this geometric matching, the epitaxial growth of graphene on Cu(1 1 1) and Ni(1 1 1) surfaces has recently been achieved via CCVD technique [23-25], which is a promising technique for the synthesis of large-area and monolayer graphene.Regarding the latter question, it is empirically known that the yield and quality of CNT products strongly depend on the choice of carbon source molecules and additives. For example, it is well known that the use of ethanol as carbon source molecules yields a large amount of SWNTs without amorphous carbons (called the alcohol CCVD (ACCVD) technique) compared with the CCVD process using hydrocarbons [4]. Moreover, the addition of a small amount of water dramatically enhances the activity and lifetime of the catalytic metal (called the supergrowth CVD technique) [26]. Recently, several experimental studies have been carried out in an attempt to understand these complicated dissociation processes. For example, Tomie et al. [27] performed in situ mass spectroscopic analysis during CNT synthesis by the ACCVD technique and revealed that ethylene molecules are formed by the dissociation of ethanol, which means that C-O bonds in the ethanol molecules are dissociated during CNT synthesis. Moreover, Xiang et al. [28] employed isotopically labeled ethanol (i.e., 12CH3-13CH2-OH, 13CH3-12CH2-OH, and so forth) to trace the carbon atoms during CNT synthesis and revealed that the carbon further away from the hydroxyl group in the ethanol is preferentially incorporated into the SNWT structure, which was confirmed from the different G band peaks of the Raman spectra. This experimental finding shows that the C-C bonds in ethanol molecules are dissociated during CNT synthesis. Although many experimental studies [29-32] have revealed part of the dissociation process during CNT growth, it is not yet well understood how the initial dissociation of carbon source molecules affects the subsequent formation process of CNTs.In parallel with the many experimental studies, there has been numerous computational works focusing on the formation process of CNTs. However, most of these studies [9-16] did not take the dissociation of carbon source molecules into account and examined the cap formation process starting from isolated carbon atoms. This is mainly due to the fact that a low-impact interatomic potential appropriately describing the dissociation of carbon source molecules has not been established for classical molecular dynamics (MD) simulation. Meanwhile, several classical MD simulations using the ReaxFF potential [33], which describes chemical reactions with a reasonable degree of accuracy but has a high computational cost, have demonstrated the dissociation of hydrocarbons on a nickel cluster [34] and a flat metal surface [35]. However, it is still challenging to treat the dissociation process of carbon source molecules in classical MD simulations in general.Under such circumstances, we have previously investigated the dissociation process of carbon source molecules at the initial stage of CNT [36,37] and graphene growth [38] by ab initio MD simulation, which simultaneously takes into account both chemical reactions with the accuracy of ab initio calculation and the dynamics of atoms. The current situation regarding the study of ethanol dissociation on Ni clusters as the initial stage of the ACCVD process [37] can be summarized as follows. Both C-C and C-O bonds in ethanol molecules are dissociated as well as C-H bonds, and subsequently various reaction products such as hydrogen atoms and molecules, carbon monoxide, oxygen atoms, water, ethylene, methane, and their fragments are formed. When dissociated hydrogen atoms cover the surface of the nickel cluster, they inhibit the additional adsorption and dissociation of ethanol molecules. Therefore, in a 10 ps simulation, C-C and C-O bond dissociation did not occur as often as C-H bond dissociation. Hence, it was not possible to clarify the preferential dissociation path of either C-C or C-O bonds in the previous study [37].On the basis of the above experience, here we investigate the energetic stability of fragment molecules before and after dissociation on a catalytic-metal surface to reveal the preferential dissociation path under CNT growth conditions via the ACCVD method. First, a subsequent ab initio MD simulation is performed starting from the atomic configuration extracted from the previous simulation [37] except for previously dissociated hydrogen atoms to enhance further C-C and C-O bond dissociations efficiently. Then, the bond dissociation energies of the C-C and C-O bonds in the fragment molecules obtained from the MD simulation are examined. Moreover, the energy difference between fragment molecules before and after dissociation on the Ni(1 1 1) surface is estimated on the basis of Hess's law. Then, the role of the metal catalyst in the dissociation process of carbon source molecules during CNT synthesis is discussed.

  7. 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).

  8. 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.

  9. Generation of pyridyl coordinated organosilicon cation pool by oxidative Si-Si bond dissociation

    PubMed Central

    Nokami, Toshiki; Soma, Ryoji; Yamamoto, Yoshimasa; Kamei, Toshiyuki; Itami, Kenichiro; Yoshida, Jun-ichi

    2007-01-01

    An organosilicon cation stabilized by intramolecular pyridyl coordination was effectively generated and accumulated by oxidative Si-Si bond dissociation of the corresponding disilane using low temperature electrolysis, and was characterized by NMR and CSI-MS. PMID:17288603

  10. Generation of pyridyl coordinated organosilicon cation pool by oxidative Si-Si bond dissociation.

    PubMed

    Nokami, Toshiki; Soma, Ryoji; Yamamoto, Yoshimasa; Kamei, Toshiyuki; Itami, Kenichiro; Yoshida, Jun-Ichi

    2007-01-01

    An organosilicon cation stabilized by intramolecular pyridyl coordination was effectively generated and accumulated by oxidative Si-Si bond dissociation of the corresponding disilane using low temperature electrolysis, and was characterized by NMR and CSI-MS. PMID:17288603

  11. 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.

  12. 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.

  13. 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.…

  14. Computational Study of Bond Dissociation Enthalpies for Lignin Model Compounds. Substituent Effects in Phenethyl Phenyl Ethers

    SciTech Connect

    Beste, Ariana; Buchanan III, A C

    2009-01-01

    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 (PhCH2CH2OPh, PPE) is the simplest example representing the dominant -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.

  15. 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 NiC/NiC(+), which are not known experimentally, we recommend the CCSDTQ(Full)/CBS predictions [D(0)(Ni-C)=4.048 eV, D(0)(Ni(+)-C)=3.360 eV, ΔH(o)(f0)(NiC)=749.0 kJ/mol, and ΔH(o)(f0)(NiC(+))=1555.1 kJ/mol]. PMID:20866136

  16. Quinoxaline-1,4-dioxide: Substituent effects on the N O bond dissociation enthalpy

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Ribeiro da Silva, Maria D. M. C.; Ribeiro da Silva, Manuel A. V.

    2006-09-01

    DFT calculations have been performed to investigate the effect of several different substituents on the N-O bond dissociation enthalpies of 2-substituted-quinoxaline-1,4-dioxides. Further, the influence of electron and proton affinities and also of N-O bond dissociation enthalpies on the antitumor activity of selected compounds is analyzed. In agreement with experimental data, the calculations suggest that Tirapazamine is more active than Quindoxin due to a much easier reduction and protonation of the former species accompanied by a weaker N-OH bond.

  17. 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.

  18. 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.

  19. Dissociation of biological catch-bond by periodic perturbation.

    PubMed

    Pereverzev, Yuriy V; Prezhdo, Oleg V

    2006-07-15

    The analysis of the P-selectin/PSGL-1 catch-slip bond that is periodically driven by a detaching force predicts that in the frequency range on the order of 1 s(-1) the bond lifetime undergoes significant changes with respect to both frequency and amplitude of the force. The result indicates how variations in the heart rate could have a substantial effect on leukocyte and lymphoid cell transport and adhesion to endothelial cells and platelets during inflammatory processes. PMID:16698784

  20. Dynamics of C-Br bond dissociation in methyl 2-bromopropionate at 235 nm: A resonance-enhanced multiphoton ionization study

    NASA Astrophysics Data System (ADS)

    Saha, Ankur; Kumar, Awadhesh; Naik, Prakash D.

    2016-01-01

    The dynamics of the C-Br bond dissociation on UV excitation of methyl 2-bromopropionate mainly to the 1(n?*) state, repulsive in the C-Br bond, has been investigated, employing resonance-enhanced multiphoton ionization. Both the ground state and spin-orbits excited bromine atoms were detected, with the former being the major channel. Bromine fragments show bimodal translational energy distributions, with slow and fast (major) bromine atoms arising mainly from the ground and excited electronic states, respectively. The measured recoil anisotropy suggests isotropic angular distributions of bromine atoms. Molecular orbital calculations reveal an important role of avoided curve crossing on C-Br bond dissociation dynamics.

  1. 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.

  2. Collision Induced Dissociation Products of Disulfide-Bonded Peptides: Ions Result from the Cleavage of More Than One Bond

    NASA Astrophysics Data System (ADS)

    Clark, Daniel F.; Go, Eden P.; Toumi, Melinda L.; Desaire, Heather

    2011-03-01

    Disulfide bonds are a post-translational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is not easy because of various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during collision induced dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a quadrupole time of flight (QTOF) instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. These data show that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/ y cleavage products could not.

  3. Effect of loading conditions on the dissociation behaviour of catch bond clusters.

    PubMed

    Sun, L; Cheng, Q H; Gao, H J; Zhang, Y W

    2012-05-01

    Under increasing tensile load, the lifetime of a single catch bond counterintuitively increases up to a maximum and then decreases exponentially like a slip bond. So far, the characteristics of single catch bond dissociation have been extensively studied. However, it remains unclear how a cluster of catch bonds behaves under tensile load. We perform computational analysis on the following models to examine the characteristics of clustered catch bonds: (i) clusters of catch bonds with equal load sharing, (ii) clusters of catch bonds with linear load sharing, and (iii) clusters of catch bonds in micropipette-manipulated cell detachment. We focus on the differences between the slip and catch bond clusters, identifying the critical factors for exhibiting the characteristics of catch bond mechanism for the multiple-bond system. Our computation reveals that for a multiple-bond cluster, the catch bond behaviour could only manifest itself under relatively uniform loading conditions and at certain stages of decohesion, explaining the difficulties in observing the catch bond mechanism under real biological conditions. PMID:21937488

  4. Force modulating dynamic disorder: a physical model of catch-slip bond transitions in receptor-ligand forced dissociation experiments.

    PubMed

    Liu, Fei; Ou-Yang, Zhong-can

    2006-11-01

    Recent experiments found that some adhesive receptor-ligand complexes have counterintuitive catch-slip transition behaviors: the mean lifetimes of these complexes first increase (catch) with initial application of a small external force, and then decrease (slip) when the force is beyond some threshold. In this work we suggest that the forced dissociation of these complexes might be a typical rate process with dynamic disorder. The one-dimensional force modulating Agmon-Hopfield model is used to describe the transitions in the single-bond P-selectin glycoprotein ligand 1-P-selectin forced dissociation experiments, which were respectively performed in the constant force [Marshall, Nature (Landon) 423, 190 (2003)] and the ramping force [Evans, Proc. Natl. Acad. Sci. U.S.A 98, 11281 (2004)] modes. We find that, an external force can not only accelerate the bond dissociation, but also modulate the complex from the lower-energy barrier to the higher one; the catch-slip bond transition can arise from a particular energy barrier shape. The agreement between our calculation and the experimental data is satisfactory. PMID:17279936

  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. Threshold dissociation energies of protonated amine/polyether complexes in a quadrupole ion trap.

    PubMed

    David, Wendi M; Brodbelt, Jennifer S

    2003-04-01

    Electrospray ionization mass spectrometry (ESI-MS) is increasingly used to probe the nature of noncovalent complexes; however, assessing the relevance of gas-phase results to structures of complexes in solution requires knowledge of the types of interactions that are maintained in a solventless environment and how these might compare to key interactions in solution. This study addresses the factors impacting the strength of hydrogen bonding noncovalent interactions in the gas phase. Hydrogen bonded complexes consisting of ammonium ions bound to polydentate ethers are transported to the gas phase with ESI, and energy-variable collisional activated dissociation (CAD) is used to map the relative dissociation energies. The measured relative dissociation energies are correlated with the gas-phase basicities and steric factors of the amine and polyether constituents. To develop correlations between hydrogen bonding strength and structural features of the donor and acceptor molecules, a variety of amines with different gas-phase basicities and structures were selected, including primary, secondary, and tertiary amines, as well as those that are bidentate to promote intramolecular hydrogen bonding. The acceptor molecules are polydentate ethers, such as 18-crown-6. Four primary factors influence the observed dissociation energies of the polyether/ammonium ion complexes: the gas-phase basicities of the polyether and amine, steric effects of the amines, conformational flexibility of the polyethers, and the inhibition of intramolecular hydrogen bonds of the guest ammonium ions in the resulting ammonium/polyether noncovalent complexes. PMID:12686485

  7. 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.

  8. On the dissociation energy of BH

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    The dissociation energy D(0) of the X 1Sigma(+) state has been determined to be 81.5 + or - 0.5 kcal/mol. This value includes an estimate for basis set incompleteness and for core-core and core-valence correlation. The barrier in the A 1Pi state potential is estimated to be 1.9 + or - 0.2 kcal/mol. By analyzing the tunneling through the barrier, it is demonstrated that D(0) and the predissociation limit differ by about 0.8-0.9 kcal/mol. Thus the experimental predissociation limit of 82.5 + or - 0.4 kcal/mol is consistent with the values computed for D(0) and the barrier in this work.

  9. 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. PMID:18517425

  10. Dissociation states of collagen functional groups and their effects on the priming efficacy of HEMA bonded to collagen.

    PubMed

    Nishiyama, N; Suzuki, K; Nagatsuka, A; Yokota, I; Nemoto, K

    2003-04-01

    Applying 2-hydroxyethylmethacrylate (HEMA) solution to etched dentin enhances the bonding of resin to dentin. However, the principal adhesion mechanisms have not yet been identified. In this study, we examined the dissociation states of the collagen functional groups of the side-chain amino acid residues and their effects on the bond strength of resin to etched dentin primed by the HEMA solution. The bond strength was strongly dependent upon the dissociation state of the collagen functional groups. Inhibiting the dissociation of the carboxylic acid or the amine of a collagen functional group resulted in increased bond strength of resin to collagen. By understanding the significance of inhibiting the dissociation state, we can better design and develop more effective and efficient primer and bonding agents. PMID:12651927

  11. Theoretical thermochemistry of homolytic C-C and C-Cl bond dissociations in unbranched perchloroalkanes

    SciTech Connect

    Cioslowski, J.; Liu, G.; Moncrieff, D.

    1998-11-26

    Proper description of the dispersion interactions that attenuate the closed-shell repulsions among chlorine atoms in n-perchloroalkanes requires an accurate treatment of long-range electron correlation effects. The presently known density functionals, which do not correctly account for such effects, grossly underestimate thermodynamic stability of these molecules, yielding the standard enthalpy {Delta}H{degree}{sub C-C} of C-C bond dissociation in n-C{sub 4}Cl{sub 10} as low as 20 kcal/mol. In contrast, the predictions of the CBS-4 scheme fail to reproduce the weakening of the C-C bonds that is experimentally observed in the higher members of the C{sub n}Cl{sub 2n+2} homologous series. For the CCl{sub 4} and C{sub 2}Cl{sub 6} the most reliable estimates of {Delta}H{degree}{sub C-C} and {Delta}H{degree}{sub C-Cl} are provided by the G2 And G2MP2 methods. The MP2/6-311G{sup **} level of theory (without ZPEs and finite-temperature corrections) appears at present to be the only viable, though quite inaccurate, theoretical approach to theoretical thermochemistry of larger chlorocarbons. At that level of theory, {Delta}H{degree}{sub C-C} is predicted to decrease by ca. 10 kcal/mol upon the addition of each -CCl{sub 2}- unit, convincingly explaining the thermal lability of higher n-perchloroalkanes. Similar conclusions are reached by examining the estimates of {Delta}H{degree}{sub C-C} derived from the CBS-4 standard enthalpies with the E{sub CBS} energy term excluded.

  12. Model-independent determination of dissociation energies: method and applications

    NASA Astrophysics Data System (ADS)

    Vogel, Manuel; Hansen, Klavs; Herlert, Alexander; Schweikhard, Lutz

    2003-03-01

    A number of methods are available for the purpose of extracting dissociation energies of polyatomic particles. Many of these techniques relate the rate of disintegration at a known excitation energy to the value of the dissociation energy. However, such a determination is susceptible to systematic uncertainties, mainly due to the unknown thermal properties of the particles and the potential existence of 'dark' channels, such as radiative cooling. These problems can be avoided with a recently developed procedure, which applies energy-dependent reactions of the decay products as an uncalibrated thermometer. Thus, it allows a direct measurement of dissociation energies, without any assumption on properties of the system or on details of the disintegration process. The experiments have been performed in a Penning trap, where both rate constants and branching ratios have been measured. The dissociation energies determined with different versions of the method yield identical values, within a small uncertainty.

  13. Hydrogen Bond and Ligand Dissociation Dynamics in Fluoride Sensing of Re(I)-Polypyridyl Complex.

    PubMed

    Verma, Sandeep; Aute, Sunil; Das, Amitava; Ghosh, Hirendra N

    2015-11-25

    Hydrogen bonding interaction plays an essential role in the early phases of molecular recognition and colorimetric sensing of various anions in aprotic media. In this work, the host-guest interaction between fac-[Re(CO)3Cl(L)] with L = 4-([2,2'-bipyridin]-4-yl)phenol and fluoride ions is investigated for the hydrogen bond dynamics and the changing local coordination environment. The stoichiometric studies using (1)H NMR and ESI-MS spectroscopies have shown that proton transfer in the H-bonded phenol-fluoride complex activates the dissociation of the CO ligand in the Re(I) center. The phenol-to-phenolate conversion during formation of HF2(-) ion induces nucleophilic lability of the CO ligand which is probed by intraligand charge transfer (ILCT) and ligand-to-metal charge transfer (LMCT) transitions in transient absorption spectroscopy. After photoexcitation, phenol-phenoxide conversion rapidly equilibrates in 280 fs time scale and the ensuing excited state [Re(II)(bpy•(-)-phenolate¯) (CO)3Cl]* undergoes CO dissociation in the ultrafast time scale of ∼3 ps. A concerted mechanism of hydrogen cleavage and coordination change is established in anion sensing studies of the rhenium complex. PMID:26514688

  14. Accurate In Bond Energies

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

    InXn atomization energies are computed for n = 1-3 and X = H, Cl, and CH3. The geometries and frequencies are determined using density functional theory. The atomization energies are computed at the coupled cluster level of theory. The complete basis set limit is obtained by extrapolation. The scalar relativistic effect is computed using the Douglas-Kroll approach. While the heats of formation for InH, InCl and InCl3 are in good agreement with experiment, the current results show that the experimental value for In(CH3)3 must be wrong.

  15. 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. PMID:26738691

  16. Sequential bond energies of water to sodium proline cation

    NASA Astrophysics Data System (ADS)

    Ye, S. J.; Moision, R. M.; Armentrout, P. B.

    2006-07-01

    Absolute bond dissociation energies of water to sodium proline cations and proline to hydrated sodium cations are determined experimentally by collision-induced dissociation of Na+Pro(H2O)x, where x = 1-4, complexes with xenon in a guided ion beam mass spectrometer. Experimental results show that the binding energies of water and proline to the complexes decrease monotonically with increasing number of water molecules. Ab initio calculations at three different levels show reasonable agreement with the experimental bond energies of water and proline for x = 1-4 except the theoretical values are higher for losing proline from x = 3 and 4. The primary binding site for Na+ is at the C terminus of proline for x = 0-4, i.e., the solvated sodiated proline complexes are in their zwitterionic forms. Calculations suggest that the first solvent shell of Na+Pro is essentially complete at four waters.

  17. Choice of Bond Dissociation Enthalpies on which to Base the Stabilization Energies of Simple Radicals: DH(R-H)is Preferred because DH(R-Me) is Perturbed by Changes in Chain Branching

    SciTech Connect

    Poutsma, Marvin L

    2008-01-01

    The relative stabilization energies of radicals, SE(R ), along the simple series methyl/ethyl/i-propyl/t-butyl are known to vary in spread and even direction dependent on which dissociation enthalpies, DH(R-X), they are based on. Using a highly electronegative X is recognized as unwise, but it is not clear whether a choice of X = Me or X = R might not be preferred over the almost universal use of R = H. The enthalpies of isomerization of C4 radical pairs that vary only in the substitution pattern at the radical center but not in carbon skeleton illustrate that R = H is indeed the better choice. Comparisons in the context of recent predictive models for alkane and radical stability indicate that, while relative DH(R-H) values highlight the desired difference in substitution pattern at the radical center, relative DH(R-Me) values are perturbed by differences in skeletal branching or protobranching which are well-known to affect thermochemistry. As a result, SE(R ) values derived from relative DH(R-Me) values are consistently too small. The same pattern is illustrated for prim, sec, and tert allylic and benzylic radicals (larger SE(R )) and for the parent vinyl, phenyl, and ethynyl radicals (negative SE(R )).

  18. 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 the ether carbon relative to the isomer with the oxygen group on a secondary carbon. Relative to alkane systems the ether oxygen decreases bond dissociation energies (BDEs) on carbon sites adjacent to the ether by ∼5 kcal mol(-1), and increases BDEs on nonether carbons ∼1 kcal mol(-1). The cyclic structures have significant effects on the C-H, CO-OH, COO-H, and CO-H bond dissociation enthalpies. These values can be used to help calibrate calculations of larger more complex bicyclic and tricyclic hydrocarbon and ether species. PMID:24660891

  19. 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. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.

  20. Selective dissociation of non-covalent bonds in biological molecules by laser spray.

    PubMed

    Takamizawa, Atsushi; Itoh, Yoshiyuki; Osawa, Ryo; Iwasaki, Noriyuki; Nishimura, Yoshifumi; Akashi, Satoko; Hiraoka, Kenzo

    2004-09-01

    The laser spray developed in our laboratory was applied to the analysis of bovine serum albumin (BSA), double-stranded DNA (dsDNA) and a protein-DNA complex. The tip of a stainless-steel capillary was irradiated with a 10.6 micro m infrared laser by increasing the laser power from 0 W (electrospray) to 1.4 W. The laser beam was focused to about 0.3 mm at the tip of the stainless-steel capillary. When BSA aqueous solution was irradiated by the laser, highly charged monomer ions were newly observed in addition to the multiply charged ions of non-denatured monomer, dimer and trimer moieties. This indicates that BSA suffers from denaturation on irradiation with an infrared laser in solution. A 1.4 W laser power is not sufficient to cause the complete denaturation of BSA under the present experimental conditions. Whereas dsDNA was found to dissociate almost completely to single-stranded DNA constituents on laser irradiation with a power of 1.2 W, no fragmentation of DNA molecules was observed. For a protein-DNA complex, i.e. a complex of c-Myb DNA binding domain and dsDNA, dissociation of the complex to the component moieties was observed. These findings indicate that the laser spray can selectively dissociate non-covalent complexes into subunits without causing dissociation of the covalent bonds of the subunits. The laser spray will be a versatile method for the investigation of the structures and stabilities of biomolecules including non-covalent complexes. PMID:15386752

  1. Molecular dissociation in the presence of catalysts: interpreting bond breaking as a quantum dynamical phase transition

    NASA Astrophysics Data System (ADS)

    Ruderman, A.; Dente, A. D.; Santos, E.; Pastawski, H. M.

    2015-08-01

    In this work we show that molecular chemical bond formation and dissociation in the presence of the d-band of a metal catalyst can be described as a quantum dynamical phase transition (QDPT). This agrees with DFT calculations that predict sudden jumps in some observables as the molecule breaks. According to our model this phenomenon emerges because the catalyst provides for a non-Hermitian Hamiltonian. We show that when the molecule approaches the surface, as occurs in the Heyrovsky reaction of H2, the bonding H2 orbital has a smooth crossover into a bonding molecular orbital built with the closest H orbital and the surface metal d-states. The same occurs for the antibonding state. Meanwhile, two resonances appear within the continuous spectrum of the d-band, which are associated with bonding and antibonding orbitals between the furthest H atom and the d-states at the second metallic layer. These move toward the band center, where they collapse into a pure metallic resonance and an almost isolated H orbital. This phenomenon constitutes a striking example of the non-trivial physics enabled when one deals with non-Hermitian Hamiltonian beyond the usual wide band approximation.

  2. Computational Study of Bond Dissociation Enthalpies for Substituted $\\beta$-O-4 Lignin Model Compounds

    SciTech Connect

    Younker, Jarod M; Beste, Ariana; Buchanan III, A C

    2011-01-01

    The biopolymer lignin is a potential source of valuable chemicals. Phenethyl phenyl ether (PPE) is representative of the dominant $\\beta$-O-4 ether linkage. Density functional theory (DFT) is used to calculate the Boltzmann-weighted carbon-oxygen and carbon-carbon bond dissociation enthalpies (BDEs) of substituted PPE. These values are important in order to understand lignin decomposition. Exclusion of all conformers that have distributions of less than 5\\% at 298 K impacts the BDE by less than 1 kcal mol$^{-1}$. We find that aliphatic hydroxyl/methylhydroxyl substituents introduce only small changes to the BDEs (0-3 kcal mol$^{-1}$). Substitution on the phenyl ring at the $ortho$ position substantially lowers the C-O BDE, except in combination with the hydroxyl/methylhydroxyl substituents, where the effect of methoxy substitution is reduced by hydrogen bonding. Hydrogen bonding between the aliphatic substituents and the ether oxygen in the PPE derivatives has a significant influence on the BDE. CCSD(T)-calculated BDEs and hydrogen bond strengths of $ortho$-substituted anisoles when compared with M06-2X values confirm that the latter method is sufficient to describe the molecules studied and provide an important benchmark for lignin model compounds.

  3. Molecular dissociation in the presence of catalysts: interpreting bond breaking as a quantum dynamical phase transition.

    PubMed

    Ruderman, A; Dente, A D; Santos, E; Pastawski, H M

    2015-08-12

    In this work we show that molecular chemical bond formation and dissociation in the presence of the d-band of a metal catalyst can be described as a quantum dynamical phase transition (QDPT). This agrees with DFT calculations that predict sudden jumps in some observables as the molecule breaks. According to our model this phenomenon emerges because the catalyst provides for a non-Hermitian Hamiltonian. We show that when the molecule approaches the surface, as occurs in the Heyrovsky reaction of H2, the bonding H2 orbital has a smooth crossover into a bonding molecular orbital built with the closest H orbital and the surface metal d-states. The same occurs for the antibonding state. Meanwhile, two resonances appear within the continuous spectrum of the d-band, which are associated with bonding and antibonding orbitals between the furthest H atom and the d-states at the second metallic layer. These move toward the band center, where they collapse into a pure metallic resonance and an almost isolated H orbital. This phenomenon constitutes a striking example of the non-trivial physics enabled when one deals with non-Hermitian Hamiltonian beyond the usual wide band approximation. PMID:26189372

  4. Computational Study of Bond Dissociation Enthalpies for Lignin Model Compounds: $\\beta$-5 Arylcoumaran

    SciTech Connect

    Beste, Ariana; Buchanan III, A C; Younker, Jarod M

    2012-01-01

    The biopolymer lignin is a potential source of valuable chemicals. The $\\beta$-5 linkage comprises $\\sim$10\\% of the linkages in lignin. Density Functional Theory (DFT) was used to calculate the $\\alpha$C-O and $\\alpha$C-$\\beta$C bond dissociation enthalpies (BDEs) for $\\beta$-5 models with varied substituents, which are important for understanding initial lignin decomposition. The $\\alpha$C-O ($\\alpha$C-$\\beta$C) BDEs were in the range of 40-44 (57-62) kcal/mol. The products resulting from either homolysis are bi-radicals with multi-determinant character in the singlet electronic state. Multiconfiguration self-consistent field (MCSCF) theory results were used to verify that unrestricted DFT and broken-symmetry DFT were sufficient to study these reactions.

  5. Timescales of N-H bond dissociation in pyrrole: a nonadiabatic dynamics study.

    PubMed

    Sapunar, Marin; Ponzi, Aurora; Chaiwongwattana, Sermsiri; Mališ, Momir; Prlj, Antonio; Decleva, Piero; Došlić, Nađa

    2015-07-15

    The excitation wavelength dependent photodynamics of pyrrole are investigated by nonadiabatic trajectory-surface-hopping dynamics simulations based on time dependent density functional theory (TDDFT) and the algebraic diagrammatic construction method to the second order (ADC(2)). The ADC(2) results confirm that the N-H bond dissociation occurring upon excitation at the origin of the first excited state, S1(πσ*), is driven by tunnelling [Roberts et al., Faraday Discuss., 2013, 163, 95] as a barrier of ΔE = 1780 cm(-1) traps the population in a quasi-bound minimum. Upon excitation to S1(πσ*) in the wavelength range of 236-240 nm, direct dissociation of the N-H bond takes place with a time constant of 28 fs. The computed time constant is in very good agreement with recently reported measurements. Excitation to the lowest B2 state in the 198-202 nm range returns a time constant for N-H fission of 48 fs at the B3LYP/def2-TZVPD level, in perfect agreement with the experiment [Roberts et al. Faraday Discuss., 2013, 163, 95]. For the same wavelength range the ADC(2)/aug-cc-pVDZ decay constant is more than three times longer than the experimentally reported one. The accuracy of the B3LYP/def2-TZVPD dynamics is checked against reference complete-active-space second-order perturbation theory (CASPT2) calculations and explained in terms of correct topography of the ππ* surface and the lack of mixing between the ππ* and the 3px Rydberg states which occurs in the ADC(2) method. PMID:26129838

  6. 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.

  7. 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.

  8. 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.

  9. Quantum scattering calculations of energy transfer and dissociation of HCO in collisions with Ar

    SciTech Connect

    Pan, B.; Bowman, J.M.

    1995-12-08

    We report a quantum scattering calculation of energy transfer and collision-induced dissociation of HCO in collisions with Ar. The HCO rotation is treated in the infinite order sudden approximation, and the HCO vibrations are treated by the coupled-channel method. Sixty {ital L}{sup 2} HCO vibrational wave functions are included in the coupled-channel basis, of which 15 correspond to bound HCO states for zero HCO angular momentum, and the remainder represent a discretized continuum, which includes ten resonances. A simple ``sum-of-pairs`` potential is used to describe the Ar--HCO interaction, and the HCO intramolecular potential is the previous Legendre polynomial fit to {ital ab} {ital initio} calculations. Vibrational state-specific and state-to-state cross sections, averaged over the orientation of Ar relative to the CO-bond axis, are calculated over a range of translational energies. Collision-induced dissociation cross sections to form H+CO from all HCO bound states are presented, and decomposed into components corresponding to dissociation via HCO resonances and dissociation via no``nresonance states. The energy transfer from selected initial states is also calculated as a function of initial relative translational energy. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  10. Bond-Selective and Mode-Specific Dissociation of CH3D and CH2D2 on Pt(111).

    PubMed

    Hundt, P Morten; Ueta, Hirokazu; van Reijzen, Maarten E; Jiang, Bin; Guo, Hua; Beck, Rainer D

    2015-12-17

    Infrared laser excitation of partially deuterated methanes (CH3D and CH2D2) in a molecular beam is used to control their dissociative chemisorption on a Pt(111) single crystal and to determine the quantum state-resolved dissociation probabilities. The exclusive detection of C-H cleavage products adsorbed on the Pt(111) surface by infrared absorption reflection spectroscopy indicates strong bond selectivity for both methane isotopologues upon C-H stretch excitation. Furthermore, the dissociative chemisorption of both methane isotopologues is observed to be mode-specific. Excitation of symmetric C-H stretch modes produces a stronger reactivity increase than excitation of the antisymmetric C-H stretch modes, whereas bend overtone excitation has a weaker effect on reactivity. The observed mode specificity and bond selectivity are rationalized by the sudden vector projection model in terms of the overlap of the reactant's normal mode vectors with the reaction coordinate at the transition state. PMID:26414099

  11. Low-energy dissociative recombination in small polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Jungen, Ch.; Pratt, S. T.

    2010-12-01

    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 H3+.

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

    PubMed

    Jungen, Ch; Pratt, S T

    2010-12-01

    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)(+). PMID:21142300

  13. 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. PMID:18062677

  14. The dissociation energy of He2(+)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Ceperley, David

    1989-01-01

    Ab initio potential energy curves for He2(+) are computed using full CI wavefunctions in conjuction with large Gaussian and Slater basis sets. The computed curves yield rotational-vibrational transitions with errors of less than 1/cm. They also yield quasi-bound levels with energies and lifetimes in reasonable agreement with translational spectroscopy measurements. The best D(e) is estimated to be 2.470 eV. Green's function Monte Carlo calculations yield a very similar value, 2.466 + or - 0.005.

  15. Indirect dissociative recombination of water molecule at low electronic energies

    NASA Astrophysics Data System (ADS)

    Fonseca, Samantha; Douguet, Nicolas; Kokoouline, Viatcheslav; Orel, Ann

    2014-05-01

    We present a theoretical study of the indirect dissociative (DR) recombination of the water molecular ion H2O+ at low collisional energies. The approach is based on the computation of the scattering matrix just above the ionization threshold and enables the explicit determination of all diabatic electronic couplings responsible for dissociative recombination. We use the multi-channel quantum- defect theory to demonstrate the precision of the scattering matrix by reproducing accurately ab initio Rydberg state energies of the neutral molecule. We also present our latest results on H2O+ with our previous results on the DR of linear molecular ions N2H+ and HCO+ and demonstrate the crucial role of the previously overlooked longitudinal modes for linear polyatomic ions with large permanent dipole moment. This work is supported by the DOE Office of Basic Energy Science and the National Science Foundation, Grant No's PHY-10-68785 and PHY-11-60611.

  16. The C-H bond dissociation enthalpies in fused N-heterocyclic compounds

    NASA Astrophysics Data System (ADS)

    Wang, Ying-Xing; Zheng, Wen-Rui; Ding, Lan-Lan

    2016-03-01

    The C-H bond dissociation enthalpies (BDEs) of the 26 N, O, S-containing mono-heterocyclic compounds were evaluated using the composite high-level ab initio methods G3 and G4. The C-H BDEs for 32 heterocyclic compounds were calculated using 8 types of density functional theory (DFT) methods. Comparing with the experimental values, the BMK method gave the lowest root mean square error (RMSE) of 7.2 kJ/mol. Therefore, the C-H BDEs of N-fused-heterocyclic compounds at different positions were investigated by the BMK method. By NBO analysis two linear relationships between the C-H BDEs of quinoline and isoquinoline with natural charges qC/ e in molecules and with natural charges qC/ e in radicals were found. The substituent effects on C(α)-H BDEs in N-fused-heterocyclic compounds were also discussed. It was found that there are two linear relationships between the C(α)-H BDEs of quinoline and isoquinoline derivatives with natural charges qC(α)/ e for the EDGs and CEGs substituents.

  17. A pass too far: dissociation of internal energy selected paracyclophane cations, theory and experiment.

    PubMed

    Hemberger, Patrick; Bodi, Andras; Schon, Christof; Steinbauer, Michael; Fischer, Kathrin H; Kaiser, Conrad; Fischer, Ingo

    2012-09-14

    The vacuum ultraviolet (VUV) photoionization and dissociative photoionization of three hydroxy-substituted [2.2]paracyclophane derivatives were studied yielding adiabatic ionization energies and dissociative photoionization energies (appearance energies). The simplest dissociation pathway is the breaking of both CH(2)-CH(2) bridge units and fragmenting the molecular ion in half to yield xylylene neutral and cationic fragments. The experimental data show that this process is outcompeted by a faster, higher energy channel, possibly yielding cyclooctatetraene derivatives. The role of the reaction coordinate, the effect of large amplitude motions on the density of states function at low and high energies and the temperature dependent 'population gap' in the internal energy distribution in large molecules are discussed in the context of applying statistical models to the dissociation. Computational approaches to the binding energy of paracyclophanes are marred with pitfalls. Noncovalent interactions play a major role in keeping paracyclophanes bound by some 200 kJ mol(-1) with respect to the two xylylene motifs, and the covalent CH(2)-CH(2) bonds are mostly counteracted by the geometric strain. The stabilizing effects are twofold: first, paracyclophanes are aromatic compounds, whereas xylylenes are not. Thus, the aromaticity of the molecule is induced by dimerization. Second, dispersive π-π interactions also stabilize the molecule. We evaluated 23 different computational chemistry approaches, and found that very few of the favorably scaling ones give an adequate description of this system. Among the DFT functionals tested, only PBE-D3 and perhaps M06-2X yielded consistently accurate results, comparable with MP3 and CCSD, or the G4 and CBS-QB3 composite methods. MP2 results in general suffer from significant overbonding. PMID:22847148

  18. 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.

  19. Pauling's electronegativity equation and a new corollary accurately predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.

    PubMed

    Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A

    2003-04-18

    Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite accurately homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not reproduce experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously observed empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant. PMID:12688786

  20. 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. Cell (2007) 128(6): 1173-11867 Smith SA. et al. PNAS (2006) 103(4): 903-908. 8 Müller F et al. Cell (2009) 139(6): 1143-11569 Ruiz FA et al. J Biol Chem (2004) 279(43): 44250-44257.

  1. The Se-H bond of benzeneselenols (ArSe-H): Relationship between bond dissociation enthalpy and spin density of radicals

    NASA Astrophysics Data System (ADS)

    Nam, Pham Cam; Nguyen, Minh Tho

    2013-03-01

    Bond dissociation enthalpies (BDE) of benzeneselenol (ArSe-H) and its para and meta-substituted derivatives are calculated using the (RO)B3LYP/6-311++G(2df,2p)//(U)B3LYP/6-311G(d,p) procedure. The computed BDE(Se-H) = 308 ± 8 kJ/mol for the parent PhSe-H is significantly smaller than the experimental value of 326.4 ± 16.7 kJ/mol [Kenttamaa and coworkers, J. Phys. Chem. 100 (1996) 6608] but larger than a previous value of 280.3 kJ/mol [Newcomb et al., J. Am. Chem. Soc. 113 (1991) 949]. The substituent effects on BDE's are analyzed in terms of a relationship between BDE(Se-H) and Mulliken atomic spin densities at the Se radical centers of ArSe (π radicals). Good correlations between Hammett's substituent constants with BDE(Se-H) are established. Proton affinity and ionization energy amount to PA(C6H5SeH) = 814 ± 4 kJ/mol and IE(C6H5SeH) = 8.0 ± 0.1 eV. IEs of the substituted benzeneselenols are also determined. Calculated results thus suggest that 4-amino-benzeneselenol derivatives emerge as efficient antioxidants.

  2. 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.

  3. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations

    SciTech Connect

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-14

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor–acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene–perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.

  4. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-01

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor-acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene-perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods.

  5. Ensemble density functional theory method correctly describes bond dissociation, excited state electron transfer, and double excitations.

    PubMed

    Filatov, Michael; Huix-Rotllant, Miquel; Burghardt, Irene

    2015-05-14

    State-averaged (SA) variants of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, SA-REKS and state-interaction (SI)-SA-REKS, implement ensemble density functional theory for variationally obtaining excitation energies of molecular systems. In this work, the currently existing version of the SA-REKS method, which included only one excited state into the ensemble averaging, is extended by adding more excited states to the averaged energy functional. A general strategy for extension of the REKS-type methods to larger ensembles of ground and excited states is outlined and implemented in extended versions of the SA-REKS and SI-SA-REKS methods. The newly developed methods are tested in the calculation of several excited states of ground-state multi-reference systems, such as dissociating hydrogen molecule, and excited states of donor-acceptor molecular systems. For hydrogen molecule, the new method correctly reproduces the distance dependence of the lowest excited state energies and describes an avoided crossing between the doubly excited and singly excited states. For bithiophene-perylenediimide stacked complex, the SI-SA-REKS method correctly describes crossing between the locally excited state and the charge transfer excited state and yields vertical excitation energies in good agreement with the ab initio wavefunction methods. PMID:25978880

  6. Accurate calculation of the dissociation energy of the highly anharmonic system ClHCl(-).

    PubMed

    Stein, Christopher; Oswald, Rainer; Botschwina, Peter; Peterson, Kirk A

    2015-05-28

    Accurate bond dissociation energies (D0) are reported for different isotopologues of the highly anharmonic system ClHCl(-). The mass-independent equilibrium dissociation energy De was obtained by a composite method with frozen-core (fc) CCSD(T) as the basic contribution. Basis sets as large as aug-cc-pV8(+d)Z were employed, and extrapolation to the complete basis set (CBS) limit was carried out. Explicitly correlated calculations with the CCSD(T)-F12b method were also performed to support the conventionally calculated values. Core-core and core-valence correlation, scalar relativity, and higher-order correlation were considered as well. Two mass-dependent contributions, namely, the diagonal Born-Oppenheimer correction and the difference in zero-point energies between the complex and the HCl fragment, were then added in order to arrive at precise D0 values. Results for (35)ClH(35)Cl(-) and (35)ClD(35)Cl(-) are 23.81 and 23.63 kcal/mol, respectively, with estimated uncertainties of 0.05 kcal/mol. In contrast to FHF(-) ( Stein , C. ; Oswald , R. ; Sebald , P. ; Botschwina , P. ; Stoll , H. , Peterson , K. A. Mol. Phys. 2013 , 111 , 2647 - 2652 ), the D0 values of the bichloride species are larger than their De counterparts, which is an unusual situation in hydrogen-bonded systems. PMID:25405989

  7. A study on electron impact dissociative ionization of organosilicon precursors for plasma processing.

    PubMed

    Yun, Yongsup; Lee, Myeonghoon; Inoue, Yasushi; Saito, Nagahiro; Takai, Osamu

    2014-12-01

    We discussed the electron impact dissociation behavior of the organosilicon molecules with methyl groups, based on the fragment pattern and molecular-orbital calculation of the bond dissociation energies for the molecules. From the calculation of bond dissociation energy of the organosilicon molecules, methyl groups, which bonded directly to the silicon atom, were found to have the weakest. Regarding the fragment patterns of the reactants investigated by a quadrupole mass spectrometer, the hexamethyldisiloxane was harder to dissociate than the trimethylmethoxysilane due to the strong Si-O bonding force, which also affected the dissociation in the plasma. From the above considerations, dissociation reactions by electron impact could be partly identified. PMID:25971114

  8. Experimental and theoretical investigations of the dissociation energy (D0) and dynamics of the water trimer, (H2O)3.

    PubMed

    Ch'ng, Lee C; Samanta, Amit K; Wang, Yimin; Bowman, Joel M; Reisler, Hanna

    2013-08-15

    We report a joint experimental-theoretical study of the predissociation dynamics of the water trimer following excitation of the hydrogen bonded OH-stretch fundamental. The bond dissociation energy (D0) for the (H2O)3 → H2O + (H2O)2 dissociation channel is determined from fitting the speed distributions of selected rovibrational states of the water monomer fragment using velocity map imaging. The experimental value, D0 = 2650 ± 150 cm(-1), is in good agreement with the previously determined theoretical value, 2726 ± 30 cm(-1), obtained using an ab initio full-dimensional potential energy surface (PES) together with Diffusion Monte Carlo calculations [ Wang ; Bowman . J. Chem. Phys. 2011 , 135 , 131101 ]. Comparing this value to D0 of the dimer places the contribution of nonpairwise additivity to the hydrogen bonding at 450-500 cm(-1). Quasiclassical trajectory (QCT) calculations using this PES help elucidate the reaction mechanism. The trajectories show that most often one hydrogen bond breaks first, followed by breaking and re-forming of hydrogen bonds (often with different hydrogen bonds breaking) until, after many picoseconds, a water monomer is finally released. The translational energy distributions calculated by QCT for selected rotational levels of the monomer fragment agree with the experimental observations. The product translational and rotational energy distributions calculated by QCT also agree with statistical predictions. The availability of low-lying intermolecular vibrational levels in the dimer fragment is likely to facilitate energy transfer before dissociation occurs, leading to statistical-like product state distributions. PMID:23536966

  9. Sequential bond energies of water to sodium glycine cation

    NASA Astrophysics Data System (ADS)

    Ye, S. J.; Moision, R. M.; Armentrout, P. B.

    2005-02-01

    Absolute bond dissociation energies of water to sodium glycine cations and glycine to hydrated sodium cations are determined experimentally by competitive collision-induced dissociation (CID) of Na+Gly(H2O)x, x = 1-4, with xenon in a guided ion beam tandem mass spectrometer. The cross sections for CID are analyzed to account for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition between reaction channels. Experimental results show that the binding energies of water and glycine to the complexes decrease monotonically with increasing number of water molecules. Ab initio calculations at four different levels show good agreement with the experimental bond energies of water to Na+Gly(H2O)x, x = 0-3, and glycine to Na+(H2O), whereas the bond energies of glycine to Na+(H2O)x, x = 2-4, are systematically higher than the experimental values. These discrepancies may provide some evidence that these Na+Gly(H2O)x complexes are trapped in excited state conformers. Both experimental and theoretical results indicate that the sodiated glycine complexes are in their nonzwitterionic forms when solvated by up to four water molecules. The primary binding site for Na+ changes from chelation at the amino nitrogen and carbonyl oxygen of glycine for x = 0 and 1 to binding at the C terminus of glycine for x = 2-4. The present characterization of the structures upon sequential hydration indicates that the stability of the zwitterionic form of amino acids in solution is a consequence of being able to solvate all charge centers.

  10. Electron Transfer Dissociation Reveals Changes in the Cleavage Frequencies of Backbone Bonds Distant to Amide-to-Ester Substitutions in Polypeptides

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas A.; Jung, Hye R.; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization.

  11. Mechanisms of Peptide Fragmentation from Time-and Energy-Resolved Surface-Induced Dissociation Studies: Dissociation of Angiotensin Analogs

    SciTech Connect

    Laskin, Julia; Bailey, Thomas H.; Futrell, Jean H.

    2006-03-01

    Energetics and mechanism of dissociation of singly protonated angiotensin III (RVYIHPF) and its analogs RVYIFPF, RVYIYPF, RVYIHAF, and RVYIHDF 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 peptide fragmentation were deduced by modeling the time- and energy-resolved survival curves for each precursor ion using an RRKM based approach developed in our laboratory. Fragmentation mechanisms were inferred from comparison of time- and energy-resolved fragmentation efficiency curves (TFECs) of different fragment ions followed by RRKM modeling of dissociation of angiotensin III into six major families of fragment ions. Detailed modeling demonstrated that dissociation of these peptides is dominated by loss of ammonia from the precursor ion and characterized by a high energy barrier of 1.6 eV. Loss of NH3 and subsequent rearrangement of the MH-NH3 ion results in proton mobilization and release of ca. 30 kcal/mol into internal excitation of the MH-NH3 ion. The resulting highly excited ion accesses a variety of non-specific dissociation pathways with very high rate constants. Fast fragmentation of excited MH-NH3 ion forms a variety of abundant bn-NH3 and an-NH3 fragment ions. Abundant XH and HX internal fragments are also formed, reflecting the stability of histidine-containing diketopiperazine structures.

  12. 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.

  13. Computational methods for the description of pharmacologically relevant platinum complexes - molecular structure and bond dissociation.

    PubMed

    Kokoschka, Malte; Galgonek, Jakub; Vondrasek, Jiri; Hobza, Pavel

    2016-01-27

    Cancer is after cardiovascular disease the most frequent cause of death in Europe. In 28 of 53 countries considered in this area it is already the leading cause of death and expected to gain even more importance until the year 2020. Amongst the large arsenal of different anti-cancer drugs, platinum drugs belong to the first developed anticancer drugs and still have a large impact on cancer therapy. Nevertheless therapy with platinum-anticancer drugs is accompanied by severe adverse effects caused by frequent interactions with the amino acids of different human proteins. Computational chemistry offers methods to study such interactions and even those of not yet synthesized drugs in silico. For such studies a profound knowledge of the prediction quality of various computational methods towards platinum-drug-like complexes is necessary. By this article we are aiming on delivering important accuracy information of the frequently used computational methods. Most important findings are the high performance of the double hybrid functional B2PLYP for the calculation of geometries, even in small basis sets, followed by BP86 and PBE and the still acceptable performance of the semi-empirical Method PM6-D3H4X for extremely large systems. To follow absolute energies of the dissociation process, LPNO-CEPA and B3LYP-D3 can be suggested while SCS-MP2 shows an extremely narrow standard deviation and a low maximum error, which make it an ideal candidate for relative energy calculations in the exploration of reaction mechanisms. PMID:26777459

  14. 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.

  15. 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)Σg (-))-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. PMID:26979687

  16. Sticky dissociative electron transfer to polychloroacetamides. In-cage ion-dipole interaction control through the dipole moment and intramolecular hydrogen bond.

    PubMed

    Costentin, Cyrille; Louault, Cyril; Robert, Marc; Teillout, Anne-Lucie

    2005-03-31

    The reductive cleavage of chloro- and polychloroacetamides in N,N-dimethylformamide gives new insights into the nature of the in-cage ion radical cluster formed upon dissociative electron transfer. Within the family of compounds investigated, the electrochemical reduction leads to the successive expulsion of chloride ions. At each stage the electron transfer is concerted with the breaking of the C-Cl bond and acts as the rate-determining step. The reduction further leads to the formation of the corresponding carbanion with the injection of a second electron, which is in turn protonated by a weak acid added to the solution. From the joint use of cyclic voltammetric data, the sticky dissociative electron-transfer model and quantum ab initio calculations, the interaction energies within the cluster fragments (*R, Cl-) resulting from the first electron transfer to the parent RCl molecule are obtained. It is shown that the stability of these adducts, which should be viewed as an essentially electrostatic radical-ion pair, is mainly controlled by the intensity of the dipole moment of the remaining radical part and may eventually be strengthened by the formation of an intramolecular hydrogen bond, as is the case with 2-chloroacetamide. PMID:16833619

  17. 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.

  18. Dissociation energy of alkali metal clusters related to inhomogeneous electron gas theory

    NASA Astrophysics Data System (ADS)

    Cordero, N. A.; Alonso, J. A.; López, J. M.; March, N. H.

    A pseudopotential model, combined with a one-centre expansion, is set up to calculate the dissociation energies D of alkali metal atom clusters LiN to CsN, when 2 ˇ- N ˇ- 10. This central field model is solved for the valence electrons using the Slater-Kohn-Sham (SKS) equations, with a local density approximation for the exchange-correlation one-body potential. Inhomogeneous electron gas theory, in terms only of the valence electron ground-state density ϱ, is then utilized, with ϱ constructed from the SKS wavefunctions, to relate D/N to the inhomogeneity kinetic energy T2 of the equilibrium cluster. For N ranging from 3 to 10, a global correlation is demonstrated, with D/N ≈ T2. A correlation between D and the density ϱ at the (equivalent) bond midpoints in the clusters is also exposed.

  19. Transition from hydrogen atom to hydride abstraction by Mn4O4(O2PPh2)6 versus [Mn4O4(O2PPh2)6]+: O-H bond dissociation energies and the formation of Mn4O3(OH)(O2PPh2)6.

    PubMed

    Carrell, Thomas G; Bourles, Emilie; Lin, Matthew; Dismukes, G Charles

    2003-05-01

    Synthesis, characterization, and reactions of the novel manganese-oxo cubane complex [Mn(4)O(4)(O(2)PPh(2))(6)](ClO(4)), 1+ (ClO(4)(-)), are described. Cation 1+ is composed of the [Mn(4)O(4)](7+) core surrounded by six bidentate phosphinate ligands. The proton-coupled electron transfer (pcet) reactions of phenothiazine (pzH), the cation radical (pzH(.+)(ClO(4)(-)), and the neutral pz* radical with 1+ are reported and compared to Mn(4)O(4)(O(2)PPh(2))(6) (1). Compound 1+ (ClO(4)(-)) reacts with excess pzH via four sequential reduction steps that transfer a total of five electrons and four protons to 1+. This reaction forms the doubly dehydrated manganese cluster Mn(4)O(2)(O(2)PPh(2))(6) (2) and two water molecules derived from the corner oxygen atoms. The first pcet step forms the novel complex Mn(4)O(3)(OH)(O(2)PPh(2))(6) (1H) and 1 equiv of the pz+ cation by net hydride transfer from pzH. Spectroscopic characterization of isolated 1H is reported. Reduction of 1 by pzH or a series of para-substituted phenols also produces 1H via net H atom transfer. A lower limit to the homolytic bond dissociation energy (BDE) (1H --> 1 + H) was estimated to be >94 kcal/mol using solution phase BDEs for pzH and para-substituted phenols. The heterolytic BDE was estimated for the hydride transfer reaction 1H --> 1+ + H(-) (BDE approximately 127 kcal/mol). These comparisons reveal the O-H bond in 1H to be among the strongest of any Mn-hydroxo complex measured thus far. In three successive H atom transfer steps, 1H abstracts three hydrogen atoms from three pzH molecules to form complex 2. Complex 2 is shown to be identical to the "pinned butterfly" cluster produced by the reaction of 1 with pzH (Ruettinger, W. F.; Dismukes, G. C. Inorg. Chem. 2000, 39, 1021-1027). The Mn oxidation states in 2 are formally Mn(4)(2II,2III), and no further reduction occurs in excess pzH. By contrast, outer-sphere electron-only reductants such as cobaltacene reduce both 1+ and 1 to the all Mn(II) oxidation level and cause cluster fragmentation. The reaction of pzH(.+) with 1+ produces 1H and the pz+ cation by net hydrogen atom transfer, and terminates at 1 equiv of pzH(.+) with no further reaction at excess. By contrast, pz* does not react with 1+ at all, indicating that reduction of 1+ by electron transfer to form pz+ does not occur without a proton (pcet to 1+ is thermodynamically required). Experimental free energy changes are shown to account for these pcet reactions and the absence of electron transfer for any of the phenothiazine series. Hydrogen atom abstraction from substrates by 1 versus hydride abstraction by 1(+ )()illustrates the transition to two-electron one-proton pcet chemistry in the [Mn(4)O(4)](7+) core that is understood on the basis of free energy consideration. This transition provides a concrete example of the predicted lowest-energy pathway for the oxidation of two water molecules to H(2)O(2) as an intermediate within the photosynthetic water-oxidizing enzyme (vs sequential one-electron/proton steps). The implications for the mechanism of photosynthetic water splitting are discussed. PMID:12716176

  20. 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.

  1. 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.

  2. 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.

  3. The mechanism of H-bond rupture: the vibrational pre-dissociation of C2H2-HCl and C2H2-DCl.

    PubMed

    Pritchard, Marisian; Parr, Jessica; Li, Guosheng; Reisler, Hanna; McCaffery, Anthony J

    2007-12-21

    Pair correlated fragment rovibrational distributions are presented following vibrational predissociation of the C2H2-DCl van der Waals dimer initiated by excitation of the asymmetric (asym) C-H stretch. The only observed fragmentation pathways are DCl (v= 0; j= 6-9)+ C2H2(nu2= 1; j= 1-5). These and previously reported data on the related C2H2-HCl species are analysed using the angular momentum (AM) method. Calculations accurately reproduce fragment rovibrational distributions following dissociation of the C2H2-HCl dimer initiated either by excitation of the asym C-H stretch or via the HCl stretch, and those from C2H2-DCl initiated via asym C-H stretch excitation. The calculations demonstrate that the dimer is bent at the moment of dissociation. Several geometries are found that lead to H-bond breakage via a clearly identified set of fragment quantum states. The results suggest a hierarchy in the disposal of excess energy and angular momentum between fragment vibration, rotation and recoil. Deposition of the largest portion of energy into a C2H2 vibrational state sets an upper limit on HCl rotation, which then determines the energy and AM remaining for C2H2 rotation and fragment recoil. Acceptor C2H2 vibrational modes follow a previously noted propensity, implying that the dissociating impulse must be able to induce appropriate nuclear motions both in the acceptor vibration and in rotation of the C2H2 fragment. PMID:18046473

  4. Towards an understanding of the bonding in polyoxometalates through bond order and bond energy analysis.

    PubMed

    Bridgeman, Adam J; Cavigliasso, Germán

    2003-01-01

    The molecular and electronic structures of transition metal complexes, [MOCl5]n- (n = 2 for M = V,Nb,Ta and n = 1 for Mo,W) and mixed-metal polyoxometalates, [M'M5O19]3-V,Nb,Ta, M = Mo,W) containing a single terminal oxo group on each metal, and of complexes of the uranyl ion [UO2]2+, [UO2(H2O)5]2+ and [UO2Cl4]2-, have been calculated using density functional methods. The calculated structures of the complexes are in good agreement with available experimental parameters. For the mixed-metal hexametalates, for which no crystallographic data is available, the calculations predict a small tetragonal compression of the clusters with only minor structural changes compared to the parent molybdate and tungstate. The metal oxygen bonding in these anions has been probed using Mayer-Mulliken, bond energy and atoms in molecule analyses (AIM). These methods provide a consistent description of the bonding in polyoxometalates. The terminal bonds between transition metal or uranium and oxygen atoms have large sigma and pi components with the pi contributions exceeding the sigma bonding. The transition metals utilize their d orbitals almost exclusively to bond to oxygen whilst uranium uses both its 5f and 6d orbitals. Oxygen atom charges increase and covalency indexes decrease with coordination number, with a marked separation of these terms according to the oxygen atom type. The total valency and AIM energies of the oxygen atoms are predicted to be almost constant for all types of oxygen site. The constancy of the bonding power of the oxygen atoms appears to be an important factor in determining the gross structures and details of the bonding in polyoxometalates. The Mayer Mulliken approach provides direct characterization of the bonding power of atoms and the extent of the interaction between pairs of atoms that is consistent with the results of the considerably more computationally demanding bond energy and AIM approaches. PMID:14527219

  5. 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…

  6. 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

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

    SciTech Connect

    Tang, Xiaofeng; National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029 ; Zhou, Xiaoguo E-mail: yanbing@jlu.edu.cn; Liu, Shilin; Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 ; Sun, Zhongfa; Liu, Fuyi; Sheng, Liusi; Yan, Bing E-mail: yanbing@jlu.edu.cn

    2014-01-28

    Dissociative photoionization of methyl bromide (CH{sub 3}Br) 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{sup 2}E of CH{sub 3}Br{sup +} is stable, and both A{sup 2}A{sub 1} and B{sup 2}E ionic excited states are fully dissociative to produce the unique fragment ion of CH{sub 3}{sup +}. From TPEPICO 3D time-sliced velocity images of CH{sub 3}{sup +} dissociated from specific state-selected CH{sub 3}Br{sup +} ion, kinetic energy release distribution (KERD) and angular distribution of CH{sub 3}{sup +} fragment ion are directly obtained. Both spin-orbit states of Br({sup 2}P) atom can be clearly observed in fast dissociation of CH{sub 3}Br{sup +}(A{sup 2}A{sub 1}) ion along C–Br rupture, while a KERD of Maxwell-Boltzmann profile is obtained in dissociation of CH{sub 3}Br{sup +}(B{sup 2}E) ion. With the aid of the re-calculated potential energy curves of CH{sub 3}Br{sup +} including spin-orbit coupling, dissociation mechanisms of CH{sub 3}Br{sup +} ion in A{sup 2}A{sub 1} and B{sup 2}E states along C–Br rupture are revealed. For CH{sub 3}Br{sup +}(A{sup 2}A{sub 1}) ion, the CH{sub 3}{sup +} + Br({sup 2}P{sub 1/2}) channel is occurred via an adiabatic dissociation by vibration, while the Br({sup 2}P{sub 3/2}) formation is through vibronic coupling to the high vibrational level of X{sup 2}E state followed by rapid dissociation. C–Br bond breaking of CH{sub 3}Br{sup +}(B{sup 2}E) ion can occur via slow internal conversion to the excited vibrational level of the lower electronic states and then dissociation.

  8. N-Cα Bond Cleavage of Zinc-Polyhistidine Complexes in Electron Transfer Dissociation Mediated by Zwitterion Formation: Experimental Evidence and Theoretical Analysis of the Utah-Washington Model.

    PubMed

    Asakawa, Daiki; Yamashita, Asuka; Kawai, Shikiho; Takeuchi, Takae; Wada, Yoshinao

    2016-02-11

    Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of gas-phase ions are widely used for peptide/protein sequencing by mass spectrometry. To understand the general mechanism of ECD/ETD of peptides, we focused on the ETD fragmentation of metal-peptide complexes in the absence of remote protons. Since Zn(2+) strongly binds to neutral histidine residues in peptides, Zn(2+)-polyhistidine complexation does not generate any remote protons. However, in the absence of remote protons, electron transfer to the Zn(2+)-polyhistidine complex induced the N-Cα bond cleavage. The formation pathway for the ETD products was investigated by density functional theory calculations. The calculations showed that the charge-reduced zinc-peptide radical, [M + Zn](•+), can exist in the low-energy zwitterionic amide π* states, which underwent homolytic N-Cα bond dissociation. The homolytic cleavage resulted in the donation of an electron from the N-Cα bond to the nitrogen atom, producing an iminoenol c' anion. The counterpart z(•) radical contained a radical site on the α-carbon atom. The iminoenol c' anion then abstracted a proton to presumably form the more stable amide c' fragment. The current experimental and computational joint study strongly suggested that the N-Cα bond cleavage occurred through the aminoketyl radical-anion formation for Zn(2+)-polyhistidine complexes in ETD. PMID:26673038

  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. Bond Energies in Models of the Schrock Metathesis Catalyst

    SciTech Connect

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

    2011-06-02

    Heats of formation, adiabatic and diabatic bond dissociation energies (BDEs) of the model Schrock-type metal complexes M(NH)(CRŔ)(OH)₂ (M = Cr, Mo, W; CRŔ = 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.

  11. Low-energy electron-induced chemistry of condensed-phase hexamethyldisiloxane: Initiating dissociative process and subsequent reactions

    NASA Astrophysics Data System (ADS)

    Ipolyi, I.; Burean, E.; Hamann, T.; Cingel, M.; Matejcik, S.; Swiderek, P.

    2009-05-01

    Thin films of condensed hexamethyldisiloxane (HMDSO) have been exposed to electron irradiation at incident energies between 5 and 15 eV and analysed afterwards by thermal desorption spectrometry (TDS). Formation of products is observed at energies at and above 11 eV and quantified at 15 eV by comparison with reference samples of known composition. Gas-phase measurements aiming at detection of dissociative electron attachment (DEA) were, in addition, performed to obtain more insight into the dominant electron-induced dissociation channel expected to initiate further reactions in the condensed phase. Apart from CH4 which is the most obvious product present in exposed films of HMDSO, tetramethylsilane (TMS) and smaller amounts of C2H6 have been detected. The quantity of the products is by one to two orders of magnitude smaller than the amount of decomposed HMDSO. In addition, signals ascribed to unquantified amounts of larger siloxanes have been observed. The present results together with previous gas-phase results from literature suggest that dissociative ionisation leading to Si-C bond rupture and release of a methyl radical is the most important electron-driven initial reaction step. Possible mechanisms of the subsequent reactions induced by the fragments of the initial dissociation reaction are reviewed and discussed in relation to the observed product quantities.

  12. Intramolecular Interaction, Photoisomerization, and Mechanical C-C Bond Dissociation of 1,2-Di(9-anthryl)benzene and Its Photoisomer: A Fundamental Moiety of Anthracene-Based π-Cluster Molecules.

    PubMed

    Nishiuchi, Tomohiko; Uno, Shin-Ya; Hirao, Yasukazu; Kubo, Takashi

    2016-03-01

    We report variable and unique properties of 1,2-di(9-anthryl)benzene 1 as a fundamental moiety of anthracene-based π-cluster molecules. Due to a through-space π-conjugation between anthracene units, excimer emission at room temperature and charge delocalized state in radical cation state of 1 could be observed. Photoirradiation to 1 afforded an intramolecular [4 + 4] cyclized anthracene dimer 1' having a high strain energy with long C-C bond that exceeded 1.68 Å, resulting in C-C bond dissociation by simple mechanical grinding. PMID:26828776

  13. 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.

  14. Threshold collision-induced dissociation and theoretical studies of hydrated Fe(II): binding energies and Coulombic barrier heights.

    PubMed

    Hofstetter, Theresa E; Armentrout, P B

    2013-02-14

    The first experimentally determined bond dissociation energies for losing water from Fe(2+)(H(2)O)(n) complexes, n = 4-11, are measured using threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer coupled to an electrospray ionization source that forms thermalized complexes. In this technique, absolute cross-sections for dissociation induced by collisions with Xe at systematically varied kinetic energies are obtained. After accounting for multiple collisions, kinetic shifts, and energy distributions, these cross-sections are analyzed to yield the energy thresholds for losing one, two, or three water ligands at 0 K. The 0 K threshold measurements are converted to 298 K values to give the hydration enthalpies and free energies for sequentially losing water ligands from each complex. Comparisons to previous results for hydration of Zn(2+) indicate that the bond energies are dominated by electrostatic interactions, with no obvious variations associated with the open shell of Fe(2+). Theoretical geometry optimizations and single-point energy calculations are performed using several levels of theory for comparison to experiment, with generally good agreement. In addition to water loss channels, the charge separation process generating hydrated FeOH(+) and protons is observed for multiple reactant complexes. Energies of the rate-limiting transition states are calculated at several levels of theory with density functional approaches (B3LYP and B3P86) disagreeing with MP2(full) results. Comparisons to our kinetic energy dependent cross-sections suggest that the energetics of the MP2(full) level are most accurate. PMID:22812673

  15. Shattering dissociation in high-energy molecular collisions between nitrate esters

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor V.; Dunlap, Brett I.

    2011-09-01

    We present ab initio molecular dynamics simulations of head-on collisions between ethyl nitrate molecules at collisional energies from 200 to 1200 kJ/mol. Above a threshold energy, an increasing fraction of the collisions led to rapid dissociation on impact—"shattering." The probability of the shattering dissociation was derived from the quasiclassical trajectories sampling the initial vibrational motion at Tvib = 300 K. Even for the zero impact parameter and a fixed orientation considered, the observed dissociation probability exhibited a wide spread (much larger than kTvib) as a function of the collision energy. This is attributed to variations in the initial vibrational phase. We propose a closed-form expression for the energy-dependent dissociation probability that captures the dependence on the phase and use it to analyze the probability of the shattering dissociation of a larger nitrate ester, pentaerythritol tetranitrate.

  16. 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.

  17. Fragmentation of doubly charged metal-acetamide complexes: Second ionization energies and dissociation chemistries

    NASA Astrophysics Data System (ADS)

    Shi, Tujin; Siu, K. W. Michael; Hopkinson, Alan C.

    2006-09-01

    The dissociation chemistries of [M(L)n]2+ (M = Mg, Ca, Mn, Fe, Co, Ni, Cu, Zn; L = acetamide; n = 2-6) have been examined experimentally by tandem mass spectrometry and theoretically by density functional theory (DFT). At low collision energies, three primary reactions were observed: loss of acetamide to produce [M(L)n-m]2+; inter-ligand proton transfer followed by dissociation to form [M(L - H)(L)n-2]+ and protonated acetamide, [L + H]+; and amide-bond cleavage, producing [M(NH2)(L)n-1]+ and [CH3CO]+. Dissociative electron transfer from acetamide to the metal forming [M(L)n-1]+ and [L]+ was only observed for [Cu(L)2,3]2+ complexes. At higher collision energies, complexes containing deprotonated acetamide [M(L - H)(L)n-2]+ (except for [Cu(L - H)(L)n-2]+) further fragmented by eliminating small molecules (H2O, CH3CN, H2CCO, HNCO) or by acetamide loss to produce [M(L - H)]+; product ions [M(NH2)(L)n-1]+ either eliminated ammonia to produce [M(L - H)(L)n-2]+ by inter-ligand proton transfer from one NH2 group to another one, or lost acetamides to form [M(NH2)]+. Collision-induced dissociations of [M(L - H)]+ yielded three common product ions, [M(CH3)]+, [M(OH)]+, and M+ by elimination of neutral molecules, HNCO, CH3CN, and a neutral radical, (L - H), respectively. Elimination of methane from [M(L - H)]+ was only observed for M = Ca, and elimination of the methyl group occurred for M = Co, Ni, and Zn. Copper complexes exhibited different chemistries; [Cu(L - H)(L)]+ fragmented to either produce [Cu(L)]+ by elimination of (L - H), or [Cu(HNCO)(L)]+ by elimination of CH3; [Cu(HNCO)(L)]+ further fragmented to produce [Cu(L)]+ by elimination of HNCO. DFT calculations show that the gas-phase reactivities of [M(L)n]2+ complexes are closely related to the second ionization energies (IE2) of the metals. For the doubly charged [M(L)n]2+ species, as IE2 increases, fragmentations involving charge separation become more competitive: inter-ligand proton transfer becomes energetically more favorable than dissociation of a neutral ligand, and amide-bond cleavage occurs more readily. For singly charged ions [M(L - H)L]+, for metals with low IE2 values, loss of L has a considerably lower enthalpy than loss of (L - H); however, for metals with higher IE2 values, loss of (L - H), which effectively reduces the oxidation state of the metal, becomes energetically competitive with the loss of L. The enthalpies for eliminating methane and the methyl radical from [M(L - H)]+ (M D Ca, Mg, and Zn) have been calculated and correlate well with the experimental observations.

  18. Size, Kinetics, and Free Energy of Clusters Formed by Ultraweak Carbohydrate-Carbohydrate Bonds.

    PubMed

    Witt, Hannes; Savić, Filip; Oelkers, Marieelen; Awan, Shahid I; Werz, Daniel B; Geil, Burkhard; Janshoff, Andreas

    2016-04-12

    Weak noncovalent intermolecular interactions play a pivotal role in many biological processes such as cell adhesion or immunology, where the overall binding strength is controlled through bond association and dissociation dynamics as well as the cooperative action of many parallel bonds. Among the various molecules participating in weak bonds, carbohydrate-carbohydrate interactions are probably the most ancient ones allowing individual cells to reversibly enter the multicellular state and to tell apart self and nonself cells. Here, we scrutinized the kinetics and thermodynamics of small homomeric Lewis X-Lewis X ensembles formed in the contact zone of a membrane-coated colloidal probe and a solid supported membrane ensuring minimal nonspecific background interactions. We used an atomic force microscope to measure force distance curves at Piconewton resolution, which allowed us to measure the force due to unbinding of the colloidal probe and the planar membrane as a function of contact time. Applying a contact model, we could estimate the free binding energy of the formed adhesion cluster as a function of dwell time and thereby determine the precise size of the contact zone, the number of participating bonds, and the intrinsic rates of association and dissociation in the presence of calcium ions. The unbinding energy per bond was found to be on the order of 1 kBT. Approximately 30 bonds were opened simultaneously at an off-rate of koff = 7 ± 0.2 s(-1). PMID:27074683

  19. Electron transfer dissociation reveals changes in the cleavage frequencies of backbone bonds distant to amide-to-ester substitutions in polypeptides.

    PubMed

    Hansen, Thomas A; Jung, Hye R; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization. PMID:21952783

  20. Resonant structure of low-energy H3+ dissociative recombination

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    High-resolution dissociative recombination rate coefficients of rotationally cool and hot H3+ 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 380-130+50 K and that this is the lowest rotational temperature so far realized in storage-ring rate-coefficient measurements on H3+. 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.

  1. HLA-DM targets the hydrogen bond between the histidine at position β81 and peptide to dissociate HLA-DR–peptide complexes

    PubMed Central

    Narayan, Kedar; Chou, Chih-Ling; Kim, AeRyon; Hartman, Isamu Z; Dalai, Sarat; Khoruzhenko, Stanislav; Sadegh-Nasseri, Scheherazade

    2010-01-01

    The peptide editor HLA-DM (DM) mediates exchange of peptides bound to major histocompatibility (MHC) class II molecules during antigen processing; however, the mechanism by which DM displaces peptides remains unclear. Here we generated a soluble mutant HLA-DR1 with a histidine-to-asparagine substitution at position 81 of the β-chain (DR1βH81N) to perturb an important hydrogen bond between MHC class II and peptide. Peptide–DR1βH81N complexes dissociated at rates similar to the dissociation rates of DM-induced peptide–wild-type DR1, and DM did not enhance the dissociation of peptide–DR1βH81N complexes. Reintroduction of an appropriate hydrogen bond (DR1βH81N βV85H) restored DM-mediated peptide dissociation. Thus, DR1βH81N might represent a `post-DM effect' conformation. We suggest that DM may mediate peptide dissociation by a `hit-and-run' mechanism that results in conformational changes in MHC class II molecules and disruption of hydrogen bonds between βHis81 and bound peptide. PMID:17143275

  2. Aromatic C-H bond activation revealed by infrared multiphoton dissociation spectroscopy.

    PubMed

    Jašíková, Lucie; Hanikýřová, Eva; Schröder, Detlef; Roithová, Jana

    2012-04-01

    Metal-oxide cations are models of catalyst mediating the C-H bond activation of organic substrates. One of the most powerful reagents suggested in the gas phase is based on CuO(+) . Here, we describe the activation of the aromatic C-H bonds of phenanthroline in its complex with CuO(+) . The reaction sequence starts with a hydrogen atom abstraction by the oxygen atom from the 2-position of the phenanthroline ring, followed by OH migration to the ring. Using infrared multiphoton spectroscopy, it is shown that the reaction can be energetically facilitated by additional coordination of a water ligand to the copper ion. As the reaction is intramolecular, a spectroscopic characterization of the product is mandatory in order to unambiguously address the reaction mechanism. PMID:22689621

  3. 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. PMID:26588277

  4. A new quantum isotope effect: Extreme local mode selectivity in unimolecular dissociations imposed by antagonism between dynamic propensities of educts and zero point energies of products

    NASA Astrophysics Data System (ADS)

    Hartke, B.; Manz, J.

    1990-01-01

    We predict a new quantum isotope effect for unimolecular dissociations of molecules with two equivalent but isotopically substituted bonds l (light isotope) and h (heavy isotope), e.g., HOT where l=HO and h=OT. Consider two near-degenerate local vibrational excitations of bonds l or h, with energies between the gap of product zero point energies. Dynamically, these excitations should induce preferential fissions of bonds l or h, but energetically, these decay channels are open and closed, respectively. Therefore, local excitation of bond h must be followed by extremely slow internal vibrational energy redistribution to bond l before dissociation, whereas local excitation of bond l induces direct, rapid decay. The resulting decay rates differ by many orders of magnitudes. The effect is demonstrated by fast Fourier transform propagation of representative wavepackets for a model system, HOT→H+OT. Extended applications to more excited educts HOT also confirm an effect discovered previously for HOD, i.e., local mode selective control of competing bond fissions H+OT←HOT→HO+T.

  5. Solvation of copper ions by acetone. structures and sequential binding energies of Cu+(acetone)x, x = 1-4 from collision-induced dissociation and theoretical studies.

    PubMed

    Chu, Y; Yang, Z; Rodgers, M T

    2002-05-01

    Collision-induced dissociation of Cu+(acetone)(x), x = 1-4, with Xe is studied as a function of kinetic energy using guided ion beam mass spectrometry. In all cases, the primary and lowest energy dissociation channel observed is endothermic loss of one acetone molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond energies after accounting for the effects of multiple ion-neutral collisions, internal energy of the complexes, and dissociation lifetimes. Density functional calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical bond dissociation energies are determined from single point calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels, using the B3LYP/6-31G* optimized geometries. The experimental bond energies determined here are in good agreement with previous experimental measurements made in a high-pressure mass spectrometer for the sum of the first and second bond energy (i.e., Cu+(acetone)2 --> Cu+ + 2 acetone) when these results are properly anchored. The agreement between theory and experiment is reasonable in all cases, but varies both with the size of the cluster and the level of theory employed. B3LYP does an excellent job for the x = 1 and 3 clusters, but is systematically low for the x = 2 and 4 clusters such that the overall trends in sequential binding energies are not parallel. In contrast, all MP2 values are somewhat low, but the overall trends parallel the measured values for all clusters. The trends in the measured Cu+(acetone), binding energies are explained in terms of 4s-3d sigma hybridization effects and ligand-ligand repulsion in the clusters. PMID:12019969

  6. Dual-Regge approach to high-energy, low-mass diffraction dissociation

    NASA Astrophysics Data System (ADS)

    Jenkovszky, L. L.; Kuprash, O. E.; Lämsä, J. W.; Magas, V. K.; Orava, R.

    2011-03-01

    A dual-Regge model with a nonlinear proton Regge trajectory in the missing mass (MX2) channel, describing the experimental data on low-mass single diffraction dissociation (SDD), is constructed. Predictions for the LHC energies are given.

  7. 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.

  8. Mass analyzed threshold ionization of phenolṡCO: Intermolecular binding energies of a hydrogen-bonded complex

    NASA Astrophysics Data System (ADS)

    Haines, Stephen R.; Dessent, Caroline E. H.; Müller-Dethlefs, Klaus

    1999-08-01

    [PhenolṡCO]+ was studied using a combination of two-color resonant zero kinetic energy (ZEKE) spectroscopy and mass analyzed threshold ionization (MATI) spectroscopy to investigate the interaction of the CO ligand with a hydrogen-bonding cation. Vibrational progressions were observed in three intermolecular modes, the in-plane bend (42 cm-1), stretch (130 cm-1), and in-plane wag (160 cm-1), and are consistent with a planar hydrogen-bonded structure where the CO bonds through the carbon atom to the phenol OH group. Dissociation energies for the S0, S1, and D0 states were determined as 659±20, 849±20, and 2425±10 cm-1, respectively. The cationic and neutral dissociation energies of the phenolṡCO complex are considerably stronger than those of phenolṡN2, demonstrating the extent to which the larger quadrupole of CO affects the strength of binding.

  9. Tubulin Bond Energies and Microtubule Biomechanics Determined from Nanoindentation in Silico

    PubMed Central

    2015-01-01

    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·nm2) 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. PMID:25389565

  10. 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.

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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 N2-N2 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.

  14. Effect of nanoscale surface roughness on the bonding energy of direct-bonded silicon wafers

    NASA Astrophysics Data System (ADS)

    Miki, N.; Spearing, S. M.

    2003-11-01

    Direct wafer bonding of silicon wafers is a promising technology for manufacturing three-dimensional complex microelectromechanical systems as well as silicon-on-insulator substrates. Previous work has reported that the bond quality declines with increasing surface roughness, however, this relationship has not been quantified. This article explicitly correlates the bond quality, which is quantified by the apparent bonding energy, and the surface morphology via the bearing ratio, which describes the area of surface lying above a given depth. The apparent bonding energy is considered to be proportional to the real area of contact. The effective area of contact is defined as the area sufficiently close to contribute to the attractive force between the two bonding wafers. Experiments were conducted with silicon wafers whose surfaces were roughened by a buffered oxide etch solution (BOE, HF:NH4F=1:7) and/or a potassium hydroxide solution. The surface roughness was measured by atomic force microscopy. The wafers were direct bonded to polished "monitor" wafers following a standard RCA cleaning and the resulting bonding energy was measured by the crack-opening method. The experimental results revealed a clear correlation between the bonding energy and the bearing ratio. A bearing depth of ˜1.4 nm was found to be appropriate for the characterization of direct-bonded silicon at room temperature, which is consistent with the thickness of the water layer at the interface responsible for the hydrogen bonds that link the mating wafers.

  15. 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.

  16. 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

    2015-01-01

    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

  17. Towards an accurate dissociative potential for water

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu

    2014-03-01

    Most models of water describe the molecule as rigid, i.e., with fixed bond angles and bond lengths, or as flexible in which the bond angles and bond lengths vary but the chemical bonds cannot be broken. In this work we present our progress in the development of a water model which allows for the breaking and formation of chemical bonds. The force field was obtained by fitting ab initio (not DFT) energies, forces, and molecular properties. The ability of the model to predict properties of water at ambient and extreme conditions will be presented. We will also report on the modeling of small clusters of water using the dissociative force field.

  18. 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.

  19. Interaction geometries and energies of hydrogen bonds to C[double bond]O and C[double bond]S acceptors: a comparative study.

    PubMed

    Wood, Peter A; Pidcock, Elna; Allen, Frank H

    2008-08-01

    The occurrence, geometries and energies of hydrogen bonds from N-H and O-H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues - ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C[double bond]S acceptors are much weaker than those to their C[double bond]O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by approximately 0.25 A. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C[double bond]S...H angle, is in the range 102-109 degrees , much lower than the analogous C[double bond]O...H angle which lies in the range 127-140 degrees . Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by approximately 12 kJ mol(-1), for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp(3))(2)C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp(3) atoms. Electron delocalization involving C[double bond]S and the N lone pairs then induces a significant >C(delta+)[double bond]S(delta-) dipole, which enables the formation of the medium-strength C[double bond]S...H bonds observed in thioureas and thioamides. PMID:18641451

  20. Study of gas-phase O-H bond dissociation enthalpies and ionization potentials of substituted phenols - Applicability of ab initio and DFT/B3LYP methods

    NASA Astrophysics Data System (ADS)

    Klein, Erik; Lukeš, Vladimír

    2006-11-01

    In this paper, the study of phenol and 37 compounds representing various ortho-, para-, and meta-substituted phenols is presented. Molecules and their radical structures were studied using ab initio methods with inclusion of correlation energy and DFT in order to calculate the O-H bond dissociation enthalpies (BDEs) and vertical ionization potentials (IPs). Calculated BDEs and IPs were compared with available experimental values to ascertain the suitability of used methods, especially for the description of the substituent induced changes in BDE and IP. MP2, MP3, and MP4 methods do not give reliable results, since they significantly underestimate substituent induced changes in BDE and do not reflect distinct effect of substituents related to para and meta position correctly. DFT/B3LYP method reflects the effect of substituents on BDE satisfactorily, though ΔBDEs are in narrower range than experimental values. BDE of phenol was calculated also using CCSD(T) method in various basis sets. Both, DFT and HF methods describe the effect of substituents on IP identically. However, DFT considerably underestimates individual values. HF method gives IPs in very good agreement with experimental data. Obtained results show that dependences of BDEs and IPs on Hammett constants of the substituents are linear. Linearity of DFT BDE vs. IP dependence is even better than the dependences on Hammett constants and obtained equations allow estimating of O-H BDEs of meta- and para-substituted phenols from calculated IPs.

  1. Surface-induced reactions and dissociations of small acetone, acetonitrile and ethanol cluster ions: competitive chemical reactions, dissociation mechanisms and determination of dissociation energy

    NASA Astrophysics Data System (ADS)

    Mair, C.; Fedor, J.; Lezius, M.; Scheier, P.; Probst, M.; Herman, Z.; Märk, T. D.

    2003-01-01

    Using a recently commissioned tandem mass spectrometer system, BESTOF, we have carried out systematic investigations (using also deuterated molecules) on the interaction of various molecular cluster ions (including stoichiometric acetone and acetonitrile cluster ions and protonated ethanol cluster ions) with a hydrocarbon-covered stainless steel surface. Besides observing competitive chemical reactions for the stoichiometric cluster ions driven by the energy transfer in the surface collision (intra-cluster reactions versus surface H-atom pick-up reactions), we were able to see clear evidence that unimolecular dissociation kinetics determines the production of the observed decay patterns in collision energy-resolved mass spectra (CERMS). From characteristic shifts in these CERMS we can deduce corresponding binding energies, i.e., {D}((CD3CN)2+ - CD3CN) = 0.66 eV, {D}((C2H5OH)2H+ - C2H5OH) = 0.95 eV, and for the protonated dimer {D}((C2H5OH)H+ - C2H5OH) = 1.6 eV. The first value is in good agreement with values currently calculated using the B3LYP (Becke-Lee-Yang-Parr) density functional and the 6-311G(d, p) basis set, the latter values are in good agreement with values derived earlier from thermochemical data. Moreover, in the case of the protonated ethanol cluster ion, it is possible to arrive at a single (universal) breakdown graph for the trimer composed of data derived from monomer, dimer and trimer CERMS. This can be achieved by renormalizing the energy scale in the CERMS for the monomer, dimer and trimer ions (taking into account the conversion from translational to internal energy and assuming that the clusters behave like a statistical ensemble with the corresponding degrees of freedom).

  2. 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). PMID:25340952

  3. Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

    SciTech Connect

    Deshlahra, Prashant; Iglesia, Enrique

    2014-11-13

    The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accurate and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.

  4. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes.

    PubMed

    Frey, Jann A; Holzer, Christof; Klopper, Wim; Leutwyler, Samuel

    2016-05-11

    The dissociation energy (D0) of an isolated and cold molecular complex in the gas-phase is a fundamental measure of the strength of the intermolecular interactions between its constituent moieties. Accurate D0 values are important for the understanding of intermolecular bonding, for benchmarking high-level theoretical calculations, and for the parametrization of force-field models used in fields ranging from crystallography to biochemistry. We review experimental and theoretical methods for determining gas-phase D0 values of M·S complexes, where M is a (hetero)aromatic molecule and S is a closed-shell "solvent" atom or molecule. The experimental methods discussed involve M-centered (S0 → S1) electronic excitation, which is often followed by ionization to the M(+)·S ion. The D0 is measured by depositing a defined amount of vibrational energy in the neutral ground state, giving M(‡)·S, the neutral S1 excited state, giving M*·S, or the M(+)·S ion ground state. The experimental methods and their relative advantages and disadvantages are discussed. Based on the electronic structure of M and S, we classify the M·S complexes as Type I, II, or III, and discuss characteristic properties of their respective potential energy surfaces that affect or hinder the determination of D0. Current theoretical approaches are reviewed, which comprise methods based on a Kohn-Sham reference determinant as well as wave function-based methods based on coupled-cluster theory. PMID:27055105

  5. Low-energy deposition and collision-induced dissociation of water ions on Pt(111)

    NASA Astrophysics Data System (ADS)

    Wang, H.; Biesecker, J. P.; Iedema, M. J.; Ellison, G. B.; Cowin, J. P.

    1997-06-01

    We studied collision-induced D 2O + dissociation on Pt(111) using a low-energy ion source (developed at PNNL and The University of Colorado) and temperature-programmed desorption (TPD). D 2O + ions were deposited on the surface at energies ranging from 3 to 27 eV. The molecular sticking probability decreases rapidly with kinetic energy, from 0.14 at 3 eV to 0.04 at 27 eV. The dissociative adsorption probability (in terms of surface D atoms produced) increases from 0 at 10 eV to 0.8 deuteriums per incident ion at 27 eV. The dissociation appears to involve oxygen ejection, since TPD after deposition shows D 2 but no oxygen other than in water. This dissociation threshold is higher than for published results for CO + and N +2 hitting metal surfaces. This is because metal electrons should neutralize D 2O + to the ground electronic state, limiting its internal energy available for dissociation.

  6. Temperature and collision energy effects on dissociation of hydrochloric acid on water surfaces.

    PubMed

    Partanen, Lauri; Murdachaew, Garold; Gerber, R Benny; Halonen, Lauri

    2016-05-21

    Collisions of HCl at the air-water interface modelled by a 72 molecule water slab are studied for a range of various impact energies and temperatures using ab initio molecular dynamics with density functional theory. A range of short-timescale events can follow the collision, from direct scattering to nondissociative trapping on the surface. In most cases, HCl dissociation occurs within a few picoseconds, followed by the formation of a solvent-separated ion pair, or rarely, the reformation of HCl. With increasing impact energy and/or system temperature, dissociation occurs more rapidly, with Cl(-) tending to diffuse deeper into the slab. At temperatures corresponding to the frozen water regime, dissociation is seen only once out of the five thermal collisions, but with the addition of a total of 4kT or more of kinetic energy to HCl, it occurs in all our trajectories within a few ps. PMID:27126973

  7. 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 the surface parallel. The latter process is due to delayed dissociation of excited ions after they have passed the collision region.

  8. Kinetic-energy release in CO dissociation caused by fast F4+ impact

    NASA Astrophysics Data System (ADS)

    Ben-Itzhak, I.; Ginther, S. G.; Krishnamurthi, Vidhya; Carnes, K. D.

    1995-01-01

    The dissociation of CO caused by 1-MeV/amu F4+ impact has been studied using the coincidence time-of-flight technique. The kinetic energy released during the dissociation of COQ+ into ion pairs Cq1+ and Oq+2 was determined from the measured difference in the times of flight of the two charged fragments. The kinetic-energy distributions of CO2+ dissociating into C+ and O+ as a result of different impinging projectiles have been compared. These distributions shift towards higher kinetic-energy release values with increasing strength of interaction. A single Gaussian kinetic-energy distribution is in good agreement with the highly charged CO dissociation, while for doubly and triply charged CO, additional Gaussians are needed. While the Coulomb-explosion model approximately predicts the most likely value of a measured distribution, the widths of all distributions are grossly underestimated by the model. The measured widths of the distributions can be explained only by invoking the existence of potential-energy curves of the multiply charged ions that have steeper and shallower slopes as compared to the Coulombic curve. The reflection method was used to calculate the kinetic-energy release for F4++CO-->CO2+* transitions to all known CO2+ states. The final kinetic-energy distribution was then fitted to the data in order to evaluate the weights of the different transitions. The calculated fit is in fair agreement with the measured one, although the high-energy tail of the measured distribution could not be accounted for, indicating that contributions from highly excited dissociating states or from curve crossings need to be included.

  9. Distinction between the three disulfide isomers of guanylin 99-115 by low-energy collision-induced dissociation.

    PubMed

    Badock, V; Raida, M; Adermann, K; Forssmann, W G; Schrader, M

    1998-01-01

    Guanylin 99-115 is a small human peptide hormone with two disulfide bonds. The four cysteinyl residues in this peptide allow the formation of two disulfide bridges in three different ways but only the 1-3/2-4 combination is able to bind to the receptor and cause an increase of intracellular cGMP, while the other isomers are biologically inactive. Using guanylin 99-115 as a model peptide, the aim of this study was to investigate whether it is possible to distinguish the differently bridged isomers directly by tandem mass spectrometry. Guanylin isomers were generated by performing an air oxidation of fully reduced guanylin 1-3/2-4 obtained by chemical synthesis. The reaction product is a mixture of guanylin 1-4/2-3 and guanylin 1-2/3-4 in a ratio of 3:1, but there is virtually no guanylin 1-3/2-4. The two biologically inactive peptides were separated by reversed-phase high pressure liquid chromatography (HPLC). Using low-energy collision-induced dissociation tandem mass spectrometry, it was possible to distinguish unambiguously between the three guanylin isomers. This was possible due to the identification of a large number of fragments with intact disulfide bonds. Accordingly, this strategy of a direct and sensitive analysis should work as well for other peptides, with the potential to determine an undefined disulfide bond pattern. PMID:9842742

  10. 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.

  11. 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.

    PubMed

    Carrasco, Javier; Lpez-Durn, David; Liu, Zongyuan; Ducho?, Tom; Evans, Jaime; Senanayake, Sanjaya D; Crumlin, Ethan J; Matoln, Vladimir; Rodrguez, Jos A; Ganduglia-Pirovano, M Vernica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Supported by experimental and density-functional theory results, the effect of the support on O?H bond cleavage activity is elucidated for nickel/ceria systems. Ambient-pressure O?1s photoemission spectra at low Ni loadings on CeO2 (111) reveal a substantially larger amount of OH groups as compared to the bare support. 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 Ni(2+) 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. PMID:25651288

  12. 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.

  13. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO? 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 CeO?(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 CeO?(111) compared with pyramidal Ni? 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 Ni? species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO? 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.

  14. 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 PAGESBeta

    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 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

  15. Effects of multidimensional potential-energy surface topology on the unimolecular dissociation of vinyl bromide

    NASA Astrophysics Data System (ADS)

    Rahaman, Asif

    Scope and method of study. The purpose of this study was to examine the effects of multidimensional potential-energy surface topology on the unimolecular dissociation and energy transfer dynamics of vinyl bromide in the gas phase using classical trajectory methods. The global potential-energy surface is parameterized and written as a sum of the different reaction channel potentials connected by switching functions. In this investigation, only the major reaction channels; namely 3-center HBr and H2, H and Br atom dissociation channels are included. The parameters of the channel potential-energy surface which represents the system either in reactant, product or in transition state for vinyl bromide undergoing dissociation, are fitted to the results of ab initio calculations using 6-31 G(d,p) basis sets for carbon and hydrogen and Huzinaga's (4333/433/4) basis set augmented with split outer s and p orbitals and f orbital with an exponent of 0.5 for bromine, at the level of fourth order Møller Plesset perturbation theory. The topological features of the potential-energy surface are changed one at a time to study the sensitivity of the dissociation and energy transfer dynamics. Findings and conclusions. The rate of dissociation, branching ratios, reaction mechanism and vibrational distribution of HBr are calculated at different excitation energy in the range 4.5-6.44 eV. Comparisons of the results obtained from the present investigation with those obtained from the previous studies on an empirical surface indicate that variation of the potential energy with respect to stretching, bending and torsion should be modeled accurately. The excellent agreement between experimental and calculated vibrational energy distribution indicates that HBr dissociation is taking place on the ground electronic state subsequent to the internal conversion. The total relaxation rate can be characterized by first order rate law. Energy-transfer pathways and relaxation rate coefficients are found to be very sensitive to small variation in the surface curvature at equilibrium and along the reaction coordinates. While intimate details of intramolecular energy transfer are very sensitive to the fine details of the potential-surface curvatures, the gross behavior of energy transfer dynamics is not.

  16. Ion appearance energies at electron-impact dissociative ionization of sulfur hexafluoride molecule and its fragments

    NASA Astrophysics Data System (ADS)

    Demesh, Shandor Sh.; Remeta, Eugene Yu.

    2015-07-01

    Theoretical analysis of appearance energies for SF{/k +} ( k = 0- n) ion fragments of SF6 molecule as well as F+ and F{2/+} ions at electron-impact dissociative ionization of SF n ( n = 1-6) molecules is presented. Theoretical methods of GAMESS software package were used to calculate the total energies of neutral and charged molecular and atomic fragments. The dissociative ionization process is concluded to occur via repulsive highly-excited electronic states of the SF6 molecule and its fragments, due to which the observed appearance energies exceed the theoretical values. The electron binding energies on the molecular orbitals in the SF6 molecule are compared with the ion fragment appearance energies.

  17. Kinetic Energy Distribution of H(2p) Atoms from Dissociative Excitation of H2

    NASA Technical Reports Server (NTRS)

    Ajello, Joseph M.; Ahmed, Syed M.; Kanik, Isik; Multari, Rosalie

    1995-01-01

    The kinetic energy distribution of H(2p) atoms resulting from electron impact dissociation of H2 has been measured for the first time with uv spectroscopy. A high resolution uv spectrometer was used for the measurement of the H Lyman-alpha emission line profiles at 20 and 100 eV electron impact energies. Analysis of the deconvolved 100 eV line profile reveals the existence of a narrow line peak and a broad pedestal base. Slow H(2p) atoms with peak energy near 80 meV produce the peak profile, which is nearly independent of impact energy. The wings of H Lyman-alpha arise from dissociative excitation of a series of doubly excited Q(sub 1) and Q(sub 2) states, which define the core orbitals. The fast atom energy distribution peaks at 4 eV.

  18. Analysis of correlation consistent wavefunctions: H 3XH bond energies (X=C, Si and Ge)

    NASA Astrophysics Data System (ADS)

    Maître, Philippe; Ohanessian, Gilles

    1992-12-01

    We have analyzed the CCCI wavefunction for the calculation of bond dissociation energies. In the first part, CCCI is reexpressed as a non-orthogonal valence bond CI wavefunction which describes bond formation as the mixing of one covalent and two ionic parent configurations. Every other configuration is considered as an improvement of one of these three building blocks. They are grouped into different classes, the contribution of which are successively analyzed. We found the dynamical correlation of ionic structures (only one for a polar bond such as HSiH 3 or HGeH 3) to be of prime importance in obtaining accurate dissociation energies. In the second part, we improve CCCI by extending both the one- and N-electron bases, which lead to an increase and decrease of the computed bond energies, respectively. We thus conclude that the high accuracy of CCCI at the DZP level results from a cancellation of limited errors. The highest level used is uniformly accurate and yields De of 110.9, 96.3 and 92.5 kcal/mol for CH 4, SiH 4 and GeH 4 respectively.

  19. 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. PMID:25353565

  20. Fragment appearance energies in dissociative ionization of a sulfur hexafluoride molecule by electron impact

    NASA Astrophysics Data System (ADS)

    Demesh, Sh. Sh.; Zavilopulo, A. N.; Shpenik, O. B.; Remeta, E. Yu.

    2015-06-01

    Theoretical analysis of the fragment appearance energies corresponding to possible channels of formation of SF{/k +} fragments in dissociative ionization of the SF6 molecule by an electron impact is carried out. The total energies of neutral and ion molecular and atomic fragments are calculated using the theoretical methods of the GAMESS program complex. It is concluded that apart from dissociative ionization via autoionizing repulsive electronic states of the SF6 molecule, the excitation channels for SF{/k +} fragments and F2 molecules play a significant role, which leads to higher values of the observed fragment appearance energy as compared to theoretical values. The dependence of the energy corresponding to the formation of SF{/k +} c fragments on the number k of fluorine atoms is considered.

  1. 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.

  2. Facilitating Protein Disulfide Mapping by a Combination of Pepsin Digestion, Electron Transfer Higher Energy Dissociation (EThcD), and a Dedicated Search Algorithm SlinkS*

    PubMed Central

    Liu, Fan; van Breukelen, Bas; Heck, Albert J. R.

    2014-01-01

    Disulfide bond identification is important for a detailed understanding of protein structures, which directly affect their biological functions. Here we describe an integrated workflow for the fast and accurate identification of authentic protein disulfide bridges. This novel workflow incorporates acidic proteolytic digestion using pepsin to eliminate undesirable disulfide reshuffling during sample preparation and a novel search engine, SlinkS, to directly identify disulfide-bridged peptides isolated via electron transfer higher energy dissociation (EThcD). In EThcD fragmentation of disulfide-bridged peptides, electron transfer dissociation preferentially leads to the cleavage of the S–S bonds, generating two intense disulfide-cleaved peptides as primary fragment ions. Subsequently, higher energy collision dissociation primarily targets unreacted and charge-reduced precursor ions, inducing peptide backbone fragmentation. SlinkS is able to provide the accurate monoisotopic precursor masses of the two disulfide-cleaved peptides and the sequence of each linked peptide by matching the remaining EThcD product ions against a linear peptide database. The workflow was validated using a protein mixture containing six proteins rich in natural disulfide bridges. Using this pepsin-based workflow, we were able to efficiently and confidently identify a total of 31 unique Cys–Cys bonds (out of 43 disulfide bridges present), with no disulfide reshuffling products detected. Pepsin digestion not only outperformed trypsin digestion in terms of the number of detected authentic Cys–Cys bonds, but, more important, prevented the formation of artificially reshuffled disulfide bridges due to protein digestion under neutral pH. Our new workflow therefore provides a precise and generic approach for disulfide bridge mapping, which can be used to study protein folding, structure, and stability. PMID:24980484

  3. Relativistic state-specific multireference perturbation theory incorporating improved virtual orbitals: Application to the ground state single-bond dissociation.

    PubMed

    Ghosh, Anirban; Chaudhuri, Rajat K; Chattopadhyay, Sudip; Mahapatra, Uttam Sinha

    2015-10-01

    Using four-component (4c) relativistic spinors, we present a computationally economical relativistic ab initio method for molecular systems employing our recently proposed second-order state-specific multireference perturbation theory (SSMRPT) incorporating the improved virtual orbital-complete active space configuration interaction (IVO-CASCI) reference wavefunction. The resulting method, 4c-IVO-SSMRPT [calculate one state at a time] is tested in pilot calculations on the homonuclear dimers including Li(2), Na(2), K(2), Rb(2), F(2), Cl(2), and Br(2) through the computations of the ground state potential energy curves (PECs). As SSMRPT curbs intruder effects, 4c-IVO-SSMRPT is numerically stable. To our knowledge, the SSMRPT in the 4c relativistic framework has not been explored in the past. Selective spectroscopic constants that are closely related to the correct shape and accuracy of the energy surfaces have been extracted from the computed PECs. For the halogen molecules, a relativistic destabilization of the bond has been found. Relativistic and electron correlation effects need to be incorporated to get reliable estimates. Our results are in good accordance with reference theoretical and experimental data which manifests the computational accuracy and efficiency of the new 4c-IVO-SSMRPT method. The method opens for an improved description of MR systems containing heavy elements. The inexpensiveness of IVO-CASCI makes 4c-IVO-SSMRPT method promising for studies on large systems of heavy elements. PMID:26272333

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

    SciTech Connect

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

    2007-06-15

    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 1 kW CO{sub 2} 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.

  5. 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.

  6. 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.

  7. The Bond Order of C2 from a Strictly N-Representable Natural Orbital Energy Functional Perspective.

    PubMed

    Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

    2016-03-14

    The bond order of the ground electronic state of the carbon dimer has been analyzed in the light of natural orbital functional theory calculations carried out with an approximate, albeit strictly N-representable, energy functional. Three distinct solutions have been found from the Euler equations of the minimization of the energy functional with respect to the natural orbitals and their occupation numbers, which expand upon increasing values of the internuclear coordinate. In the close vicinity of the minimum energy region, two of the solutions compete around a discontinuity point. The former, corresponding to the absolute minimum energy, features two valence natural orbitals of each of the following symmetries, σ, σ*, π and π*, and has three bonding interactions and one antibonding interaction, which is very suggestive of a bond order large than two but smaller than three. The latter, features one σ-σ* linked pair of natural orbitals and three degenerate pseudo-bonding like orbitals, paired each with one triply degenerate pseudo-antibonding orbital, which points to a bond order larger than three. When correlation effects, other than Hartree-Fock for example, between the paired natural orbitals are accounted for, this second solution vanishes yielding a smooth continuous dissociation curve. Comparison of the vibrational energies and electron ionization energies, calculated on this curve, with their corresponding experimental marks, lend further support to a bond order for C2 intermediate between acetylene and ethylene. PMID:26822104

  8. Novel 2-alkyl-1-ethylpyridinium ionic liquids: synthesis, dissociation energies and volatility.

    PubMed

    Vilas, Miguel; Rocha, Marisa A A; Fernandes, Ana M; Tojo, Emilia; Santos, Luís M N B F

    2015-01-28

    This work presents the synthesis, volatility study and electrospray ionization mass spectrometry with energy-variable collision induced dissociation of the isolated [(cation)2(anion)](+) of a novel series of 2-alkyl-1-ethyl pyridinium based ionic liquids, [(2)CN-2(1)C2Py][NTf2]. Compared to the imidazolium based ionic liquids, the new ionic liquid series presents a higher thermal stability and lower volatility. The [(cation)2(anion)](+) collision induced dissociation energies of both [(2)CN-2(1)C2Py][NTf2] and [CNPy][NTf2] pyridinium series show an identical trend with a pronounced decrease of the relative cation-anion interaction energy towards an almost constant value for N = 6. It was found that the lower volatility of [(2)CN-2(1)C2Py][NTf2] with a shorter alkyl chain length is due to its higher enthalpy of vaporization. Starting from [(2)C3(1)C2Py][NTf2], the lower volatility is governed by the combination of slightly lower entropies and higher enthalpies of vaporization, an indication of a higher structural disorder of the pyridinium based ionic liquids than the imidazolium based ionic liquids. Dissociation energies and volatility trends support the cohesive energy interpretation model based on the overlapping of the electrostatic and van der Waals functional interaction potentials. PMID:25493639

  9. 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.

  10. Comparison of hexamethyldisiloxane dissociation processes in plasma.

    PubMed

    Jauberteau, J L; Jauberteau, I

    2012-09-01

    Different hexamethyldisiloxane (HMDSO) dissociation processes are investigated by means of absorption spectroscopy and mass spectrometry. All of these processes are expected to occur in plasma containing Ar-HMDSO gas mixture. We successively study interactions of the HMDSO molecule with electrons (energy ranges from 15 to 70 eV), with Ar((3)P(2)) metastable species (internal energy 11.55 eV) and with VUV photon (7.3 to 10.79 eV). The studies of HMDSO interactions with Ar((3)P(2)) and VUV photon provide new results concerning the dissociation pathways and the collision cross-sections. In the case of Ar((3)P(2)), the dissociation mechanisms result mainly in Si-C or Si-O bond breaking, producing SiMe(2,1) radicals. Less efficient mechanisms involve also Si-C and Si-O bond breaking producing Me, Si(2)Me(5)O, or SiMe(3), on one hand, and, on the other hand, Si-C and C-H bond breaking producing Si(2)Me(4)OH. In the case of photon interaction, the dissociation process is more selective and mainly produces Si(2)OMe(5) pentadisiloxane and methyl radicals due to Si-C bond breaking. Si-O bond breaking produces also SiMe(3) in a lower concentration. Dissociation cross-section values of HMDSO ranging from σ = 45 × 10(-20) m(2) to 180 × 10(-20) m(2) and from σ = 0.7 × 10(-22) m(2) to 18.3 × 10(-22) m(2), correspond to a global dissociation mechanism by Ar((3)P(2)) collision and to a selective dissociation mechanism (producing Si(2)OMe(5) and Me) by VUV photon interaction, respectively. All results are compared and discussed. PMID:22812650

  11. 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

  12. 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

  13. 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…

  14. On the dissociation energy of CaOH and LiOH

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Partridge, H.

    1984-01-01

    A technique for computing the dissociation energy of ionic diatomics is extended to the ionic triatomics LiOH and CaOH. The calculated Do values (with the recommended experimental values in parentheses) are 4.72 plus or minus 0.06 eV (4.53 plus or minus 0.04) for LiOH and 4.13 plus or minus 0.07 (4.23 eV) for CaOH.

  15. 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.

    1988-01-01

    The dissociation energy D0 is determined here for the CN ground-state and radiative lifetimes for the A 2Pi and B 2Sigma(+) states. D0 is found to be 7.65 + or - 0.06 eV, corresponding to Delta Hf (CN) = 105.3 + or - 1.5 kcal/mole. These results are compared with current experimental estimates and with previous theoretical calculations.

  16. How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

    PubMed

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867

  17. 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 surface parallel. The latter process is due to delayed dissociation of excited ions after they have passed the collision region and the energy analyzer as excited parent ions.

  18. 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.

  19. 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.

  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. 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})

  2. The dissociation energy of the new diatomic molecules SiPb and GePb

    NASA Astrophysics Data System (ADS)

    Ciccioli, A.; Gigli, G.; Meloni, Giovanni; Testani, E.

    2007-08-01

    The diatomic molecules SiPb and GePb were for the first time identified by producing high temperature vapors of the constituent pure elements in a "double-oven-like" molecular-effusion assembly. The partial pressures of the atomic, heteronuclear, and homonuclear gaseous species observed in the vapor, namely, Si, Ge, Pb, SiPb, GePb, Pb2, Gen, and Sin (n=2-3), were mass-spectrometrically measured in the overall temperature ranges 1753-1961K (Ge-Pb) and 1992-2314K (Si-Pb). The dissociation energies of the new species were determined by second- and third-law analyses of both the direct dissociation reactions and isomolecular exchange reactions involving homonuclear molecules. The selected values of the dissociation energies at 0K (D0°) are 165.1±7.3 and 141.6±6.9kJ/mol, respectively, for SiPb and GePb, and the corresponding enthalpies of formation (ΔfH0°) are 476.4±7.3 and 419.3±6.9kJ/mol. The ionization efficiency curves of the two species were measured, giving the following values for the first ionization energies: 7.0±0.2eV (SiPb) and 7.1±0.2eV (GePb). A computational study of the species SiPb and GePb was also carried out at the CCSD(T) level of theory using the relativistic electron core potential approach. Molecular parameters, adiabatic ionization energies, adiabatic electron affinities, and dissociation energies of the title species were calculated, as well as the enthalpy changes of the exchange reactions involving the other Pb-containing diatomics of group 14. Finally, a comparison between the experimental and theoretical results is presented, and from a semiempirical correlation the unknown dissociation energies of the SiSn and PbC molecules are predicted as 234±7 and 185±11kJ/mol, respectively.

  3. 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.

  4. Bond resonance energy and verification of the isolated pentagon rule

    SciTech Connect

    Aihara, Jun Ichi

    1995-04-12

    The isolated pentagon rule (IPR) states that fullerenes with isolated pentagons are kinetically much more stable than their fused pentagon counterparts. This rule can be verified in terms of a graph-theoretically defined bond resonance energy. In general, a {pi} bond shared by two pentagons has a large negative bond resonance energy, thus contributing significantly to the increase in kinetic instability or chemical reactivity of the molecule. The existence of such highly antiaromatic local structures sharply distinguishes IPR-violating fullerenes from isolated-pentagon isomers. {pi}bonds shared by two pentagons are shared by many antiaromatic conjugated circuits but not by relatively small aromatic conjugated circuits. 39 refs., 3 figs., 5 tabs.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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 ? 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.

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

    PubMed

    Oghbaie, Shabnam; Gisselbrecht, Mathieu; Laksman, Joakim; Mnsson, 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 ? 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. PMID:26395707

  7. 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.

  8. 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 weakens. In this way, as Tv decreases, rotational energy appears to compensate for the decline in average vibrational energy in promoting dissociation. In both the equilibrium and nonequilibrium test sets, in every case, the average total internal energy loss in the dissociating trajectories is between 10.2 and 11.0 eV, slightly larger than the equilibrium potential energy change of N2 dissociation.

  9. 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

    2015-08-01

    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 × 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's dependence on v weakens. In this way, as T(v) decreases, rotational energy appears to compensate for the decline in average vibrational energy in promoting dissociation. In both the equilibrium and nonequilibrium test sets, in every case, the average total internal energy loss in the dissociating trajectories is between 10.2 and 11.0 eV, slightly larger than the equilibrium potential energy change of N2 dissociation. PMID:26254650

  10. Energetics and Dynamics of the Fragmentation Reactions of Protonated Peptides Containing Methionine Sulfoxide or Aspartic Acid via Energy- and Time-Resolved Surface Induced Dissociation

    SciTech Connect

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E.; O'Hair, Richard Aj

    2007-10-25

    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility on these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (non-mobile proton conditions) to lysine (partially-mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFEC) reveals that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 12 orders of magnitude lower than non-selective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to non-selective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.

  11. The Chemical Bond in C2.

    PubMed

    Hermann, Markus; Frenking, Gernot

    2016-03-14

    Quantum chemical calculations using the complete active space of the valence orbitals have been carried out for Hn CCHn (n=0-3) and N2 . The quadratic force constants and the stretching potentials of Hn CCHn have been calculated at the CASSCF/cc-pVTZ level. The bond dissociation energies of the C-C bonds of C2 and HC≡CH were computed using explicitly correlated CASPT2-F12/cc-pVTZ-F12 wave functions. The bond dissociation energies and the force constants suggest that C2 has a weaker C-C bond than acetylene. The analysis of the CASSCF wavefunctions in conjunction with the effective bond orders of the multiple bonds shows that there are four bonding components in C2 , while there are only three in acetylene and in N2 . The bonding components in C2 consist of two weakly bonding σ bonds and two electron-sharing π bonds. The bonding situation in C2 can be described with the σ bonds in Be2 that are enforced by two π bonds. There is no single Lewis structure that adequately depicts the bonding situation in C2 . The assignment of quadruple bonding in C2 is misleading, because the bond is weaker than the triple bond in HC≡CH. PMID:26756311

  12. Low energy water ion deposition and collision-induced dissociation on Pt(111)

    SciTech Connect

    Cowin, J.P.; Wang, H.; Iedema, M.J.

    1996-12-31

    A mass selected molecular ion source built to deposit aqueous-like ions (H{sup 3}O{sub +},H{sub +},NH{sup 4}+, and anions) at low energy (2 ev) has been completed. A study of D{sup 2}O ion deposition on clean Pt(111) is reported on, as well as preliminary results for D{sup +3}O{sub +} deposition on ice layers. For D{sup 2}O{sub +}, the ion was deposited on the surface at energies from 3 to 27 eV. It is expected to neutralize by resonant charge transfer near the surface. We found that D{sup 2}O{sub +} dissociates at higher kinetic energy with high probability, but stays intact below a threshold energy of 10 {+-} eV. The molecular sticking probability decreases rapidly with kinetic energy, being 0.14 at 3 eV and 0.04 at 20{sub 2}eV. The dissociation involves oxygen ejection since TPD after deposition shows D{sup 2} but no oxygen desorbing, other than in water. Probably this is simply a type of {open_quotes}spectator{close_quotes} collision, whereby the oxygen, carrying most of the momentum, bounces oblivious to the deuterium`s fate.

  13. 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.

  14. Experimental and theoretical investigations of energy transfer and hydrogen-bond breaking in small water and HCl clusters.

    PubMed

    Samanta, Amit K; Czakó, Gábor; Wang, Yimin; Mancini, John S; Bowman, Joel M; Reisler, Hanna

    2014-08-19

    Water is one of the most pervasive molecules on earth and other planetary bodies; it is the molecule that is searched for as the presumptive precursor to extraterrestrial life. It is also the paradigm substance illustrating ubiquitous hydrogen bonding (H-bonding) in the gas phase, liquids, crystals, and amorphous solids. Moreover, H-bonding with other molecules and between different molecules is of the utmost importance in chemistry and biology. It is no wonder, then, that for nearly a century theoreticians and experimentalists have tried to understand all aspects of H-bonding and its influence on reactivity. It is somewhat surprising, therefore, that several fundamental aspects of H-bonding that are particularly important for benchmarking theoretical models have remained unexplored experimentally. For example, even the binding strength between two gas-phase water molecules has never been determined with sufficient accuracy for comparison with high-level electronic structure calculations. Likewise, the effect of cooperativity (nonadditivity) in small H-bonded networks is not known with sufficient accuracy. An even greater challenge for both theory and experiment is the description of the dissociation dynamics of H-bonded small clusters upon acquiring vibrational excitation. This is because of the long lifetimes of many clusters, which requires running classical trajectories for many nanoseconds to achieve dissociation. In this Account, we describe recent progress and ongoing research that demonstrates how the combined and complementary efforts of theory and experiment are enlisted to determine bond dissociation energies (D0) of small dimers and cyclic trimers of water and HCl with unprecedented accuracy, describe dissociation dynamics, and assess the effects of cooperativity. The experimental techniques rely on IR excitation of H-bonded X-H stretch vibrations, measuring velocity distributions of fragments in specific rovibrational states, and determining product state distributions at the pair-correlation level. The theoretical methods are based on high-level ab initio potential energy surfaces used in quantum and classical dynamical calculations. We achieve excellent agreement on D0 between theory and experiments for all of the clusters that we have compared, as well as for cooperativity in ring trimers of water and HCl. We also show that both the long-range and the repulsive parts of the potential must be involved in bond breaking. We explain why H-bonds are so resilient and hard to break, and we propose that a common motif in the breaking of cyclic trimers is the opening of the ring following transfer of one quantum of stretch excitation to form open-chain structures that are weakly bound. However, it still takes many vibrational periods to release one monomer fragment from the open-chain structures. Our success with water and HCl dimers and trimers led us to embark on a more ambitious project: studies of mixed water and HCl small clusters. These clusters eventually lead to ionization of HCl and serve as prototypes of acid dissociation in water. Measurements and calculations of such ionizations are yet to be achieved, and we are now characterizing these systems by adding monomers one at a time. We describe our completed work on the HCl-H2O dimer and mention our recent theoretical results on larger mixed clusters. PMID:25072730

  15. Absolute cross sections for dissociative electron attachment and dissociative ionization of cobalt tricarbonyl nitrosyl in the energy range from 0 eV to 140 eV.

    PubMed

    Engmann, Sarah; Stano, Michal; Papp, Peter; Brunger, Michael J; Matej?k, tefan; Inglfsson, Oddur

    2013-01-28

    We report absolute dissociative electron attachment (DEA) and dissociative ionization (DI) cross sections for electron scattering from the focused electron beam induced deposition (FEBID) precursor Co(CO)(3)NO in the incident electron energy range from 0 to 140 eV. We find that DEA leads mainly to single carbonyl loss with a maximum cross section of 4.1 10(-16) cm(2), while fragmentation through DI results mainly in the formation of the bare metal cation Co(+) with a maximum cross section close to 4.6 10(-16) cm(2) at 70 eV. Though DEA proceeds in a narrow incident electron energy range, this energy range is found to overlap significantly with the expected energy distribution of secondary electrons (SEs) produced in FEBID. The DI process, on the other hand, is operative over a much wider energy range, but the overlap with the expected SE energy distribution, though significant, is found to be mainly in the threshold region of the individual DI processes. PMID:23387582

  16. Geometrical structures, vibrational frequencies, force constants and dissociation energies of isotopic water molecules (H2O, HDO, D2O, HTO, DTO, and T2O) under dipole electric field

    NASA Astrophysics Data System (ADS)

    Shi, Shun-Ping; Zhang, Quan; Zhang, Li; Wang, Rong; Zhu, Zheng-He; Jiang, Gang; Fu, Yi-Bei

    2011-06-01

    The dissociation limits of isotopic water molecules are derived for the ground state. The equilibrium geometries, the vibrational frequencies, the force constants and the dissociation energies for the ground states of all isotopic water molecules under the dipole electric fields from -0.05 a.u. to 0.05 a.u. are calculated using B3P86/6-311++G(3df,3pf). The results show that when the dipole electric fields change from -0.05 a.u. to 0.05 a.u., the bond length of H—O increases whereas the bond angle of H—O—H decreases because of the charge transfer induced by the applied dipole electric field. The vibrational frequencies and the force constants of isotopic water molecules change under the influence of the strong external torque. The dissociation energies increase when the dipole electric fields change from -0.05 a.u. to 0.05 a.u. and the increased dissociation energies are in the order of H2O, HDO, HTO, D2O, DTO, and T2O under the same external electric fields.

  17. Storing Renewable Energy in Chemical Bonds

    ScienceCinema

    Helm, Monte; Bullock, Morris

    2014-06-13

    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.

  18. 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.

  19. 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.

  20. The unimolecular dissociation of H2CO on the lowest triplet potential-energy surface

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yukio; Wesolowski, Steven S.; Van Huis, Timothy J.; Schaefer, Henry F.

    1998-04-01

    The unimolecular dissociation reaction of H2CO on the triplet potential-energy surface has been studied via ab initio electronic structure theory. The stationary point geometries for the equilibrium and transition state are determined employing the configuration interaction with single and double excitations (CISD), coupled cluster with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] levels of theory with large basis sets up to the correlation consistent (cc)-pVQZ basis. With the best method, cc-pVQZ CCSD(T), the first excited triplet ( 3A?) state lies 72.2 kcal/mol (25 260 cm-1) above the ground (X 1A1) state of H2CO, which is in excellent agreement with the experimental observation of 72.03 kcal/mol (25 194 cm-1). The dissociation limit (H?+HCO?) is located at 86.3 kcal/mol (30 170 cm-1) above the ground state of H2CO, which is again in good agreement with the two experimentally determined values of 86.57 kcal/mol (30 280 cm-1) and 86.71 kcal/mol (30 328.5 cm-1). With the same method the triplet dissociation transition state lies 92.4 kcal/mol (32 300 cm-1) above the ground state. Consequently, the activation energy for the dissociation reaction of H2CO on the triplet surface is determined ab initio to be 18.9-20.1 kcal/mol (6620-7040 cm-1) (including an estimated error bar of 1.2 kcal/mol or 420 cm-1). The zero-point vibrationally corrected exit barrier height is predicted to be 4.9-6.1 kcal/mol (1710-2130 cm-1). These newly predicted energies are consistent with the recent experimental observations by the Moore group at University of California-Berkeley (1987) and by the Wittig group at University of Southern California (1997).

  1. 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. PMID:25142324

  2. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds.

    PubMed

    Warshel, A; Papazyan, A

    1996-11-26

    Low-barrier hydrogen bonds have recently been proposed as a major factor in enzyme catalysis. Here we evaluate the feasibility of transition state (TS) stabilization by low-barrier hydrogen bonds in enzymes. Our analysis focuses on the facts that (i) a low-barrier hydrogen bond is less stable than a regular hydrogen bond in water, (ii) TSs are more stable in the enzyme active sites than in water, and (iii) a nonpolar active site would destabilize the TS relative to its energy in water. Combining these points and other experimental and theoretical facts in a physically consistent frame-work shows that a low-barrier hydrogen bond cannot stabilize the TS more than an ordinary hydrogen bond. The reason for the large catalytic effect of active site hydrogen bonds is that their formation entails a lower reorganization energy than their solution counterparts, due to the preorganized enzyme environment. PMID:8942991

  3. 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.

  4. How Many Water Molecules Does it Take to Dissociate HCl?

    PubMed

    Vargas-Caamal, Alba; Cabellos, Jose Luis; Ortiz-Chi, Filiberto; Rzepa, Henry S; Restrepo, Albeiro; Merino, Gabriel

    2016-02-01

    The potential energy surfaces of the HCl(H2 O)n (n is the number of water molecules) clusters are systematically explored using density functional theory and high-level ab initio computations. On the basis of electronic energies, the number of water molecules needed for HCl dissociation is four as reported by some experimental groups. However, this number is five owing to the inclusion of entropic factors. Wiberg bond indices are calculated and analyzed, and the results provide a quadratic correlation and classification of clusters according to the nondissociated, partially dissociated, and fully dissociated character of the H-Cl bond. Our computations show that if temperature is not controlled during the experiment, the values obtained for the dipole moment (or for any measurable property) are susceptible to change, providing a different picture of the number of water molecules needed for HCl dissociation in a nanoscopic droplet. PMID:26774026

  5. Intermolecular transfer of vibrational energy in matrix isolated NO. High vibrational states, electronic excitation and dissociation

    NASA Astrophysics Data System (ADS)

    Hadj Bachir, I.; Charneau, R.; Dubost, H.

    1993-12-01

    Nitric oxide dispersed in solid argon and krypton is vibrationally excited by a cw modulated infrared laser resonant with the fundamental or first overtone absorption. The energy deposited into ν = 1 or ν = 2 is redistributed to higher levels by intermolecular vibration to vibration transfer. The vibrational population distributions obtained from overtone emission spectra in both IR and visible regions or probed using a pulsed dye laser extend over a broad range. The topmost detected level is ν = 27. In addition to the vibrational fluorescence, electronic luminescence emanating from the lowest excited valence states a 4Π and B 2Π of NO is found to be induced by IR laser irradiation. The slow irreversible decay of the electronic emissions followed by thermoluminescence shows that a small fraction of the NO molecules is dissociated. Time and frequency resolved analysis of the various emissions is performed as a function of the relevant parameters. The results show that X 2Π→a 4Π intersystem crossing and X 2Π→B 2Π internal conversion do not occur in matrix isolated NO. A new mechanism of intermolecular vibrational to electronic energy transfer involving the exchange "en bloc" of a large number of vibrational quanta between highly vibrationally excited molecules is proposed. The excitation of NO to predissociated vibronic levels of the B 2Π state results in electronic emission and dissociation.

  6. 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.

  7. Sub-femtosecond dynamics and dissociation of C-H bonds in the condensed phase: Effects of entangled protonic states

    NASA Astrophysics Data System (ADS)

    Chatzidimitriou-Dreismann, C. A.; Abdul-Redah, T.; Sperling, J.

    2000-08-01

    According to quantum theory, adjacent particles of condensed systems may exhibit quantum interference and/or correlation phenomena being caused by interparticle interactions. Here we present, for the first time, direct experimental evidence for short-lived quantum entanglement of protons of C-H bonds. Neutron Compton scattering results from solid polystyrene reveal that, in the sub-femtosecond time scale, the measured cross-section density of the protons is "anomalously" reduced by ca. 20%. A first-principles theoretical treatment of this effect is given, which is based on the well-known van Hove formalism, and also takes explicitly into account quantum entanglement of protonic states and its decoherence. Besides its fundamental physical character, the effect may have considerable chemical and biological applications, and also be of technical importance, e.g., for the engineering of some neutron moderators.

  8. 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.

  9. 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. PMID:19309157

  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. 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). PMID:17975856

  12. High-energy electron transfer dissociation (HE-ETD) using alkali metal targets for sequence analysis of post-translational peptides.

    PubMed

    Hayakawa, Shigeo; Matsumoto, Shinya; Hashimoto, Mami; Iwamoto, Kenichi; Nagao, Hirofumi; Toyoda, Michisato; Shigeri, Yasushi; Tajiri, Michiko; Wada, Yoshinao

    2010-09-01

    Post-translational modifications (PTMs) of proteins are important in the activation, localization, and regulation of protein function in vivo. The usefulness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) in tandem mass spectrometry (MS/MS) using low-energy (LE) trap type mass spectrometer is associated with no loss of a labile PTM group regarding peptide and protein sequencing. The experimental results of high-energy (HE) collision induced dissociation (CID) using the Xe and Cs targets and LE-ETD were compared for doubly-phosphorylated peptides TGFLT(p)EY(p)VATR (1). Although HE-CID using the Xe target did not provide information on the amino acid sequence, HE-CID using the Cs target provided all the z-type ions without loss of the phosphate groups as a result of HE-ETD process, while LE-ETD using fluoranthene anion gave only z-type ions from z(5) to z(11). The difference in the results of HE-CID between the Xe and Cs targets demonstrated that HE-ETD process with the Cs target took place much more dominantly than collisional activation. The difference between HE-ETD using Cs targets and LE-ETD using the anion demonstrated that mass discrimination was much weaker in the high-energy process. HE-ETD was also applied to three other phosphopeptides YGGMHRQEX(p)VDC (2: X = S, 3: X = T, 4: X = Y). The HE-CID spectra of the doubly-protonated phosphopeptides (= [M + 2H](2+)) of 2, 3, and 4 using the Cs target showed a very similar feature that the c-type ions from c(7) to c(11) and the z-type ions from z(7) to z(11) were formed via N-C alpha bond cleavage without a loss of the phosphate group. PMID:20598903

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

    PubMed

    Gawthrop, Peter J; Crampin, Edmund J

    2014-11-01

    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

  14. 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

  15. 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.

  16. How Well Can New-Generation Density Functionals Describe the Energetics of Bond-Dissociation Reactions Producing Radicals?

    SciTech Connect

    Zhao, Yan; Truhlar, Donald G.

    2008-02-14

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The performance of various density functionals has been tested for three sets of reaction energies involving radicals. It is shown that two recently designed functionals, M05-2X and M06-2X, provide the best performance. These functionals provide useful and affordable methods for future mechanistic studies involving organic radicals.

  17. Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

    PubMed

    Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

    2011-12-01

    Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. PMID:22052831

  18. Dissociation of acetaldehyde in intense laser field: Coulomb explosion or field-assisted dissociation?

    NASA Astrophysics Data System (ADS)

    Elshakre, Mohamed E.; Gao, Lirong; Tang, Xiaoping; Wang, Sufan; Shu, Yafei; Kong, Fanao

    2003-09-01

    Dissociation of acetaldehyde in moderate strong laser field of 1013-1014W/cm2 was investigated. Singly charged parent ion CH3CHO+ and fragmental ions CH3+, CHO+, C2H4+, O+, CH2CHO+, and H+ were produced by 800 nm laser of 100 fs pulse duration and recorded by time-of-flight mass spectrometer. The CH3+ fragment further dissociated to CH2+, CH+, and C+ ions at higher intensity. Ab initio calculated results show that the singly-, doubly-, and triply charged parent ions are stable. So, the dissociation mechanism was not due to Coulomb explosion of multicharged ion. A field-assisted dissociation (FAD) theory, which assumes that only one bond undergoes dissociation while the rest of the molecular geometry stays unchanged, was employed to treat the dissociation dynamics. Accordingly, the dressed potential energy surfaces of the ground state for the parent and the fragment ions were calculated. Corresponding quasiclassical trajectory calculations show that the bond ruptures take place in the order of C-C, C-O, and C-H, agreeing with the observation. The observed angular dependence and charge distribution of the product ions can also be interpreted by the FAD theory.

  19. 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.

  20. Low energy electron induced cytosine base release in 2'-deoxycytidine-3'-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Renjith; Sarma, Manabendra

    2014-09-01

    Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2'-deoxycytidine-3'-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3' C-O bond cleavage from the lowest π* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π* orbital of the base to the σ* orbital of the glycosidic N-C bond. In addition, the metastable state formed after impinging LEE (0-1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N-C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ˜35-55 fs. Comparison of salient features of the two dissociation events, i.e., 3' C-O single strand break and glycosidic N-C bond cleavage in 3'-dCMPH molecule are also provided.

  1. Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

    SciTech Connect

    Bhaskaran, Renjith; Sarma, Manabendra

    2014-09-14

    Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed after impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.

  2. Analysis of liquid metal embrittlement from a bond energy viewpoint

    NASA Technical Reports Server (NTRS)

    Kelley, M. J.; Stoloff, N. S.

    1975-01-01

    Absorption induced embrittlement of solid metals by certain liquid metals is analyzed through an Engel-Brewer calculation of the solid-liquid interaction energy, and of the effect of the latter in reducing fracture surface energy. The reduction in fracture surface energy is estimated by comparison of the electronic contribution to the solid-liquid interaction energy with solid-solid bond energy for some 40 liquid-solid couples. Regular solution theory is used to estimate mutual solubility as the relative difference in parameter values. Embrittlement can be predicted by using reduction in fracture surface energy and solubility parameter difference as critical variables. The effect of solute additions to the liquid on the degree of embrittlement is interpreted via the same two variables; the principal effect of solutes is to modify solubility relationships at the solid-liquid interface.

  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. Tailoring Bond Cleavage in Gas-Phase Biomolecules by Low Energy Electrons

    NASA Astrophysics Data System (ADS)

    Ptasinska, Sylwia

    2014-10-01

    The high energy quanta of impinging radiation can generate a large number (about 5x104) of secondary electrons per 1 MeV of energy deposited. When ejected in condensed phase water, the kinetic energy distribution of these free or quasi-free electrons is peaked below 10 eV. Low energy electrons also dominate in the secondary emission from biomolecular targets exposed to different energies of primary radiation. Due to the complexity of the radiation-induced processes in the condensed-phase environment, mechanisms of secondary electrons induced damage in biomolecules (BM) still need to be investigated. However, based on results from theory and different experiments accumulated within the last decade, it is now possible to determine the fundamental mechanisms that are involved in many chemical reactions induced in isolated gas-phase biomolecules by low energy electrons. The central finding of earlier research was the discovery of the bond- and site- selectivity in the dissociative electron attachment (DEA) process to biomolecules. It has been demonstrated that by tuning the energy of the incoming electron we can gain control over the location of the bond cleavage. These studies showed the selectivity in single bond cleavage reactions leading to the formation of the dehydrogenated closed shell anion (BM-H)- or the complementary reaction leading to H-. The loss of a hydrogen atom or an anion is fast compared with ring cleavage and the excision of heavier fragments and, hence, this reaction can compete efficiently with autodetachment. Moreover, site selectivity has been also observed in the metastable anion formation via the DEA process. Such delayed fragmentation was studied recently for the dehydrogenated closed-shell anion conversion into NCO- upon DEA proceeded a few μ sec after electron attachment, indicating a rather slow unimolecular decomposition. Interestingly, site selectivity was observed in the prompt as well as the metastable NCO- formation in DEA. The research described herein was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Basic Energy Sciences, Office of Science, United States Department of Energy through Grant Number DE-FC02-04ER15533.

  5. Structures, energies, and bonding in the water heptamer

    NASA Astrophysics Data System (ADS)

    Acelas, Nancy; Hincapié, Gina; Guerra, Doris; David, Jorge; Restrepo, Albeiro

    2013-07-01

    In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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 (2Σ+)←X (2Σ+) continuum leading to direct, near-threshold dissociation generating Ag* (2P3/2) + RG (1S0) products. Images recorded at excitation wavelengths throughout the C (2Σ+)←X (2Σ+) continuum, coupled with known atomic energy levels, permit determination of the ground X (2Σ+) state dissociation energies of 85.9 ± 23.4 cm-1 (Ag-Ar), 149.3 ± 22.4 cm-1 (Ag-Kr), and 256.3 ± 16.0 cm-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-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 Ag2.

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

    PubMed

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

    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 ((2)Σ(+))←X ((2)Σ(+)) continuum leading to direct, near-threshold dissociation generating Ag* ((2)P3/2) + RG ((1)S0) products. Images recorded at excitation wavelengths throughout the C ((2)Σ(+))←X ((2)Σ(+)) continuum, coupled with known atomic energy levels, permit determination of the ground X ((2)Σ(+)) state dissociation energies of 85.9 ± 23.4 cm(-1) (Ag-Ar), 149.3 ± 22.4 cm(-1) (Ag-Kr), and 256.3 ± 16.0 cm(-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(-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 Ag2. PMID:26429006

  8. Anchor Points Reactive Potential for Bond-Breaking Reactions.

    PubMed

    Yang, Ke R; Xu, Xuefei; Truhlar, Donald G

    2014-03-11

    We present a new method for fitting potential energy surfaces in molecular-mechanics-like internal coordinates based on data from electronic structure calculations. The method should be applicable to chemical reactions involving either bond dissociation or isomerization and is illustrated here for bond dissociation, in particular the breaking of an O-H bond in methanol and the breaking of an N-H bond in dimethylamine. As compared to previously available systematic methods for fitting global potential energy surfaces, it extends the maximum size of the system than can be treated by at least an order of magnitude. PMID:26580172

  9. 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.

  10. Determination of the collisional energy transfer distribution responsible for the collision-induced dissociation of NO2 with Ar

    NASA Astrophysics Data System (ADS)

    Steill, Jeffrey D.; Jasper, Ahren W.; Chandler, David W.

    2015-09-01

    Collisional energy transfer is an essential aspect of chemical reactivity and maintenance of thermal equilibrium. Here we report the shape (energy-dependence) of the collisional energy transfer probability function for collisions of vibrationally excited NO2 entrained in a molecular beam and photoexcited to within 40 cm-1 of its dissociation threshold. The internally excited molecules undergo collisions with Ar atoms in a crossed beam apparatus. Dissociative collisions rapidly produce the NO(J) fragment, which is observed by velocity-mapped ion imaging and REMPI techniques. The measured collisional energy transfer function is obtained via energy conservation and is compared with the results of classical trajectory calculations. Good agreement between the theory and experiment is found for collisions that transfer small amounts of energy, but the theory predicts a higher likelihood of energetic collisions than is observed experimentally. We explore possible explanations for this discrepancy in the dynamics of the collision excitation process.

  11. Projectile energy dependence in the molecular excitation of th H3+, D3+ molecular ions in their polar dissociation

    SciTech Connect

    Yousif, F.B.; Hinojosa, G.; Dominguez, I.

    1996-05-01

    The laboratory energy distributions of H{sup +} and D{sup +} in coincidence with H{sup {minus}} and D{sup {minus}} ions, resulting from the collision-induced-dissociation of H{sup 3+} and D{sup 3+} on He target for incoming beam energies ranging from 2.5 to 9.0 keV has been measured. The energy-analyzed-spectra of ionic fragments were measured both independently and in coincidence with each other. From these, the energy absorbed by the dissociating molecular ions in the excitation process induced by the collision with He prior to its breakup, was evaluated as a function of the projectile energy and it was found that it is not constant but it is consistent with the identified H{sup 3+} excited states which have adiabatic Born-Oppenheimer energies of 21-50 eV above the H{sup 3+} ground state.

  12. 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. PMID:26661033

  13. 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 =…

  14. Bond length and local energy density property connections for non-transition-metal oxide-bonded interactions.

    PubMed

    Gibbs, G V; Spackman, M A; Jayatilaka, D; Rosso, K M; Cox, D F

    2006-11-01

    For a variety of molecules and earth materials, the theoretical local kinetic energy density, G(r(c)), increases and the local potential energy density, V(r(c)), decreases as the M-O bond lengths (M = first- and second-row metal atoms bonded to O) decrease and the electron density, rho(r(c)), accumulates at the bond critical points, r(c). Despite the claim that the local kinetic energy density per electronic charge, G(r(c))/rho(r(c)), classifies bonded interactions as shared interactions when less than unity and closed-shell when greater, the ratio was found to increase from 0.5 to 2.5 au as the local electronic energy density, H(r(c)) = G(r(c)) + V(r(c)), decreases and becomes progressively more negative. The ratio appears to be a measure of the character of a given M-O bonded interaction, the greater the ratio, the larger the value of rho(r(c)), the smaller the coordination number of the M atom and the more shared the bonded interaction. H(r(c))/rho(r(c)) versus G(r(c))/rho(r(c)) scatter diagrams categorize the M-O bonded interactions into domains with the local electronic energy density per electron charge, H(r(c))/rho(r(c)), tending to decrease as the electronegativity differences for the bonded pairs of atoms decrease. The values of G(r(c)) and V(r(c)), estimated with a gradient-corrected electron gas theory expression and the local virial theorem, are in good agreement with theoretical values, particularly for the bonded interactions involving second-row M atoms. The agreement is poorer for shared C-O and N-O bonded interactions. PMID:17078623

  15. 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).

  16. Dissociation mechanisms of the Ar trimer induced by a third atom in high-energy electron-impact ionization

    NASA Astrophysics Data System (ADS)

    Yan, S.; Zhang, P.; Ma, X.; Xu, S.; Tian, S. X.; Li, B.; Zhu, X. L.; Feng, W. T.; Zhao, D. M.

    2014-06-01

    We experimentally studied the dissociation dynamics of a highly charged Ar3 cluster initiated by a high-energy electron. The dissociation patterns of the correlated ions from a two-body and a three-body Coulombic explosion (CE) of (Ar3)2+ suggest that predissociation alters the evolution of radiative charge transfer. The three-body CE in (Ar3)4+ and (Ar3)5+ is driven, after double ionization of one constituent Ar atom, by single ionization with a simultaneous interatomic Coulombic decay process.

  17. 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 intensities. PMID:16159109

  18. Electron-impact dissociative double ionization of N2 and CO: Dependence of transition probability on impact energy

    NASA Astrophysics Data System (ADS)

    Pandey, A.; Kumar, P.; Banerjee, S. B.; Subramanian, K. P.; Bapat, B.

    2016-04-01

    We present an experimental and computational analysis of dissociative double ionization of N2 and CO molecules under electron impact. Experiments are performed at three energies, viz. 1, 3, and 5 keV, in order to observe the effect of impact energy on the dissociative ionization kinematics. We compare the kinetic energy release (KER) distributions of the charge symmetric dissociation channels of N22 + and CO2 + at these impact energies. An approximately linear trend between the transition energy and the expected KER values is inferred on the basis of the calculated potential energy curves of the dications. Experimentally, the normalized differential KER cross sections for these channels show an increasing trend in the low KER range and a decreasing trend in the high KER range as the electron-impact energy is increased. This observation indicates that the transition probability for excitation to different molecular ion states is not only a function of energy difference between the ground and excited states, but also a complicated function of the impact energy. In addition, nature of the observed trend in the differential KER cross sections differs significantly from their differential transition probability, which are calculated using inelastic collision model for fast-electron-impact case.

  19. 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.

  20. 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 intermediates was observed on the Pt and Pt/WC surfaces. For CH3OH decomposition, DFT calculations suggested that the bond scission sequence could be controlled using monolayer coverage of Pt on WC. The Ni/Pt bimetallic system was studied as an example for using oxygenates as a hydrogen source. There are two well characterized surface structures for the Ni/Pt system: the surface configuration, in which the Ni atoms reside primarily on the surface of the Pt bulk, and the subsurface configuration, in which the second atomic layer is enriched in Ni atoms and the surface is enriched in Pt atoms. These configurations are denoted NiPtPt and PtNiPt, respectively. DFT results revealed that trends established for the Ni/Pt(111) system extend to the Ni/Pt(100) analogue. TPD studies revealed that the NiPtPt surface was more active for oxygenate reforming than the Pt or PtNiPt surfaces. HREELS confirmed the presence of strongly bound reaction intermediates, including aldehyde-like species, and suggested that the first decomposition step was likely O-H bond scission. Thus, the binding energies of the deprotonated reaction intermediates are important parameters in controlling the decomposition pathways of oxygenates. These studies have demonstrated that the bond scission sequence of oxygenate decomposition can be controlled using bimetallic and transition metal carbide catalysts. While this study has focused on oxygenate decomposition for energy applications, the principles and methodology applied herein are universally applicable to the development of novel and marketable value-added products. The value in such a methodology is in the combination of both calculations to predict catalytic and chemical properties, and experiments to fine-tune theoretical predictions.

  1. Excitation and dissociation of tungsten hexacarbonyl W(CO)6: statistical and nonstatistical dissociation processes.

    PubMed

    Martin, S; Chen, L; Brédy, R; Bernard, J; Montagne, G; Zhu, X

    2011-01-21

    We have studied the excitation and dissociation processes of the molecule W(CO)(6) in collisions with low kinetic energy (3 keV) protons, monocharged fluorine, and chlorine ions using double charge transfer spectroscopy. By analyzing the kinetic energy loss of the projectile anions, we measured the excitation energy distribution of the produced transient dications W(CO)(6)(2+). By coincidence measurements between the anions and the stable or fragments of W(CO)(6)(2+), we determined the energy distribution for each dissociation channel. Based on the experimental data, the emission of the first CO was tentatively attributed to a nonstatistical direct dissociation process and the emission of the second or more CO ligands was attributed to the statistical dissociation processes. The dissociation energies for the successive breaking of the W-CO bond were estimated using a cascade model. The ratio between charge separation and evaporation (by the loss of CO(+) and CO, respectively) channels was estimated to be 6% in the case of Cl(+) impact. PMID:21261350

  2. 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.

  3. 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…

  4. 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

  5. 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.

  6. Response to the Comment by J. Grunenberg on "The Nature of the Fourth Bond in the Ground State of C2: The Quadruple Bond Conundrum''.

    PubMed

    Shaik, Sason; Danovich, David; Hiberty, Philippe C

    2015-11-16

    The quadruple bond structure in C2 emerges from solid quantum-chemical calculations and won't go away! There is no mystery in the rather small bond dissociation energy, and this cannot constitute the reason to reconsider the whole concept of quadruple bonding. PMID:26482677

  7. 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.

  8. 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.

  9. 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.

  10. Formation energy of dangling bonds on hydrogenated diamond surfaces: A first-principles study

    NASA Astrophysics Data System (ADS)

    Zilibotti, G.; Corni, S.; Righi, M. C.

    2012-01-01

    We calculate the energy cost to create dangling bonds on hydrogenated diamond (001) surfaces by means of spin-polarized first-principle calculations. We demonstrate that the dangling bond formation energy depends on both the density and the arrangement of the dangling bonds already present on the surface. In particular, at low dangling bond density, hydrogen removal is less energetically costly than at high dangling bond density. We also find that adjacent dangling bonds are more stable in the antiferromagnetic configuration than in the ferromagnetic one. We provide quantitative information and a physical rationale of these phenomena.

  11. 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 linked together and stabilized by the pathways of electron density comprising S-S bonded interactions. Such interactions not only exist between the S atoms for adjacent S8 rings in native sulfur, but their bond critical point properties are similar to those displayed by the metal sulfides.

  12. Dynamic disorder in receptor-ligand forced dissociation experiments.

    PubMed

    Liu, Fei; Ou-Yang, Zhong-can; Iwamoto, Mitsumasa

    2006-01-01

    Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative models have been proposed to explain the intriguing transitions from the "catch bond" to the "slip bond." In this work we propose that the dynamic disorder of the force-dependent dissociation rate can account for the counterintuitive behaviors of the bonds. A Gaussian stochastic rate model is used to quantitatively describe the transitions observed recently in the single bond P-selctin glycoprotein ligand 1-P-selectin force rupture experiment [Marshall, Nature 423, 190 (2003)]. Our model agrees well with the experimental data. We conclude that the catch bonds could arise from the stronger positive correlation between the height of the intrinsic energy barrier and the distance from the bound state to the barrier; classical pathway scenario or a priori catch bond assumption is not essential. PMID:16486112

  13. Dissociative electron attachment, electron transmission, and electron energy-loss study of the temporary negative ion of acetylene

    SciTech Connect

    Dressler, R.; Allan, M.

    1987-10-15

    The three title electron-impact techniques are used to study the ground and excited states of acetylene negative ion and their decay processes. The ..pi..* resonance at 2.6 eV predissociates into C/sub 2/H/sup -/ and H. Four narrow resonances are observed in the transmission spectrum in the 7.5--9.5 eV region and assigned to Feshbach and core-excited shape resonances with double occupation of Rydberg orbitals and ground state positive ion core. These four resonances decay into low-lying Rydberg states of neutral acetylene, the first two undergo quasiresonant autodetachment ejecting low energy (<0.7 eV) electrons, and the lowest also dissociates to yield C/sup -//sub 2/. One additional resonance is observed in the C/sup -//sub 2/ yield, which is not observable in other decay channels. The shapes of the dissociative attachment bands differ qualitatively from the band shapes of the parent and grandparent states, indicating either a strong v dependence of the dissociation rate or the admixture of sigma* orbitals in some of the dissociating anion states.

  14. 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.

  15. Bond Length and Local Energy Density Property Connections for Non-transition- Metal-Oxide-Bonded Interactions

    SciTech Connect

    Gibbs, Gerald V.; Spackman, M. A.; Jayatilaka, Dylan; Rosso, Kevin M.; Cox, David F.

    2006-11-09

    For a variety of molecules and Earth materials, the theoretical local kinetic energy density, G(rc), increases and the local potential energy density, V(rc), decreases as the MO bond lengths (M = first and second row metal atoms) decrease and electron density, ρ(rc), is localized at the bond critical points, rc. Despite claims that the ratio, G(rc)/ρ(rc), classifies bonded interactions as shared covalent when less than unity and closed shell ionic when greater than unity, the ratio was found to increase from 0.5 to 2.5 a.u. as the local electronic energy density H(rc) = G(rc) + V(rc) decreases and becomes progressively more negative. In any event, the ratio is indicated to be a measure of the character for a given M-O bond, the greater the ratio, the larger the value of ρ(rc), the smaller the coordination number of the M atom and the more covalent the bond. H(rc)/ρ(rc) vs. G(rc)/ρ(rc) scatter diagrams categorize the M-O bond data into domains with the H(rc)/ρ(rc) ratio tending to increase as the electronegativity of the M atoms increase. Estimated values of G(rc) and V(rc), using an expression based on gradient corrected electron gas theory, are in good agreement with theoretical values, particularly for bonded interactions involving second row M atoms. The agreement is poorer for the more covalent C-O and N-O bonds.

  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; stin, Anders; Nygren, Yvonne; Juhlin, Lars; Nilsson, Calle; stot, 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. PMID:21915956

  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. PMID:26360734

  18. 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.

  19. Absence of CO dissociation on Mo(112)

    NASA Astrophysics Data System (ADS)

    Yakovkin, I. N.; Petrova, N. V.

    2009-05-01

    We revisit the problem of CO adsorption and thermal dissociation on the Mo(112) surface by means of density-functional calculations of binding energies, local densities of states, and CO vibrational frequencies for various configurations of equilibrated adlayers. The bridge-on-row adsorption sites on the Mo(112) surface are found to be the most favorable and CO molecules will occupy less stable in-furrow sites only after the completing of the first monolayer. At low coverages, CO molecules are tilted by ˜40° with respect to the normal to the surface (the β state), but with increasing coverage, due to lateral interactions, attain an upright orientation with the carbon end down (the α state). The tilting of CO results in a significant elongation of the C-O bond (to 1.20 Å) and, consequently, the C-O stretching vibration frequency decreases to 1159 cm-1. Nonetheless, the β state cannot be attributed to the precursor to CO dissociation, because the estimated potential barrier for the dissociation (˜2.8 eV) substantially exceeds the chemisorption energy (2.1 eV), which makes the thermally induced CO dissociation on Mo improbable. With estimated chemisorption energies, Monte Carlo simulations have shown that the two-peak shape of TPD spectra can be explained without involving the CO dissociation. We predict also that the lack of dissociation can be detected in photoemission studies for CO on Mo(112) by the presence of the -23 and -7 eV peaks, characteristic of chemisorbed CO, and absence of the -18 and -5 eV peaks characteristic of adsorbed O atoms.

  20. Strong photon energy dependence of the photocatalytic dissociation rate of methanol on TiO2(110).

    PubMed

    Xu, Chenbiao; Xu, Chengbiao; Yang, Wenshao; Ren, Zefeng; Dai, Dongxu; Guo, Qing; Minton, Timothy K; Yang, Xueming

    2013-12-18

    Photocatalytic dissociation of methanol (CH3OH) on a TiO2(110) surface has been studied by temperature programmed desorption (TPD) at 355 and 266 nm. Primary dissociation products, CH2O and H atoms, have been detected. The dependence of the reactant and product TPD signals on irradiation time has been measured, allowing the photocatalytic reaction rate of CH3OH at both wavelengths to be directly determined. The initial dissociation rate of CH3OH at 266 nm is nearly 2 orders of magnitude faster than that at 355 nm, suggesting that CH3OH photocatalysis is strongly dependent on photon energy. This experimental result raises doubt about the widely accepted photocatalysis model on TiO2, which assumes that the excess potential energy of charge carriers is lost to the lattice via strong coupling with phonon modes by very fast thermalization and the reaction of the adsorbate is thus only dependent on the number of electron-hole pairs created by photoexcitation. PMID:24299197

  1. 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.

  2. Production of hydrated metal ions by fast ion or atom beam sputtering. Collision-induced dissociation and successive hydration energies of gaseous Cu sup + with 1-4 water molecules

    SciTech Connect

    Magnera, T.F.; David, D.E.; Stulik, D.; Orth, R.G.; Jonkman, H.T.; Michl, J. )

    1989-07-05

    Low-temperature sputtering of frozen aqueous solutions of metal salts, of hydrated crystalline transition-metal salts, of frosted metal surfaces, and of frosted metal salts with kiloelectronvolt energy rare gas atoms or ions produces copious amounts of cluster ions, among which M{sup +}(H{sub 2}O){sub n} and/or M{sup +}OH(H{sub 2}O){sub n} frequently dominate. Variable-energy collision-induced dissociation of these ions in a triple quadrupole mass spectrometer yields the successive gas-phase solvation energies. Several known hydration and bond energies have been reproduced, and the first and second hydration energies of the Cu{sup +} ion have been determined as 35 {plus minus} 3 and 39 {plus minus}3 kcal/mol, respectively.It is concluded that gaseous Cu{sup +} prefers discoordination.

  3. 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, the average electron temperature is expected to be between 10,000 and 20,000 K. Thus only data for low energy electrons are relevant to the model.

  4. Dissociative recombination and low-energy inelastic electron collisions of the helium dimer ion

    SciTech Connect

    Pedersen, H.B.; Buhr, H.; Altevogt, S.; Andrianarijaona, V.; Kreckel, H.; Lammich, L.; Schwalm, D.; Wolf, A.; Ruette, N. de; Staicu-Casagrande, E.M.; Urbain, X.; Strasser, D.; Zajfman, D.

    2005-07-15

    The dissociative recombination (DR) of {sup 3}He {sup 4}He{sup +} has been investigated at the heavy-ion Test Storage Ring (TSR) in Heidelberg by observing neutral products from electron-ion collisions in a merged beams configuration at relative energies from near-zero (thermal electron energy about 10 meV) up to 40 eV. After storage and electron cooling for 35 s, an effective DR rate coefficient at near-zero energy of 3x10{sup -9} cm{sup 3}s{sup -1} is found. The temporal evolution of the neutral product rates and fragment imaging spectra reveals that the populations of vibrational levels in the stored ion beam are nonthermal with fractions of {approx}0.1-1 % in excited levels up to at least v=4, having a significant effect on the observed DR signals. With a pump-probe-type technique using DR fragment imaging while switching the properties of the electron beam, the vibrational excitation of the ions is found to originate mostly from ion collisions with the residual gas. Also, the temporal evolution of the DR signals suggests that a strong electron induced rotational cooling occurs in the vibrational ground state, reaching a rotational temperature near or below 300 K. From the absolute rate coefficient and the shape of the fragment imaging spectrum observed under stationary conditions, the DR rate coefficient from the vibrational ground state is determined; converted to a thermal electron gas at 300 K it amounts to (3.3{+-}0.9)x10{sup -10} cm{sup 3}s{sup -1}. The corresponding branching ratios from v=0 to the atomic final states are found to be (3.7{+-}1.2) % for 1s2s {sup 3}S,(37.4{+-}4.0) % for 1s2s {sup 1}S,(58.6{+-}5.2) % for 1s2p {sup 3}P, and (2.9{+-}3.0) % for 1s2p {sup 1}P. A DR rate coefficient in the range of 2x10{sup -7} cm{sup 3}s{sup -1} or above is inferred for vibrational levels v=3 and higher. As a function of the collision energy, the measured DR rate coefficient displays a structure around 0.2 eV. At higher energies, it has one smooth peak around 7.3 eV and a highly structured appearance at 15-40 eV. The small size of the observed effective DR rate coefficient at near-zero energy indicates that the electron induced rotational cooling is due to inelastic electron-ion collisions and not due to selective depletion of rotational levels by DR.

  5. 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.

  6. 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.

  7. A big data approach to the ultra-fast prediction of DFT-calculated bond energies

    PubMed Central

    2013-01-01

    Background The rapid access to intrinsic physicochemical properties of molecules is highly desired for large scale chemical data mining explorations such as mass spectrum prediction in metabolomics, toxicity risk assessment and drug discovery. Large volumes of data are being produced by quantum chemistry calculations, which provide increasing accurate estimations of several properties, e.g. by Density Functional Theory (DFT), but are still too computationally expensive for those large scale uses. This work explores the possibility of using large amounts of data generated by DFT methods for thousands of molecular structures, extracting relevant molecular properties and applying machine learning (ML) algorithms to learn from the data. Once trained, these ML models can be applied to new structures to produce ultra-fast predictions. An approach is presented for homolytic bond dissociation energy (BDE). Results Machine learning models were trained with a data set of >12,000 BDEs calculated by B3LYP/6-311++G(d,p)//DFTB. Descriptors were designed to encode atom types and connectivity in the 2D topological environment of the bonds. The best model, an Associative Neural Network (ASNN) based on 85 bond descriptors, was able to predict the BDE of 887 bonds in an independent test set (covering a range of 17.67–202.30 kcal/mol) with RMSD of 5.29 kcal/mol, mean absolute deviation of 3.35 kcal/mol, and R2 = 0.953. The predictions were compared with semi-empirical PM6 calculations, and were found to be superior for all types of bonds in the data set, except for O-H, N-H, and N-N bonds. The B3LYP/6-311++G(d,p)//DFTB calculations can approach the higher-level calculations B3LYP/6-311++G(3df,2p)//B3LYP/6-31G(d,p) with an RMSD of 3.04 kcal/mol, which is less than the RMSD of ASNN (against both DFT methods). An experimental web service for on-line prediction of BDEs is available at http://joao.airesdesousa.com/bde. Conclusion Knowledge could be automatically extracted by machine learning techniques from a data set of calculated BDEs, providing ultra-fast access to accurate estimations of DFT-calculated BDEs. This demonstrates how to extract value from large volumes of data currently being produced by quantum chemistry calculations at an increasing speed mostly without human intervention. In this way, high-level theoretical quantum calculations can be used in large-scale applications that otherwise would not afford the intrinsic computational cost. PMID:23849655

  8. 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. PMID:25903223

  9. 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 be independently shown that these species are co-spatial.

  10. 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.

  11. Chemical control through dissociative electron attachment - A study on pentafluorotoluene, pentafluoroaniline and pentafluorophenol

    NASA Astrophysics Data System (ADS)

    Ómarsson, Benedikt; Bjarnason, Elías H.; Ingólfsson, Oddur; Haughey, Sean; Field, Thomas A.

    2012-06-01

    In a combined experimental and theoretical study on dissociative electron attachment (DEA) to pentafluorotoluene, pentafluoroaniline and pentafluorophenol in the energy range 0-3 eV we reveal the role of rearrangement and hydrogen bonded intermediates in the DEA process and show that HF formation can be used to enable otherwise inaccessible, efficient low energy DEA processes.

  12. Dissociative electron attachments to ethanol and acetaldehyde: A combined experimental and simulation study

    NASA Astrophysics Data System (ADS)

    Wang, Xu-Dong; Xuan, Chuan-Jin; Feng, Wen-Ling; Tian, Shan Xi

    2015-02-01

    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-/OH- and CH3- are recorded, indicating the low kinetic energies of O-/OH- for ethanol while the low and high kinetic energy distributions of O- ions for acetaldehyde. The CH3- 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- ion via the dehydrogenated intermediate, CH3CHO- (acetaldehyde anion), is proposed for the dissociative electron attachment to ethanol. After the electron attachment to acetaldehyde molecule, the slow CH3- is produced quickly in the two-body dissociation with the internal energy redistributions in different aspects before bond cleavages.

  13. Discovery and Mechanistic Studies of Facile N-Terminal Cα–C Bond Cleavages in the Dissociation of Tyrosine-Containing Peptide Radical Cations

    SciTech Connect

    Mu, Xiaoyan; Song, Tao; Xu, Minjie; Lai, Cheuk-Kuen; Siu, Chi-Kit; Laskin, Julia; Chu, Ivan K.

    2014-03-28

    Gas phase fragmentations of protein and peptide (M) ions in a mass spectrometer—induced by, for example, electron-capture dissociation1-2 and electron-transfer dissociation3-422 —form the foundation for top-down amino acid sequencing approaches for the rapid identification of protein components in complex biological samples. During these processes, protonated protein and peptide radicals ([M + nH]•(n – 1)+)5–8 are generated; their fragmentations are governed largely by the properties of the unpaired electron. Because of their importance in modern bioanalytical chemistry, considerable attention has been drawn recently toward understanding the radical cation chemistry behind the fragmentations of these odd-electron biomolecular ions in the gas phase.

  14. 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.

  15. 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.

  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. Threshold collision-induced dissociation of hydrated magnesium: experimental and theoretical investigation of the binding energies for Mg(2+)(H2O)x complexes (x=2-10).

    PubMed

    Carl, Damon R; Armentrout, Peter B

    2013-03-18

    The sequential bond energies of Mg(2+)(H2O)x complexes, in which x=2-10, are measured by threshold collision-induced dissociation in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Mg(2+)(H2O)x complexes in which x=7-10, complexes down to x=3 are formed by using an in-source fragmentation technique. Complexes smaller than Mg(2+)(H2O)3 cannot be formed in this source because charge separation into MgOH(+)(H2O) and H3O(+) is a lower-energy pathway than simple water loss from Mg(2+)(H2O)3. The kinetic energy dependent cross sections for dissociation of Mg(2+)(H2O)x complexes, in which x=3-10, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Mg(2+) for x=2-10 and the first experimental values for x=2-4. Additionally, the thermodynamic onsets leading to the charge-separation products from Mg(2+)(H2O)3 and Mg(2+)(H2O)4 are determined for the first time. Our experimental results for x=3-7 agree well with quantum chemical calculations performed here and previously calculated binding enthalpies, as well as previous measurements for x=6. The present values for x=7-10 are slightly lower than previous experimental results and theory, but within experimental uncertainties. PMID:23239534

  18. Experimental investigation of the complete inner shell hydration energies of Ca2+: threshold collision-induced dissociation of Ca(2+)(H2O)x Complexes (x = 2-8).

    PubMed

    Carl, Damon R; Armentrout, P B

    2012-04-19

    The sequential bond energies of Ca(2+)(H(2)O)(x) complexes, where x = 1-8, are measured by threshold collision-induced dissociation (TCID) in a guided ion beam tandem mass spectrometer. From an electrospray ionization source that produces an initial distribution of Ca(2+)(H(2)O)(x) complexes where x = 6-8, complexes down to x = 2 are formed using an in-source fragmentation technique. Ca(2+)(H(2)O) cannot be formed in this source because charge separation into CaOH(+) and H(3)O(+) is a lower energy pathway than simple water loss from Ca(2+)(H(2)O)(2). The kinetic energy dependent cross sections for dissociation of Ca(2+)(H(2)O)(x) complexes, where x = 2-9, are examined over a wide energy range to monitor all dissociation products and are modeled to obtain 0 and 298 K binding energies. Analysis of both primary and secondary water molecule losses from each sized complex provides thermochemistry for the sequential hydration energies of Ca(2+) for x = 1-8 and the first experimental values for x = 1-4. Additionally, the thermodynamic onsets leading to the charge separation products from Ca(2+)(H(2)O)(2) and Ca(2+)(H(2)O)(3) are determined for the first time. Our experimental results for x = 1-6 agree well with previously calculated binding enthalpies as well as quantum chemical calculations performed here. Agreement for x = 1 is improved when the basis set on calcium includes core correlation. PMID:22452741

  19. 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.

  20. Exploring trends in strong-field dissociation of small polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Jochim, Bethany; Zohrabi, M.; Ablikim, U.; Berry, B.; Severt, T.; Carnes, K. D.; Ben-Itzhak, I.

    2013-05-01

    Using a 3-D coincidence momentum imaging technique, we examine trends in intense ultrafast laser-induced two-body dissociation and dissociative ionization of an N2O+ ion beam. As an example, it is observed that in both dissociation and dissociative ionization, the N-N bond is more likely to break than the N-O bond for typical laser pulses (Fourier transform-limited, 800 nm, ~30 fs, ~1015 W/cm2). This finding is perhaps counterintuitive in light of the stronger bond between the two N atoms in the ground state of N2O+. Utilizing our measured kinetic energy release and angular distribution spectra and the molecule's published electronic structure, we explain this and other trends in bond cleavage and charge localization preference. We also draw comparisons to other triatomic molecular ions, such as CO2+, and attempt to gain insight into the relative importance of chemical bond strength and the spacing of the relevant potential energy surfaces. Supported by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy. BJ is also supported by DOE SCGF (DE-AC05-06OR23100).

  1. Seniority number description of potential energy surfaces: Symmetric dissociation of water, N2, C2, and Be2.

    PubMed

    Bytautas, Laimutis; Scuseria, Gustavo E; Ruedenberg, Klaus

    2015-09-01

    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), N2 (6-31G), C2 (6-31G), and Be2 (cc-pVTZ). We find that the potential energy profile for H2O dissociation can be reasonably well described using only the Ω = 0 sector of the CI wave function. For the Be2 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 N2 and C2, 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 correlated molecular orbitals, simultaneously. We discuss the usefulness of the seniority number concept in addressing both static and dynamic electron correlation problems along dissociation paths. PMID:26342357

  2. Seniority number description of potential energy surfaces: Symmetric dissociation of water, N2, C2, and Be2

    NASA Astrophysics Data System (ADS)

    Bytautas, Laimutis; Scuseria, Gustavo E.; Ruedenberg, Klaus

    2015-09-01

    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), N2 (6-31G), C2 (6-31G), and Be2 (cc-pVTZ). We find that the potential energy profile for H2O dissociation can be reasonably well described using only the Ω = 0 sector of the CI wave function. For the Be2 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 N2 and C2, 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 correlated molecular orbitals, simultaneously. We discuss the usefulness of the seniority number concept in addressing both static and dynamic electron correlation problems along dissociation paths.

  3. The unimolecular dissociation of H{sub 2}CO on the lowest triplet potential-energy surface

    SciTech Connect

    Yamaguchi, Y.; Wesolowski, S.S.; Van Huis, T.J.; Schaefer, H.F. III

    1998-04-01

    The unimolecular dissociation reaction of H{sub 2}CO on the triplet potential-energy surface has been studied via {ital ab initio} electronic structure theory. The stationary point geometries for the equilibrium and transition state are determined employing the configuration interaction with single and double excitations (CISD), coupled cluster with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] levels of theory with large basis sets up to the correlation consistent (cc)-pVQZ basis. With the best method, cc-pVQZ CCSD(T), the first excited triplet ({tilde a}{sup 3}A{sup {double_prime}}) state lies 72.2kcal/mol (25260cm{sup {minus}1}) above the ground ({tilde X}{sup 1}A{sub 1}) state of H{sub 2}CO, which is in excellent agreement with the experimental observation of 72.03kcal/mol (25194cm{sup {minus}1}). The dissociation limit (H{center_dot}+HCO{center_dot}) is located at 86.3kcal/mol (30170cm{sup {minus}1}) above the ground state of H{sub 2}CO, which is again in good agreement with the two experimentally determined values of 86.57kcal/mol (30280cm{sup {minus}1}) and 86.71kcal/mol (30328.5cm{sup {minus}1}). With the same method the triplet dissociation transition state lies 92.4kcal/mol (32300cm{sup {minus}1}) above the ground state. Consequently, the activation energy for the dissociation reaction of H{sub 2}CO on the triplet surface is determined {ital ab initio} to be 18.9{endash}20.1kcal/mol (6620{endash}7040cm{sup {minus}1}) (including an estimated error bar of 1.2kcal/mol or 420cm{sup {minus}1}). The zero-point vibrationally corrected exit barrier height is predicted to be 4.9{endash}6.1kcal/mol (1710{endash}2130cm{sup {minus}1}). These newly predicted energies are consistent with the recent experimental observations by the Moore group at University of California-Berkeley (1987) and by the Wittig group at University of Southern California (1997). {copyright} {ital 1998 American Institute of Physics.}

  4. Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.

    PubMed

    Agius, Rudi; Torchala, Mieczyslaw; Moal, Iain H; Fernández-Recio, Juan; Bates, Paul A

    2013-01-01

    Predicting the effects of mutations on the kinetic rate constants of protein-protein interactions is central to both the modeling of complex diseases and the design of effective peptide drug inhibitors. However, while most studies have concentrated on the determination of association rate constants, dissociation rates have received less attention. In this work we take a novel approach by relating the changes in dissociation rates upon mutation to the energetics and architecture of hotspots and hotregions, by performing alanine scans pre- and post-mutation. From these scans, we design a set of descriptors that capture the change in hotspot energy and distribution. The method is benchmarked on 713 kinetically characterized mutations from the SKEMPI database. Our investigations show that, with the use of hotspot descriptors, energies from single-point alanine mutations may be used for the estimation of off-rate mutations to any residue type and also multi-point mutations. A number of machine learning models are built from a combination of molecular and hotspot descriptors, with the best models achieving a Pearson's Correlation Coefficient of 0.79 with experimental off-rates and a Matthew's Correlation Coefficient of 0.6 in the detection of rare stabilizing mutations. Using specialized feature selection models we identify descriptors that are highly specific and, conversely, broadly important to predicting the effects of different classes of mutations, interface regions and complexes. Our results also indicate that the distribution of the critical stability regions across protein-protein interfaces is a function of complex size more strongly than interface area. In addition, mutations at the rim are critical for the stability of small complexes, but consistently harder to characterize. The relationship between hotregion size and the dissociation rate is also investigated and, using hotspot descriptors which model cooperative effects within hotregions, we show how the contribution of hotregions of different sizes, changes under different cooperative effects. PMID:24039569

  5. 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

  6. Dissociative ionization of H2+ : Few-cycle effect in the joint electron-ion energy spectrum

    NASA Astrophysics Data System (ADS)

    Mosert, V.; Bauer, D.

    2015-10-01

    Joint electron-ion energy spectra for the dissociative ionization of a model H2+ in few-cycle, infrared laser pulses are calculated via the numerical ab initio solution of the time-dependent Schrödinger equation. A strong, pulse-dependent modulation of the ionization probability for certain values of the protons' kinetic energy (but almost independent of the electron's energy) is observed. With the help of models with frozen ions, this feature, which mistakenly might be attributed to vibrational excitations, is traced back to the transient population of electronically excited states, followed by ionization. This assertion is further corroborated employing a two-level model incorporating strong-field ionization from the excited state.

  7. Theoretical aspects of the biological catch bond.

    PubMed

    Prezhdo, Oleg V; Pereverzev, Yuriy V

    2009-06-16

    The biological catch bond is fascinating and counterintuitive. When an external force is applied to a catch bond, either in vivo or in vitro, the bond resists breaking and becomes stronger instead. In contrast, ordinary slip bonds, which represent the vast majority of biological and chemical bonds, dissociate faster when subjected to a force. Catch-bond behavior was first predicted theoretically 20 years ago and has recently been experimentally observed in a number of protein receptor-ligand complexes. In this Account, we review the simplest physical-chemical models that lead to analytic expressions for bond lifetime, the concise universal representations of experimental data, and the explicit requirements for catch binding. The phenomenon has many manifestations: increased lifetime with growing constant force is its defining characteristic. If force increases with time, as in jump-ramp experiments, catch binding creates an additional maximum in the probability density of bond rupture force. The new maximum occurs at smaller forces than the slip-binding maximum, merging with the latter at a certain ramp rate in a process resembling a phase transition. If force is applied periodically, as in blood flows, catch-bond properties strongly depend on force frequency. Catch binding results from a complex landscape of receptor-ligand interactions. Bond lifetime can increase if force (i) prevents dissociation through the native pathway and drives the system over a higher energy barrier or (ii) alters protein conformations in a way that strengthens receptor-ligand binding. The bond deformations can be associated with allostery; force-induced conformational changes at one end of the protein propagate to the binding site at the other end. Surrounding water creates further exciting effects. Protein-water tension provides an additional barrier that can be responsible for significant drops in bond lifetimes observed at low forces relative to zero force. This strong dependence of bond properties on weak protein-water interactions may provide universal activation mechanisms in many biological systems and create new types of catch binding. Molecular dynamics simulations provide atomistic insights: the molecular view of bond dissociation gives a foundation for theoretical models and differentiates between alternative interpretations of experimental data. The number of known catch bonds is growing; analogs are found in enzyme catalysis, peptide translocation through nanopores, DNA unwinding, photoinduced dissociation of chemical bonds, and negative thermal expansion of bulk materials, for example. Finer force resolution will likely provide many more. Understanding the properties of catch bonds offers insight into the behavior of biological systems subjected to external perturbations in general. PMID:19331389

  8. Dissociative recombination of LiH2+

    NASA Astrophysics Data System (ADS)

    Thomas, R. D.; Ehlerding, A.; Geppert, W. D.; Hellberg, F.; Zhaunerchyk, V.; Larsson, M.; Bahati, E.; Bannister, M. E.; Fogle, M. R.; Vane, C. R.

    2014-05-01

    In this paper, we report results regarding how LiH2+ fragments as a result of a low-energy collision with an electron (dissociative recombination), a reaction that contains only elements and particles created during the very first phase of the universe. The collision-energy-dependent reaction rate and cross sections show detailed structures, more so than predicted by theory, suggesting significant rovibrational coupling in the ion and a complex reaction surface. From the structure of the molecule, the reaction predominantly results in the formation of Li + H2. However, 23% of the reaction flux leads to more interesting products, with 17% producing Li + 2H and 6% producing LiH + H. These last two channels break the strongest molecular bond in the system and, in the case of the latter channel, form a significantly weaker ionic bond. Possible reasons behind this interesting behavior are discussed, together with the interaction between the available reaction channels.

  9. Low energy collision-induced dissociation and photodissociation studies of the (N2O,H2O) + cluster ion

    NASA Astrophysics Data System (ADS)

    Bastian, Michael J.; Dressler, Rainer A.; Levandier, Dale J.; Murad, Edmond; Muntean, Felician; Armentrout, P. B.

    1997-06-01

    Low energy collision-induced dissociation (CID) and photodissociation measurements of monohydrated nitrous oxide cluster ions are presented. The CID measurements have been conducted with ions produced in both thermal and supersonic jet sources, and with both Ne and Ar as collision gases. In all experiments, H2O+, N2O+, and N2OH+ fragments are observed, for which CID thresholds (0 K) of 1.04±0.06, 1.43±0.12 and 1.32±0.10 eV are determined, respectively. The thermal source experimental thresholds are consistent with all fragment ions originating from a single isomeric precursor ion, [N2OṡH2O]+. Whereas both N2O+ and N2OH+ CID curves are comparable in the thermal source and supersonic jet source experiments, considerable differences are observed in the H2O+ CID measurements. The differences are attributed to loosely bound cluster-ion isomeric forms produced in the jet source experiment. In the photodissociation experiments, branching ratios measured with the present jet source are very similar to those observed in previously reported thermal experiments [S. T. Graul, H-S. Kim, and M. T. Bowers, Int. J. Mass Spectrom. Ion Proc. 117, 507 (1992)]. All of the fragment ions can be accounted for by invoking an optical transition from ground state [N2OṡH2O]+ to an excited state associated with the N2O+H2O+ (Ã) dissociation limit. The H2O+ and N2O+ branching ratios are primarily governed by predissociation of the upper state followed by charge-transfer dynamics along a repulsive dissociation coordinate. Formation of N2OH+ is postulated to be controlled by a competing internal conversion process that leads to a longer-lived complex that decays to proton transfer products.

  10. Influence of Electron Molecule Resonant Vibrational Collisions over the Symmetric Mode and Direct Excitation-Dissociation Cross Sections of CO2 on the Electron Energy Distribution Function and Dissociation Mechanisms in Cold Pure CO2 Plasmas.

    PubMed

    Pietanza, L D; Colonna, G; Laporta, V; Celiberto, R; D'Ammando, G; Laricchiuta, A; Capitelli, M

    2016-05-01

    A new set of electron-vibrational (e-V) processes linking the first 10 vibrational levels of the symmetric mode of CO2 is derived by using a decoupled vibrational model and inserted in the Boltzmann equation for the electron energy distribution function (eedf). The new eedf and dissociation rates are in satisfactory agreement with the corresponding ones obtained by using the e-V cross sections reported in the database of Hake and Phelps (H-P). Large differences are, on the contrary, found when the experimental dissociation cross sections of Cosby and Helm are inserted in the Boltzman equation. Comparison of the corresponding rates with those obtained by using the low-energy threshold energy, reported in the H-P database, shows differences up to orders of magnitude, which decrease with the increasing of the reduced electric field. In all cases, we show the importance of superelastic vibrational collisions in affecting eedf and dissociation rates either in the direct electron impact mechanism or in the pure vibrational mechanism. PMID:27064438

  11. 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! PMID:26880488

  12. CO dissociation on iron nanoparticles: Size and geometry effects

    NASA Astrophysics Data System (ADS)

    Melander, Marko; Latsa, Ville; Laasonen, Kari

    2013-10-01

    The reactivity of 0.5-1.4 nm iron nanoparticles and corresponding bulk surfaces has been systematically studied using density functional theory. The study includes both ideally symmetric and more realistic rugged nanoparticles. The activation energies for CO dissociation vary between 1.1 and 2.1 eV. An increasing particle size and roughness result in lower activation energies. For a single particle, variations as large as 0.9 eV occur indicating the importance of local particle morphology. Depending on the nanoparticle size, geometry, and CO dissociation pathway the reaction rates span five orders of magnitude at conditions relevant for gas-phase chemical vapor deposition synthesis of carbon nanotubes. Studies on the smallest particles and bulk surfaces show that these systems cannot be used as reliable models for catalysis on larger iron nanoparticles. It has also been demonstrated that predictive d-band and linear-energy relationships cannot be used to explain the reactivity of iron for CO dissociation as reaction mechanisms vary from one particle to another. The changes in reaction mechanisms can be rationalized by the varying Fe-Fe bond lengths in different particles leading to changes in back-bonding between the iron surface and CO. CO dissociation on nano-sized iron seems to be more complex than that seen on more conventional non-magnetic noble metal particles.

  13. Electron-induced ionization and dissociative ionization of iron pentacarbonyl molecules

    NASA Astrophysics Data System (ADS)

    Lacko, Michal; Papp, Peter; Wnorowski, Karol; Matejčík, Štefan

    2015-03-01

    Electron ionization (EI) and dissociative ionization (DI) of Iron pentacarbonyl molecule (Fe(CO)5) was studied using a crossed molecular and electron beam mass spectrometry technique. Positive ions FeO(CO)+, FeC(CO)2+ and CO+ of Fe(CO)5 were detected for the first time. We have determined the experimental appearance energies of positive ions, the thresholds for dissociative reactions, the experimental bond dissociation energies for (CO)nFe+-CO bond breaks (for n = 4,..., 0) and their average value for Fe-C bond energy 1.25 eV in Fe(CO)5+. We have performed extensive density functional theory (DFT) studies of the ground states of neutral molecule and fragments 1 A1' Fe(CO)5, 3B1 Fe(CO)4, 3A1Fe(CO)3, 3∑g Fe(CO)2, 3 ∑FeCO as well as positive ions 2A1 Fe(CO)5+, 4A1 Fe(CO)4+, 4A1 Fe(CO)3+, 4∑g Fe(CO)2+ and 4 ∑ FeCO+. The structures and energies of the states have beendetermined and the calculated bond dissociation energies (BDEs) were compared with present experiments as well as with previous works. Contribution to the Topical Issue "Elementary Processes with Atoms and Molecules in Isolated and Aggregated States", edited by Friedrich Aumayr, Bratislav Marinkovic, Stefan Matejick, John Tanis and Kurt H. Becker.

  14. 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 Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26754126

  15. 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.

  16. 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

    2003-07-01

    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. PMID:12823025

  17. Site-specific lithium ion attachment directs low-energy dissociation pathways of dinucleotides in the gas phase. Application to nucleic acid sequencing by mass spectrometry

    NASA Astrophysics Data System (ADS)

    Rodgers, M. T.; Campbell, Sherrie A.; Beauchamp, J. L.

    1997-02-01

    Fourier transform ion cyclotron resonance mass spectroscopy has been used to examine the low-energy collision-induced dissociation pathways of lithiated dinucleotides. Collisional activation using continuous off-resonance excitation permits observation of energetically-favorable dissociation pathways. Dissociation products were examined under multiple collision conditions for center of mass collision energies from 0 eV to the minimum energy required to bring about complete dissociation of the reactant ion (7.0 eV). The lithiated molecular ions dissociate to yield several characteristic products. The major fragmentation pathways observed in most systems are directed by localization of charge on the phosphate moiety leading to cleavage of the 3'-phosphate diester linkage to produce the 3'-sequence ion. In some systems, loss of the 5'-terminus base from the lithiated parent ion is also observed. Exceptions are observed only in systems where guanine is the 3'-terminus base. In these systems, the major products observed are the ion resulting from loss of the neutral 3'-terminus base along with its dehydrated decedent ion, the 5'-sequence ion and the ion resulting from loss of water from the 5'-sequence ion. Reaction mechanisms which account for the observed products are proposed. The present results suggest that collisional activation of lithiated oligonucleotides may provide useful sequence information.

  18. The Bond Energy of CH3-H: A Physical Chemistry Experiment.

    ERIC Educational Resources Information Center

    Dorain, Paul B.

    1979-01-01

    Describes an experiment, designed for use in the undergraduate laboratory, that measures the bond energies of molecules using a small commercial mass spectrometer and low-cost digital voltmeters. (BT)

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

    PubMed

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

    2015-09-01

    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

  20. Protein unfolding from free-energy calculations: Integration of the Gaussian network model with bond binding energies

    NASA Astrophysics Data System (ADS)

    Srivastava, Amit; Granek, Rony

    2015-02-01

    Motivated by single molecule experiments, we study thermal unfolding pathways of four proteins, chymotrypsin inhibitor, barnase, ubiquitin, and adenylate kinase, using bond network models that combine bond energies and elasticity. The protein elasticity is described by the Gaussian network model (GNM), to which we add prescribed bond binding energies that are assigned to all (nonbackbone) connecting bonds in the GNM of native state and assumed identical for simplicity. Using exact calculation of the Helmholtz free energy for this model, we consider bond rupture single events. The bond designated for rupture is chosen by minimizing the free-energy difference for the process, over all (nonbackbone) bonds in the network. Plotting the free-energy profile along this pathway at different temperatures, we observe a few major partial unfolding, metastable or stable, states, that are separated by free-energy barriers and change role as the temperature is raised. In particular, for adenylate kinase we find three major partial unfolding states, which is consistent with single molecule FRET experiments [Pirchi et al., Nat. Commun. 2, 493 (2011), 10.1038/ncomms1504] for which hidden Markov analysis reveals between three and five such states. Such states can play a major role in enzymatic activity.

  1. 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.

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

    PubMed

    Jacobsen, Heiko

    2009-06-01

    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. PMID:19452076

  3. 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.

  4. 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.

  5. Dissociative electron attachment and vibrational excitation of H2 by low-energy electrons: Calculations based on an improved nonlocal resonance model

    NASA Astrophysics Data System (ADS)

    Horáček, J.; Čížek, M.; Houfek, K.; Kolorenč, P.; Domcke, W.

    2004-11-01

    An improved nonlocal resonance model proposed by Čížek, Horáček, and Domcke [J. Phys. B 31, 2571 (1998)] is used for the calculation of cross sections of electron dissociative attachment and vibrational excitation of molecular hydrogen by the impact of low-energy electrons in the range of Σu+2 resonance. The model is based on ab initio data and takes full account of the nonlocality of the effective potential for the nuclear motion. The dissociative attachment cross sections and rate constants are calculated for all target states (v,J) of relevance and compared with other theoretical and experimental data. It is found that the present dissociative attachment cross section calculated under the conditions of the experiment carried out by Schulz and Asundi reproduces the larger of the two values proposed by them, i.e.- 2.8×10-21cm2 . A detailed discussion of the dissociative attachment cross section as a function of the vibrational and rotational target states is given. Very narrow peaks, with a width of 1meV , are observed in the dissociative attachment cross section for large values of the orbital quantum number J . These structures are interpreted as shape resonances in H-+H collision dynamics. It is shown that for large values of J rotational excitation of the hydrogen molecule enhances the dissociative attachment more efficiently than vibrational excitation. The largest dissociative attachment cross section of 28.3×10-16cm2 is obtained for v=1 and J=29 . The process of vibrational excitation will be discussed in a separate paper.

  6. 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.

  7. The dissociation of low energy 1,2-propanediol ions: an intriguing mechanism revisited

    NASA Astrophysics Data System (ADS)

    Burgers, Peter C.; Fell, Lorne M.; Milliet, Arielle; Rempp, Muriel; Ruttink, Paul J. A.; Terlouw, Johan K.

    1997-11-01

    The fascinating unimolecular chemistry of ionized 1,2-propanediol, CH3C(H)OHCH2OH[middle dot]+, 1, has been re-examined using computational chemistry (ab initio MO and density functional theories) in conjunction with modern tandem mass spectrometric and 13C labelling experiments. The calculations allow a considerable simplification of a previously proposed complex mechanism (Org. Mass Spectrom., 23 (1988) 355). Again, the central intermediates are proposed to be stable hydrogen bridged ion--dipole complexes, but our present calculations indicate that the key transformation now is the rearrangement CH3C(H)OH+[middle dot][middle dot][middle dot]O(H)-CH2. --> CH3C(H)OH+[middle dot][middle dot][middle dot].OCH3, which can best be viewed as the cation-catalyzed 1,2-hydrogen shift .CH2OH --> CH3O., a rearrangement which does not occur so easily in the unassisted system. Another important process is the electron transfer CH3C(H)=O[middle dot][middle dot][middle dot]CH3OH[middle dot]+ --> O=CH(CH3)[middle dot]+[middle dot][middle dot][middle dot]O(H)CH3 which allows proton transfer to generate CH3OH2+ + CH3C=O.. Other dissociation processes (loss of CH3., H2O, H2O + CH3., H2O + CH4) are interpreted in terms of Bohme's `methyl cation shuttle' (J. Am. Chem. Soc., 118 (1996) 4500) taking place in ion-dipole complexes. The most stable intermediate is the hydrogen bridged ion-dipole complex CH2=CHOH.+[middle dot][middle dot][middle dot]O(H)CH3, which is the reacting configuration for loss of methanol.

  8. 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

  9. Bond graph modeling and validation of an energy regenerative system for emulsion pump tests.

    PubMed

    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

  10. Theoretical study of adsorption and dissociation of NH3 on pentanuclear Fe(111) surface

    NASA Astrophysics Data System (ADS)

    Purwiandono, G.; Triyono; Wijaya, K.

    2016-02-01

    Theoretical study regarding the adsorption and dissociation of NH3 molecule on Fe(111) surface has been carried out. The method used was DFT-B3LYP, and the basis sets used were ECP and 6-311G**. This research aimed at giving the theoretical understanding of adsorption and dissociation of NH3 molecule on Fe(111) surface. The adsorption and dissociation were studied based on the energetic parameter, bond length, electron population, vibration and orbital interaction. The result of theoretical calculation revealed that the on top position is the interaction position with the minimum energy for the adsorption of NH3 molecule on Fe(111) surface. The analysis of electron population of the two composing molecular orbitals indicated that the transfer of electron has an important role in the mechanism of adsorption. The visualization of molecular orbital showed that the transfer of electron occurred in the electron pairs of the interacting orbital. Relating to the adsorption mechanism and the overlapping of interaction orbitals, NH3 molecule provides the Highest Occupied Molecular Orbital (HOMO) as the interaction pair for the Lowest Unoccupied Molecular Orbital (LUMO) on Fe surface. The insignificant difference between the oxidation state of N and H atoms as well as the higher hemolytic N-H bond dissociation energy (compared to heterolytic dissociation) cause the adsorption mechanism of NH3 on Fe(111) model to occur through homolytic-dissociative chemisorption.

  11. Hydrogen bond cooperativity in water hexamers: atomic energy perspective of local stabilities.

    PubMed

    Albrecht, Laura; Chowdhury, Saptarshi; Boyd, Russell J

    2013-10-17

    Atomic energies are used to describe local stability in eight low-lying water hexamers: prism, cage, boat 1, boat 2, bag, chair, book 1, and book 2. The energies are evaluated using the quantum theory of atoms in molecules (QTAIM) at MP2/aug-cc-pVTZ geometries. It is found that the simple, stabilizing cooperativity observed in linear hydrogen-bonded water systems is diminished as clusters move from nearly planar to three-dimensional structures. The prism, cage, and bag clusters can have local water stabilities differing up to 5 kcal mol(-1) as a result of mixed cooperative and anticooperative interactions. At the atomic level, in many cases a water may have a largely stabilized oxygen atom but the net water stability will be diminished due to strong destabilization of the water's hydrogen atoms. Analysis of bond critical point (BCP) electron densities shows that the reduced cooperativity results in a decrease in hydrogen bond strength and an increase in covalent bond strength, most evident in the prism. The chair, with the greatest cooperativity, has the largest average electron density at the BCP per hydrogen bond, whereas the cage has the largest total value for BCP density at all hydrogen bonds. The cage also has the second largest value (after the prism) for covalent bond critical point densities and an oxygen-oxygen BCP which may factor into the experimentally observed stability of the structure. PMID:24067198

  12. Photofragment translational spectroscopy of three body dissociations and free radicals

    SciTech Connect

    North, S.W.

    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 is invariant to the available energy. A fraction of the nascent CH{sub 3}CO radicals spontaneously dissociate following rotational averaging. The 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, CH{sub 3}CO 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 CH{sub 2} ({sup 1}A{sub l}) and H ({sup 2}S) was the only single photon dissociation pathway observed at both wavelengths.

  13. 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.

  14. 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.

  15. Theoretical insights into the structures and mechanical properties of HMX/NQ cocrystal explosives and their complexes, and the influence of molecular ratios on their bonding energies.

    PubMed

    Li, Yong-Xiang; Chen, Shu-Sen; Ren, Fu-de

    2015-09-01

    Molecular dynamics (MD) methods were employed to study the binding energies and mechanical properties of selected crystal planes of 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/nitroguanidine (NQ) cocrystals at different molecular molar ratios. The densities and detonation velocities of the cocrystals at different molar ratios were estimated. The intermolecular interaction and bond dissociation energy (BDE) of the N-NO2 bond in the HMX:NQ (1:1) complex were calculated using the B3LYP, MP2(full) and M06-2X methods with the 6-311++G(d,p) and 6-311++G(2df,2p) basis sets. The results indicated that the HMX/NQ cocrystal prefers cocrystalizing in a 1:1 molar ratio, and the cocrystallization is dominated by the (0 2 0) and (1 0 0) facets. The K, G, and E values of the ratio of 1:1 are smaller than those of the other ratios, and the 1:1 cocrystal has the best ductility. The N-NO2 bond becomes stronger upon the formation of the intermolecular H-bonding interaction and the sensitivity of HMX decreases in the cocrystal. This sensitivity change in the HMX/NQ cocrystal originates not only from the formation of the intermolecular interaction but also from the increment of the BDE of N-NO2 bond in comparison with isolated HMX. The HMX/NQ (1:1) cocrystal exhibits good detonation performance. Reduced density gradient (RDG) reveals the nature of cocrystallization. Analysis of the surface electrostatic potential further confirmed that the sensitivity decreases in complex (or cocrystal) in comparison with that in isolated HMX. PMID:26318201

  16. Hadron cross sections at ultra high energies and unitarity bounds on diffraction dissociation

    NASA Technical Reports Server (NTRS)

    Yodh, G. B.; Gaisser, T. K.

    1985-01-01

    It was shown that if unitarity bounds on diffractive cross sections are valid at ultra high energies then diffractive dominance models which ascribe the increase in total hadron-hadron cross sections to diffractive processes only are ruled out. Calculations also show that cosmic ray cross sections derived from air shower experiments at ultra high energies clearly rule out models for hadron-hadron cross sections with nat.log ns energy dependence and favor those with nat.log n(2)s variation.

  17. High-energy Collision-induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

    PubMed Central

    Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

    2014-01-01

    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. PMID:24781458

  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. 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. PMID:27141555

  20. 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. PMID:27086657

  1. Guided ion beam studies of the reactions of Co{sub n}{sup +} (n=1-18) with N{sub 2}: Cobalt cluster mononitride and dinitride bond energies

    SciTech Connect

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

    2008-05-21

    The reactions of Co{sub n}{sup +} (n=1-18) with N{sub 2} are measured as a function of kinetic energy over a range of 0-15 eV in a guided ion beam tandem mass spectrometer. A variety of Co{sub m}{sup +}, Co{sub m}N{sup +}, and Co{sub m}N{sub 2}{sup +} (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 Co{sub 13}{sup +}-N bond energy is relatively weak. The bond energies of Co{sub n}{sup +}-N for larger clusters suggest that a reasonable value for the desorption energy of atomic nitrogen from bulk phase cobalt is 6.3{+-}0.2 eV, 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, D{sub 0}(Co{sub n}{sup +}-Co), and to D{sub 0}(Fe{sub n}{sup +}-N). Implications for catalytic ammonia production using cobalt versus iron are discussed.

  2. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations.

    PubMed

    Shimamura, K; Shibuta, Y; Ohmura, S; Arifin, R; Shimojo, F

    2016-04-13

    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. PMID:26953616

  3. 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.

  4. 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 take place under quasi-stationary state conditions. This suggest the necessity of explicitly including some rovibrational levels, when solving a global kinetic rate equation. PMID:23387589

  5. 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.

  6. Bond descriptors based on kinetic energy densities reveal regions of slow electrons - Another look at aromaticity

    NASA Astrophysics Data System (ADS)

    Jacobsen, Heiko

    2013-09-01

    An analysis of the kinetic energy density within a molecule identifies patterns within its electronic structure that are intuitively linked to familiar concepts of chemical bonding. Proposed are bond descriptors based on local kinetic energies in an extended mapping onto a finite range of values, so called RoSE-indicators. The usefulness and performance of RoSE-indicators is judged in applications on aromaticity. Results are presented for benzene, cyclobutadiene, borazine and the cyclic hydrogen fluoride trimer as examples for agreed-upon aromaticity and antiaromaticity, as well as for questionable aromaticity. All-metal aromaticity is discussed based on results obtained for tetra aluminum dianion.

  7. A comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes.

    PubMed

    Haldar, Susanta; Gnanasekaran, Ramachandran; Hobza, Pavel

    2015-10-28

    Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as the sum of interaction energies and the change of zero-point vibrational energies (ΔZPVE). The structures of H-bonded complexes were optimized at the RI-MP2/cc-pVTZ level, at which deformation and harmonic ΔZPVE energies were also calculated. The structures of dispersion-bound complexes were optimized at the DFT-D3 level, and harmonic ΔZPVE energies were determined at the same level as well. For comparison, CCSD(T)/CBS D0 energies were also evaluated for both types of complexes. The CCSD(T)/CBS interaction energy was constructed as the sum of MP2/CBS interaction energy, extrapolated from aug-cc-pVTZ and aug-cc-pVQZ basis sets, and ΔCCSD(T) correction, determined with the aug-cc-pVDZ basis set. The ΔZPVE energies were determined for all complexes at the harmonic level and for selected complexes, these energies were also calculated using second-order vibration perturbation (VPT2) theory. For H-bonded complexes, the harmonic CCSD(T)/CBS D0 energies were in better agreement with the experimental values (with a mean relative error (MRE) of 6.2%) than the RI-MP2/cc-pVTZ D0 (a MRE of 12.3%). The same trend was found for dispersion-bound complexes (6.2% (MRE) at CCSD(T)/CBS and 7.7% (MRE) at the DFT-D3 level). When the anharmonic ΔZPVE term was included instead of harmonic one, the agreement between theoretical and experimental D0 deteriorated for H-bonded as well as dispersion-bound complexes. Finally, the applicability of "diagonal approximation" for determining the anharmonic ΔZPVE was shown. For the phenolH2O complex, the ΔZPVE energy calculated at the VPT2 level and on the basis of "diagonal approximation" differed by less than 0.1 kcal mol(-1). PMID:26392236

  8. Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

    PubMed Central

    Mommen, Geert P. M.; Frese, Christian K.; Meiring, Hugo D.; van Gaans-van den Brink, Jacqueline; de Jong, Ad P. J. M.; van Els, Cécile A. C. M.; Heck, Albert J. R.

    2014-01-01

    The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides. PMID:24616531

  9. Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD).

    PubMed

    Mommen, Geert P M; Frese, Christian K; Meiring, Hugo D; van Gaans-van den Brink, Jacqueline; de Jong, Ad P J M; van Els, Cécile A C M; Heck, Albert J R

    2014-03-25

    The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides. PMID:24616531

  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. 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.

  12. Potential energy surfaces for CH bond cleavage reactions

    SciTech Connect

    Harding, L.B.

    1996-12-31

    Ab initio, multi-reference, configuration interaction calculations are reported for CH{sub 4}{leftrightarrow}CH{sub 3}+H, CH{sub 3}F{leftrightarrow}CH{sub 2}F+H, CH{sub 2}F{sub 2}{leftrightarrow}CHF{sub 2}+H, and CHF{sub 3}{leftrightarrow}CF{sub 3}+H. Two equivalent, barrier-less paths are found for the CH{sub 3}+H recombination, two inequivalent, barrier-less paths are found for the CH{sub 2}F+H and CHF{sub 2}+H recombinations (depending on which side of the radical the H atom approaches), and only one barrier-less path is found for the CF{sub 3}+H recombination. Minimum energy path for H atom approaching CF{sub 3} from the concave side is predicted to have a barrier of 27 kcal/mole. Both minimum energy path energies and transitional frequencies as function of R{sub CH} for all 4 reactions are predicted to be similar.

  13. An experimental study of SO3 dissociation as a mechanism for converting and transporting solar energy

    NASA Technical Reports Server (NTRS)

    Mccrary, J. H.; Mccrary, G. E.; Chubb, T. A.; Won, Y. S.

    1981-01-01

    The high temperature catalytic dissocation of SO3 is an important chemical process being considered in the development and application of solar-thermal energy conversion, transport, and storage systems. A facility for evaluating chemical converter-heat exchangers at temperatures to 1000 C with high flow rates of gaseous SO3 feedstock has been assembled and operated on the NMSU campus. Several quartz and metal reactors containing different catalyst configurations have been tested. Descriptions of the test facility and of the reactors are given along with a presentation and discussion of experimental results.

  14. Analysis of low complex region peptides derived from mollusk shell matrix proteins using CID, high-energy collisional dissociation, and electron transfer dissociation on an LTQ-orbitrap: implications for peptide to spectrum match.

    PubMed

    Marie, Arul; Alves, Sandra; Marie, Benjamin; Dubost, Lionel; Bédouet, Laurent; Berland, Sophie

    2012-10-01

    Identification of proteins involved in mollusk biomineralization by proteomics approach is gaining importance. These proteins are often characterized by low-complexity regions (LCRs) made of repeating motifs that are constituted by few amino acids (e.g. IGG, DD, KK, and GGG). In this work, we have analyzed the fragmentation of model LCR peptides under different fragmentation regimes (CID, high-energy collisional dissociation [HCD], and electron transfer dissociation [ETD]) and its consequences on peptide to spectrum matches (PSMs) using two search algorithms (Mascot and PEAKS DB). For both search tools, higher number of PSMs was obtained using CID spectra, followed by HCD and ETD. Intense fragment ions present in the lower m/z region of HCD led to lower PSM scores and absence of low mass cut off seems to offer little advantage for the identification of LCR peptides. Generally, doubly charged peptides under ETD conditions did not fragment to yield sequence information rich spectra. The spectral quality is affected by the nature of the repeating motifs in the peptide. The performance of both Mascot and PEAKS DB (de novo based search tool) vary according to the fragment regime employed to acquire MS/MS spectra. PMID:22888092

  15. Chemical bond as a test of density-gradient expansions for kinetic and exchange energies

    NASA Astrophysics Data System (ADS)

    Perdew, John P.; Levy, Mel; Painter, G. S.; Wei, Siqing; Lagowski, Jolanta B.

    1988-01-01

    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 N2 and F2, 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.

  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. Methane dissociation on Ni(111): A fifteen-dimensional potential energy surface using neural network method

    NASA Astrophysics Data System (ADS)

    Shen, Xiangjian; Chen, Jun; Zhang, Zhaojun; Shao, Kejie; Zhang, Dong H.

    2015-10-01

    In the present work, we develop a highly accurate, fifteen-dimensional potential energy surface (PES) of CH4 interacting on a rigid flat Ni(111) surface with the methodology of neural network (NN) fit to a database consisted of about 194 208 ab initio density functional theory (DFT) energy points. Some careful tests of the accuracy of the fitting PES are given through the descriptions of the fitting quality, vibrational spectrum of CH4 in vacuum, transition state (TS) geometries as well as the activation barriers. Using a 25-60-60-1 NN structure, we obtain one of the best PESs with the least root mean square errors: 10.11 meV for the entrance region and 17.00 meV for the interaction and product regions. Our PES can reproduce the DFT results very well in particular for the important TS structures. Furthermore, we present the sticking probability S0 of ground state CH4 at the experimental surface temperature using some sudden approximations by Jackson's group. An in-depth explanation is given for the underestimated sticking probability.

  18. 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.

  19. A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems

    NASA Astrophysics Data System (ADS)

    Raupach, Marc; Tonner, Ralf

    2015-05-01

    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.

  20. 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.

  1. 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.

  2. Covalent bonding effect on the mean excitation energy of H2 with the local plasma model

    NASA Technical Reports Server (NTRS)

    Kamaratos, E.

    1984-01-01

    Chemical bonding is taken into account explicitly in the determination of the mean excitation energy (I) for stopping power of H2 with the local plasma approximation by employing molecular electronic wave functions for H2 for the first time. This procedure leads to a new value for IH2 that is higher than all accepted experimental and theoretical values.

  3. 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.

  4. Total π-Electron Energy of Conjugated Molecules with Non-bonding Molecular Orbitals

    NASA Astrophysics Data System (ADS)

    Gutman, Ivan

    2016-02-01

    Lower and upper bounds for the total π-electron energy are obtained, which are applicable to conjugated π-electron systems with non-bonding molecular orbitals (NBMOs). These improve the earlier estimates, in which the number of NBMOs has not been taken into account.

  5. 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.

  6. 3Σ- and 3Π states of GeC and GeSi: The problematic dissociation energy of GeC

    NASA Astrophysics Data System (ADS)

    Sari, Levent; Yamaguchi, Yukio; Schaefer, Henry F.

    2003-10-01

    The 3Σ- and 3Π states for the GeC and GeSi diatomics have been investigated at the highly correlated coupled-cluster levels of theory. Large basis sets [including TZ3P(2d,2f)+2diff, cc-pVQZ, and aug-cc-pVQZ] were employed in order to predict reliable values for the experimentally unknown spectroscopic properties. The ground states were confirmed to be the 3Π state for GeC and the 3Σ- state for GeSi. Advanced theoretical treatments such as inclusion of core-valence correlation, scalar relativity, and complete basis set extrapolations have been performed to determine accurate energetic properties. The dissociation energies (D0) of 91.4 kcal/mol and 72.9 kcal/mol have been predicted for the X 3Π state of GeC and X 3Σ- state of GeSi, respectively. It is observed that the theoretical value of 72.9 kcal/mol for GeSi is in very good agreement with the experimental value of 71±5 kcal/mol. However, the predicted dissociation energy for the X 3Π state of GeC is found to be 18 kcal/mol smaller than the mass spectrometric measurements. Both the X 3Π and A 3Σ- state potential energy surfaces for GeC have been examined by the full valence configuration interaction technique to search for a possible transition state that might explain this discrepancy. However, it has been found that both states smoothly dissociate to the ground 3P states of carbon and germanium without any transition state. Several theoretical and experimental aspects related to the determination of the dissociation energy of GeC have been discussed. It is concluded that the theoretically determined value of 91.4 kcal/mol should be more reliable than the reported experimental values.

  7. 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.

  8. 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.

  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. Bonding Motifs of Noble-Gas Compounds As Described by the Local Electron Energy Density.

    PubMed

    Borocci, Stefano; Giordani, Maria; Grandinetti, Felice

    2015-06-18

    The bonding situation of some exemplary noble-gas (Ng) compounds, including HNg(+), HNgF, FNgO(-), Ng-HF, and NgBeO (Ng = He-Xe) was assayed by examining their local electron energy density H(r). In general, this function partitions the space of atomic species (neutral and ionic) into inner regions of negative values and outer regions of positive values. In the formation of chemical bonds, these atomic regions combine so to form a molecular H(r), Hmol(r), whose plotted form naturally shows the "covalent" and "noncovalent" regions of the molecular species and allows also the recognition of different types of noncovalent interactions such van der Waals, hydrogen, and ionic or partially ionic bonds. The qualitative assignment of the various bonding motifs is corroborated by the topological analysis of Hmol(r), which typically includes several critical points of rank 3 and variable signature. These points are, in particular, characterized here in terms of their bond degree (BD). From a previous definition (Espinosa J. Chem. Phys. 2002, 117, 5529-5542), this quantity is taken as the ratio between the energy density calculated at the critical point of H(r), H(rc), and the corresponding electron density ρ(rc): BD = -H(rc)/ρ(rc). Thus, the BD is positive for covalent interactions (H(rc) < 0) and negative for noncovalent interactions (H(rc) > 0). For structurally related species, the BD result, in general, positively correlated with the binding energies and is, therefore, a semiquantitative index of stability. The present study suggests the general validity of the Hmol(r) to effectively assay the bonding motifs of noble-gas compounds. PMID:25988571

  11. Trans-reflection thermal driven deformable mirror with flexible bonding in high energy laser system

    NASA Astrophysics Data System (ADS)

    Ma, Xingkun; Huang, Lei; Gong, Mali; Xue, Qiao

    2014-09-01

    Deformable mirrors used in high energy laser system suffer from problems like the stress from adhesive solidification or the relatively expensive unit price of piezoceramic actuator. The thermal driven deformable mirror (TDDM) investigated here provided a promising prospect to solve these problems. Four scenarios of TDDM were studied and compared. Results showed that the trans-reflection TDDM with flexible bonding best met the requirement in practical use. The flexible bonding excluded the stress problem in the solidification of adhesives, trans-reflection brought about enough correction range, and the choice of thermo-electric cooler as actuator could greatly bring down the cost of adaptive optics apparatus as well.

  12. Interlayer bonding energy of layered minerals: Implication for the relationship with friction coefficient

    NASA Astrophysics Data System (ADS)

    Sakuma, Hiroshi; Suehara, Shigeru

    2015-04-01

    The frictional strength of layered minerals is an important component of fault slip physics. A low-friction coefficient of these minerals has been attributed to the interlayer bonding energy (ILBE) of their weak interlayer bonding. The ILBE used for discussing the friction coefficient is based on a simple electrostatic calculation; however, the values should be revisited by precise calculations based on quantum mechanics. In this study, the ILBEs of layered minerals were calculated by using the density functional theory (DFT) method with van der Waals correction. The ILBEs calculated by the simple electrostatic method for hydrogen-bonding minerals such as kaolinite, lizardite, gibbsite, and brucite strongly overestimated the reliable energies calculated by the DFT method. This result should be ascribed to the inaccurate approximation of the point charges at the basal plane. A linear relationship between the experimentally measured friction coefficients of layered minerals and the ILBEs determined by the simple method was not confirmed by using the reliable ILBEs calculated by our DFT method. The results, however, do not remove the possibility of a relationship between interlayer bonding energy and the friction coefficient because the latter, used for comparing the former, was obtained through experiments conducted under various conditions.

  13. Real-Time Evolution of the Valence Electronic Structure in a Dissociating Molecule

    SciTech Connect

    Wernet, Ph.; Godehusen, K.; Gaudin, J.; Schwarzkopf, O.; Eberhardt, W.; Odelius, M.

    2009-07-03

    Time-resolved valence band photoelectron spectroscopy with a temporal resolution of 135 fs is used to map the entire occupied valence electronic structure of photoexcited gas-phase Br{sub 2} molecules during dissociation. The observed shifting and mixing of valence energy levels defines a transition period where the system appears to be intermediate between atoms and molecules. The surprisingly short bond breaking or dissociation time is determined by monitoring in real time how the photoelectron multiplet structure of the free atom arises from the valence states of the photoexcited molecule.

  14. 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.

  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. PMID:25639210

  16. Collision-Induced Dissociation and Theoretical Studies of Ag+(methanol)(n) , n= 1 - 4

    SciTech Connect

    Koizumi, Hideya; Larsen, Melissa; Armentrout, Peter B.; Feller, David F. )

    2003-04-24

    Collision-induced dissociations of the Ag+(methanol)n complexes for n= 1 - 4 are studied using kinetic energy dependent guided ion beam tandem mass spectrometry. In all cases, the primary products are endothermic loss of an intact neutral ligand from the complex. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-molecule collisions, internal energy of the complexes, and unimolecular decay rates. These values are compared with theoretical values obtained using high level ab initio calculations. Generally good agreement is found except for the third ligand. The nature of the bonding in these complexes and their BDEs are examined in detail. Although the effect is not as dramatic as in singly or doubly ligated copper complexes, 5s-4ds hybridization found in the Ag+(methanol)n complexes, n= 1 and 2, enhances the BDEs.

  17. Electron-energy-loss spectroscopy characterization of the sp2 bonding fraction within carbon thin films

    NASA Astrophysics Data System (ADS)

    Papworth, A. J.; Kiely, C. J.; Burden, A. P.; Silva, S. R. P.; Amaratunga, G. A. J.

    2000-11-01

    When using electron-energy-loss spectroscopy (EELS) to quantify the sp2/sp3 bonding fraction in thin film carbon, the spectrum taken from the film must be compared to that of a suitable known standard. In contrast to the work of Berger [S. D. Berger and D. R. McKenzie, Philos. Mag. Lett. 57, 285 (1988)], C60 fullerite is used in this work as the standard since highly oriented pyrolytic graphite (HOPG) is highly anisotropic, and can therefore lead to preferential orientation effects in EELS. It was found that C60 had a shoulder on the high-energy side of the 1s-->π* peak, which was centered at 287 eV. In theory, many Gaussian peaks can be fitted to the near edge structure (NES) of the energy-loss spectrum. In practice, we show that only three, centered at energies of 285, 287, and 293 eV, are necessary for semiquantitative analysis. The 285 eV peak is indicative of the sp2 bonding fraction; the second peak at 287 eV is attributed to molecular structure within the sample; the third at 293 eV is determined by sp3 bonding contributions in the sample. We show that by fitting these three peaks to C60 fullerite and evaporated amorphous carbon (a-C), that the a-C has a 0.99 sp2 bonding fraction compared with the C60 fullerite standard. The importance of considering the 287 eV peak in highly sp2 bonded amorphous carbon is further illustrated by analysis of a-C:H:N thin films.

  18. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine.

    PubMed

    Wu, R R; Chen, Yu; Rodgers, M T

    2016-01-20

    Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ?25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond. PMID:26740232

  19. Autocatalytic water dissociation on Cu(110) at near ambient conditions

    SciTech Connect

    Mulleregan, Alice; Andersson, Klas; Ketteler, Guido; Bluhm, Hendrik; Yamamoto, Susumu; Ogasawara, Hirohito; Pettersson, Lars G.M.; Salmeron, Miquel; Nilsson, Anders

    2007-05-16

    Autocatalytic dissociation of water on the Cu(110) metal surface is demonstrated based on X-ray photoelectron spectroscopy studies carried out in-situ under near ambient conditions of water vapor pressure (1 Torr) and temperature (275-520 K). The autocatalytic reaction is explained as the result of the strong hydrogen-bond in the H{sub 2}O-OH complex of the dissociated final state, which lowers the water dissociation barrier according to the Broensted-Evans-Polanyi relations. A simple chemical bonding picture is presented which predicts autocatalytic water dissociation to be a general phenomenon on metal surfaces.

  20. General formulation of the vibrational kinetic energy operator in internal bond-angle coordinates

    NASA Astrophysics Data System (ADS)

    Frederick, John H.; Woywod, Clemens

    1999-10-01

    A general formulation of the vibrational kinetic energy operator expressed in internal bond-angle coordinates is presented. This formulation is based on Podolsky's expression for the covariant form of the Laplace-Beltrami operator. When a valid set of internal bond-angle coordinates is employed, it is possible to adapt a systematic approach to solve for the Jacobian determinant governing the coordinate transformation from Cartesian coordinates. In the general case of an arbitrary N-atom system, this Jacobian always factorizes to a simple form. This allows one to evaluate all the terms that contribute to V̂', the effective potential that arises from transforming the kinetic energy operator to internal coordinates. We discuss restrictions on the choice of internal vibrational coordinates that may be included in a valid set. We then provide tabular information from which the vibrational kinetic energy operator for any molecular system can be constructed directly with no matrix inversion or chain rule manipulation required.

  1. Six-dimensional quantum dynamics of dissociative chemisorption of H2 on Co(0001) on an accurate global potential energy surface.

    PubMed

    Jiang, Bin; Hu, Xixi; Lin, Sen; Xie, Daiqian; Guo, Hua

    2015-09-28

    Cobalt is a widely used catalyst for many heterogeneous reactions, including the Fischer-Tropsch (FT) process, which converts syngas (H2 and CO) to higher hydrocarbons. As a result, a better understanding of the key chemical steps on the Co surface, such as the dissociative chemisorption of H2 as an initial step of the FT process, is of fundamental importance. Here, we report an accurate full-dimensional global potential energy surface for the dissociative chemisorption of H2 on the rigid Co(0001) surface constructed from more than 3000 density functional theory points. The high-fidelity potential energy surface was obtained using the permutation invariant polynomial-neural network method, which preserves both the permutation symmetry of H2 and translational symmetry of the Co(0001) surface. The reaction path features a very low barrier on the top site. Full-dimensional quantum dynamical calculations provide insights into the dissociation dynamics and influence of the initial vibrational, rotational, and orientational degrees of freedom. PMID:26286861

  2. 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.

  3. Five-membered ring formation in unimolecular reactions of peptides: a key structural element controlling low-energy collision-induced dissociation of peptides.

    PubMed

    Schlosser, A; Lehmann, W D

    2000-12-01

    Unimolecular fragmentation reactions of peptides in low-energy collision-induced dissociation are reviewed in the mechanistic context of five-membered ring formation. This structure of intermediates or of fragment ions is recognized as a key element that governs unimolecular peptide fragmentation within the structural framework determined by the peptide backbone and its side-chains. A collection of collision-induced dissociation reactions is presented covering (i) b-ion formation, (ii) the fragmentation of N-terminally acylated peptides, (iii) neutral loss of the C-terminal amino acid in alkali or silver cationized peptides, (iv) the fragmentation of isoAsp-containing peptides and (v) the fragmentation of negatively charged Asp- or Glu-containing peptides. It appears that for all possible nucleophile-electrophile interactions leading to a five-membered ring structure an associated unimolecular peptide fragmentation reaction can be observed. PMID:11180628

  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. 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. PMID:27114315

  6. 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.

  7. Cascade Dissociations of Peptide Cation-Radicals. Part 2. Infrared Multiphoton Dissociation and Mechanistic Studies of z-Ions from Pentapeptides

    NASA Astrophysics Data System (ADS)

    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 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 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 MS4 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.

  8. Dissociation of 8He

    NASA Astrophysics Data System (ADS)

    Iwata, Y.; Ieki, K.; Galonsky, A.; Kruse, J. J.; Wang, J.; White-Stevens, R. H.; Tryggestad, E.; Zecher, P. D.; Deák, F.; Horváth, Á.; Kiss, Á.; Seres, Z.; Kolata, J. J.; von Schwarzenberg, J.; Warner, R. E.; Schelin, H.

    2000-12-01

    We have performed kinematically complete measurements of dissociation of 8He into 6He and two neutrons at E/A=24 MeV. The targets were Sn and Pb. A prominent peak around 0.4 MeV in the relative energy distribution of the 6He+n system is consistent with the ground state of 7He, suggesting sequential decay via 7He in 8He dissociation. Further evidence of the sequential decay was found in neutron momentum distributions. The excitation energy distributions of 8He were reconstructed. For the Sn target, it shows a peak which is suggestive of the first excited state of 8He (Ex=3.6 MeV, Γ=0.5 MeV, and Jπ=2+). The distribution for the Pb target was found to have a broad structure, indicating the E1 continuum, as observed in measurements of other halo nuclei. The photonuclear cross section σE1(Ex) and the dipole strength function dB(E1)/dEd were deduced for the first time. The integrated dipole strength up to 3 MeV decay energy is 0.091+/-0.026 e2fm2. Insignificant energy-weighted strength, compared to the cluster sum rule, indicates that 8He does not have the 6He+2n structure. Agreement of the measured neutron momentum distributions with the COSMA model is in favor of the 4He+4n structure.

  9. Ab initio molecular dynamics of high-temperature unimolecular dissociation of gas-phase RDX and its dissociation products.

    PubMed

    Schweigert, Igor V

    2015-03-26

    Unimolecular dynamics of gas-phase hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and its dissociation products were simulated using density functional theory (DFT) at the M06-L level. The simulations of RDX at 2000 K showed that dissociation proceeds from multiple conformers, mostly via homolytic fission of an N-N bond with a minor contribution from elimination of HONO, in agreement with previous transition state theory calculations. However, the simulations of the fission and elimination products revealed that secondary N-N fission is facile and, at the simulated temperature of 1750 K, dominant over other mechanisms. The simulations of the resulting intermediates revealed a number of new unimolecular pathways that have not been previously considered. The transition structures and minimal energy paths were calculated for all reactions to confirm these observations. Based on these findings, a revised set of the unimolecular reactions contributing to gas-phase RDX decomposition is proposed. PMID:25738393

  10. The mechanism of excited state proton dissociation in microhydrated hydroxylamine clusters.

    PubMed

    Thisuwan, Jittima; Suwannakham, Parichart; Lao-Ngam, Charoensak; Sagarik, Kritsana

    2016-02-21

    The dynamics and mechanism of excited-state proton dissociation and transfer in microhydrated hydroxylamine clusters are studied using NH2OH(H2O)n (n = 1-4) as model systems and the DFT/B3LYP/aug-cc-pVDZ and TD-DFT/B3LYP/aug-cc-pVDZ methods as model calculations. This investigation is based on the Frster acidity scheme and emphasizes the photoacid dissociation in the ground (S0) and lowest singlet-excited states (S1) and the interplay between the photo and thermal excitations. The quantum chemical results suggest that the intermediate complexes are formed only in the S1 state in a low local-dielectric environment (e.g., ? = 1) and that upon the S0? S1 transition, the photon energy excites mostly NH2OH, which leads to a homolytic cleavage of the O-H bond and to dynamically stable charge-separated Rydberg-like H-bond complexes (e.g., NH2O?-H3O(+)?). The potential energy surfaces for proton displacement in the smallest Rydberg-like H-bond complex support the intersection of the S0 and S1 states in low local-dielectric environments, whereas in a high local-dielectric environment (e.g., ? = 78), these two states are completely separated. Based on the static results, a photoacid-dissociation mechanism that involves Rydberg-like H-bond complex formation, an H-bond chain extension and fluctuations in the local-dielectric environment is proposed. NVT-BOMD simulations confirm the static results and show that the dynamic behavior of the dissociating proton in the S1 state is not different from that of the protonated H-bond systems in the ground state, which consists of the oscillatory shuttling and structural diffusion motions. These findings allow our theoretical methods, which have been used successfully in protonated H-bond systems in the ground state, to be applied in the study of the photoacid-dissociation processes. The current theoretical study suggests effective steps as well as guidelines for the investigation of the dynamics of the photoacid-dissociation and transfer processes in the Frster acidity scheme, provided that the exciting photon does not lead to a significant change in the structure of the intermediate complex in the excited state. PMID:26862862

  11. Dissociation of H{sub 2}{sup +} and D{sub 2}{sup +} in an intense laser field

    SciTech Connect

    Ludwig, J.; Rottke, H.; Sandner, W.

    1997-09-01

    We report experimental investigations on dissociation of H{sub 2} and D{sub 2} in intense subpicosecond laser pulses at 1053 and 526.5 nm. Intensities in the range from {approx}5{times}10{sup 13} up to {approx}5{times}10{sup 14} W/cm{sup 2} were applied. The kinetic-energy distributions of the photoions H{sup +} and D{sup +}, which change dramatically with the light pulse peak intensity, give a detailed insight into the dissociation mechanisms. At 526.5 nm and low light intensity, ions from bond-softening dissociation and probably seven-photon resonant dissociative multiphoton ionization dominate the spectra. The resonant intermediate states are Rydberg states of the neutral molecules. At 1053 nm, above-threshold dissociation makes the main contribution to the spectra. Independent of the excitation wavelength, Coulomb explosion dissociation is found in the high-intensity limit. H{sub 2}{sup +} and D{sub 2}{sup +} photoionization, triggering this process, proceeds in the quasistatic limit by preferred tunnel or above-barrier ionization in a limited range of internuclear separations around 7.5 a.u. The ion kinetic-energy distributions seem to indicate that at 526.5 nm ionization starts from molecular ions light stabilized in a certain range of internuclear distances. In contrast, at 1053 nm, ionization seems to start from dissociating molecular ions. {copyright} {ital 1997} {ital The American Physical Society}

  12. Effects of in-plane. pi. prime bonding on electronic transition energies for inorganic polymers

    SciTech Connect

    Ferris, K.F.; Risser, S.M.; Hanson, A.K.

    1990-03-01

    The electronic structure of organic and inorganic polymeric systems are well described in terms of their molecular symmetry, even with the large bond polarity shown by such systems as polyphosphazenes. We have performed calculations using the semi-empirical CNDO/1 method to determine the valence electronic structure for a series of model phosphonitrilic and organic compounds. The optical transition energies for phosphonitrilic compounds are greater than their organic counterparts as a result of in-plane {pi}{prime} bonding interactions. The extent of these interactions is modulated by the electronegativity of the substituent groups on the phosphorus atoms. We report values for the vertical ionization energy and electronic absorption wavelengths, and use molecular orbital contour analysis to show the effects of ligand electronegativity on the {pi}{prime} network. 15 refs., 3 tabs.

  13. Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

    NASA Astrophysics Data System (ADS)

    Poudel, Lokendra; Rulis, Paul; Liang, Lei; Ching, W. Y.

    2014-08-01

    We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)10,(GC)10, (AT)5(GC)5, and (AT-GC)5 where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)5(GC)5 and (AT-GC)5 models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO4 + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

  14. 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.

  15. Bond breaking in a Morse chain under tension: fragmentation patterns, higher index saddles, and bond healing.

    PubMed

    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. PMID:23574219

  16. High-energy collision-activated and electron-transfer dissociation of gas-phase complexes of tryptophan with Na+, K+, and Ca2+

    NASA Astrophysics Data System (ADS)

    Fujihara, Akimasa; Sha, Yuki; Matsuo, Sou; Toyoda, Michisato; Hayakawa, Shigeo

    2014-10-01

    The structure and reactivity of gas-phase complexes of tryptophan (Trp) with Na+, K+, and Ca2+ were examined by high-energy collision-activated dissociation (CAD) and electron transfer dissociation (ETD) using alkali metal targets. In the CAD spectra of M+Trp (M = Na and K), neutral Trp loss was the primary dissociation pathway, and the product ion of collision-induced intracomplex electron transfer from the indole π ring of Trp to the alkali metal ion was observed, indicating a charge-solvated structure in which Trp is non-zwitterionic. The NH3 loss observed in the CAD spectrum of Ca2+Trp2 is ascribed to a CZ (mixed charge-solvated/zwitterionic)-type structure, in which one Trp is non-zwitterionic and the other Trp adopts a zwitterionic structure with an NH3+ moiety. The H atom and NH3 losses observed in the ETD spectrum of Ca2+Trp2 indicate the formation of a hypervalent radical in the complex, R-NH3, via electron transfer from the alkali metal target to the NH3+ group of the CZ-type structure. Ca2+ attachment to Trp cluster induces the zwitterionic structure of Trp in the gas phase, and an electron transfer to the zwitterionic Trp forms the hypervalent radical as a reaction intermediate.

  17. Shock-induced initiation and energy release behavior of polymer bonded explosive materials

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Cai, Xuanming; Hypervelocity Impact Research Center Team

    2015-06-01

    In this paper, an initially sealed vented test chamber and a test projectile with a recessed hole 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 impact pressure of the projectile was measured by the PVDF sensors. Based on the earlier work that the constitutive equation of polymer bonded explosive materials was established, the impact pressure of the projectile was obtained through the numerical simulation. The experimental results reveal that the impact pressure is significant to the energy release behavior, and in some extent the gas pressure improves with the velocity of the projectile. The impact pressure obtained by the experiments is comparing with which obtained through the numerical simulation, and the results of the comparing is that the value of them are closely relative. The experimental results also indicate that the constitutive equation of polymer bonded explosive materials used in the numerical simulation can correctly describe the mechanical behavior of PBX materials.

  18. Free Energy Landscapes for S-H Bonds in (Cp2Mo2S4)-Mo-star Complexes

    SciTech Connect

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

    2009-03-23

    Extensive thermochemical data have been determined for a series of complexes derived from Cp*Mo(μ S)2(μ SMe)(μ SH)MoCp* and Cp*Mo(μ S)2(μ SH)2MoCp*. These data include electrochemical potentials, pKa 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 FeCp2+/o for electrochemical potentials, 5 to 31 for pKa 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 wealth of thermochemical data are presented in free energy landscapes as a useful approach to visualizing and understanding the relative stabilities of all of the species under specified conditions. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.

  19. Quantum enhancement of vibrational predissociation near the dissociation threshold

    NASA Astrophysics Data System (ADS)

    Côté, 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.

  20. Statistical modeling of competitive threshold collision-induced dissociation

    NASA Astrophysics Data System (ADS)

    Rodgers, M. T.; Armentrout, P. B.

    1998-08-01

    Collision-induced dissociation of (R1OH)Li+(R2OH) with xenon is studied using guided ion beam mass spectrometry. R1OH and R2OH include the following molecules: water, methanol, ethanol, 1-propanol, 2-propanol, and 1-butanol. In all cases, the primary products formed correspond to endothermic loss of one of the neutral alcohols, with minor products that include those formed by ligand exchange and loss of both ligands. The cross-section thresholds are interpreted to yield 0 and 298 K bond energies for (R1OH)Li+-R2OH and relative Li+ binding affinities of the R1OH and R2OH ligands after accounting for the effects of multiple ion-molecule collisions, internal energy of the reactant ions, and dissociation lifetimes. We introduce a means to simultaneously analyze the cross sections for these competitive dissociations using statistical theories to predict the energy dependent branching ratio. Thermochemistry in good agreement with previous work is obtained in all cases. In essence, this statistical approach provides a detailed means of correcting for the "competitive shift" inherent in multichannel processes.

  1. 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.

  2. 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

    2015-12-01

    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. PMID:26646889

  3. 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, 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. Electronic supplementary information (ESI) available: Further experimental spectra and theoretical calculations. See DOI: 10.1039/c3nr06799h

  4. Vibrationally resolved structure in O{sub 2}{sup +} dissociation induced by intense ultrashort laser pulses

    SciTech Connect

    Zohrabi, M.; McKenna, J.; Gaire, B.; Johnson, Nora G.; Carnes, K. D.; De, S.; Bocharova, I. A.; Magrakvelidze, M.; Ray, D.; Litvinyuk, I. V.; Cocke, C. L.; Ben-Itzhak, I.

    2011-05-15

    Laser-induced dissociation of O{sub 2}{sup +} is studied in the strong-field limit using two independent methods, namely a crossed laser-ion-beam coincidence 3D momentum imaging method and a supersonic gas jet velocity map imaging technique (790 and 395 nm, 8-40 fs, {approx}10{sup 15} W/cm{sup 2}). The measured kinetic energy release spectra from dissociation of O{sub 2}{sup +} and dissociative ionization of O{sub 2} reveal vibrational structure which persists over a wide range of laser intensities. The vibrational structure is similar for O{sub 2}{sup +} produced incoherently in an ion source and coherently by laser pulses. By evaluation of the potential energy curves, we assign the spectral energy peaks to dissociation of the v=10-15 vibrational states of the metastable a {sup 4}{Pi}{sub u} state via the dissociation pathway |a {sup 4}{Pi}{sub u}>{yields}|f {sup 4}{Pi}{sub g}-1{omega}>--a mechanism equivalent to bond softening in H{sub 2}{sup +}.

  5. Absolute cross sections for the dissociation of hydrogen cluster ions in high-energy collisions with helium atoms

    SciTech Connect

    Eden, S.; Tabet, J.; Samraoui, K.; Louc, S.; Farizon, B.; Farizon, M.; Ouaskit, S.; Maerk, T. D.

    2006-02-15

    Absolute dissociation cross sections are reported for H{sub n}{sup +} clusters of varied mass (n=3,5,...,35) following collisions with He atoms at 60 keV/amu. Initial results have been published previously for a smaller range of cluster sizes [Ouaskit et al., Phys. Rev. A 49, 1484 (1994)]. The present extended study includes further experimental results, reducing the statistical errors associated with the absolute cross sections. The previously suggested quasilinear dependence of the H{sub n}{sup +} dissociation cross sections upon n is developed with reference to expected series of geometrical shells of H{sub 2} molecules surrounding a H{sub 3}{sup +} core. Recent calculations identify n=9 as corresponding to the first closed H{sub 2} shell [e.g., Stich et al., J. Chem. Phys. 107, 9482 (1997)]. Recurrence of the distinct characteristics observed in the dissociation-cross-section dependence upon cluster size around n=9 provides the basis for the presently proposed subsequent closed shells at n=15, 21, 27, and 33, in agreement with the calculations of Nagashima et al. [J. Phys. Chem. 96, 4294 (1992)].

  6. Theoretical Studies of Small Molecules Containing Aluminum-Nitrogen Dative Bonds

    NASA Astrophysics Data System (ADS)

    Marsh, Craig Melvin Bourvic

    1995-01-01

    Ab initio quantum mechanical methods have been applied to several systems which contain aluminum-nitrogen dative bonds, including ammonia alane [ AlH_3NH_3], trimethylamine alane [ AlH _3N(CH_3)_3], and bisammonia alane [ AlH_3(NH _3)_2], as well as their dissociation products: alane [ AlH_3], ammonia [ NH_3], and trimethylamine ] N(CH_3)_3] . Dissociation energies, equilibrium geometries, harmonic vibrational frequencies, infrared intensities, atomic charges, dipole moments are reported. Hyperconjugative effects in trimethylamine and trimethylamine alane are also reported. Differences between the dative bond in ammonia alane and in bisammonia alane are also presented.

  7. 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)

  8. 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.

  9. Mechanistic studies of processes involving C-C bond cleavage in gas-phase organometallic reactions using product kinetic energy release distributions: Co sup + reacting with cyclopentane

    SciTech Connect

    van Koppen, P.A.M.; Bowers, M.T. ); Beauchamp, J.L. )

    1990-03-01

    A reverse-geometry mass spectrometer is used to obtain product ion kinetic energy release distributions to probe the energetics and mechanisms of several gas-phase organometallic reactions. In particular, we examine the mechanism for C{sub 2}H{sub 4} and C{sub 3}H{sub 6} elimination from Co(cyclopentane){sup +}. The kinetic energy release distribution associated with these processes can be modeled by using phase space calculations assuming, for the C{sub 3}H{sub 6} elimination process, propene rather than cyclopropane is being eliminated as the product neutral, and for the C{sub 2}H{sub 4} elimination process, Co(propene){sup +} rather than (cobaltacyclobutane){sup +} is being formed as the product ion. In addition, we obtain a heat of formation for the cobalt ethylene ion of 255 kcal/mol at 0 K, corresponding to a bond dissociation energy of 42 kcal/mol at 0 K, by fitting the theoretical results to the experimental distribution.

  10. 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.

  11. Photodissociation of CO sup minus sub 3 : Product kinetic energy measurements as a probe of excited state potential surfaces and dissociation dynamics

    SciTech Connect

    Snodgrass, J.T.; Roehl, C.M.; van Koppen, P.A.M.; Palke, W.E.; Bowers, M.T. )

    1990-05-15

    The photodissociation process CO{sup {minus}}{sub 3} +{ital h}{nu}{r arrow}O{sup {minus}}+CO{sub 2} has been investigated at photon energies of 2.41, 2.50, 2.54, 2.60, and 2.71 eV. Experiments were conducted by crossing a mass-selected, 8 keV ion beam with a linearly polarized laser beam, and measuring the kinetic energy distributions of the charged photodissociation products. By varying the angle between the ion beam and laser polarization, angular distributions were obtained at photon energies of 2.41 and 2.54 eV. The photon energy dependence of the average photofragment kinetic energies shows conclusively that photodissociation at these photon energies does not proceed by a direct dissociation process on a repulsive potential surface, or by a statistical vibrational predissociation process on a bound surface. The photofragment angular distributions are isotropic, providing further evidence that precludes direct photodissociation on a repulsive potential surface. {ital Ab} {ital initio} calculations were performed using the GAUSSIAN86 programs. These calculations indicate that ground state CO{sup {minus}}{sub 3} has a planar {ital D}{sub 3}{sub {ital h}} geometry, and {sup 2}{ital A}{sup {prime}}{sub 2} electronic symmetry. This ground state correlates adiabatically to the CO{sup {minus}}{sub 2} +O dissociation asymptote, not the lower energy O{sup {minus}}+CO{sub 2} asymptote. Taken together, these new experimental and theoretical results suggest that the photodissociation of CO{sup {minus}}{sub 3} at these energies occurs via the interaction of bound and repulsive excited state potential surfaces. A new model of the potential surfaces of CO{sup {minus}}{sub 3} is proposed.

  12. Dissociation and dissociative phase transition in dense hydrogen

    SciTech Connect

    Khomkin, A. L. Shumikhin, A. S.

    2012-01-15

    A simple physical model is proposed for dissociating dense fluid hydrogen. We propose that free dissociated atoms interact via quantum electron-electron exchange analogously to the interaction in the liquid-metal phase of alkali metals. The density dependence of a hydrogen atom's binding energy in such a quasi-liquid is calculated. It is shown that the transition from the molecular fluid to liquid hydrogen is a first-order phase transition. The critical parameters of the transition are determined: P{sub c} = 72 GPa, T{sub c} = 10500 K, and {rho}{sub c} = 0.5 g/cm{sup 3}. The possibility of the metastable existence of atomic liquid hydrogen in a dissociated molecular fluid under decreased pressure is established.

  13. Ab initio multireference configuration interaction study of CH2NNO2. HONO elimination vs NN bond fragmentation

    NASA Astrophysics Data System (ADS)

    Mowrey, R. C.; Page, M.; Adams, G. F.; Lengsfield, B. H., III

    1990-08-01

    Features of the potential energy surface pertinent to the thermal decomposition mechanism of methylenenitramine (CH2NNO2) are investigated. At issue are the activation energies both for concerted molecular dissociation leading to HCN and HONO and for the simple NN bond cleavage leading to CH2N and NO2. We use multiconfiguration (MC)SCF wave functions with double-zeta and double-zeta plus polarization quality basis sets to locate minimum energy and transition state structures as well as determine harmonic vibrational frequencies and resulting zero-point vibrational energies. The energetics are determined using configuration interaction wave functions which include single and double excitations from a selected set of reference configurations constructed with the MCSCF molecular orbitals. Our best calculations, without adjustment, predict the molecular dissociation to have an activation energy slightly lower than that for simple bond rupture. Calculations at the level of those reported here are known, however, to underestimate bond dissociation energies by several kcal/mol. Based on trends from past calculations, and new calculations on a related compound, we estimate the activation energy for the HONO elimination path to be 31±4 kcal/mol and the NN bond dissociation energy to be 35±4 kcal/mol. This reverses the energetic ordering of previous theoretical predictions and is consistent with recent molecular beam experiments.

  14. C2 in a Box: Determining Its Intrinsic Bond Strength for the X(1) Σg (+) Ground State.

    PubMed

    Zou, Wenli; Cremer, Dieter

    2016-03-14

    The intrinsic bond strength of C2 in its (1) Σg (+) ground state is determined from its stretching force constant utilizing MR-CISD+Q(8,8), MR-AQCC(8,8), and single-determinant coupled cluster calculations with triple and quadruple excitations. By referencing the CC stretching force constant to its local counterparts of ethane, ethylene, and acetylene, an intrinsic bond strength half way between that of a double bond and a triple bond is obtained. Diabatic MR-CISD+Q results do not change this. Confinement of C2 and suitable reference molecules in a noble gas cage leads to compression, polarization, and charge transfer effects, which are quantified by the local CC stretching force constants and differences of correlated electron densities. These results are in line with two π bonds and a partial σ bond. Bond orders and bond dissociation energies of small hydrocarbons do not support quadruple bonding in C2 . PMID:26742466

  15. Diffraction dissociation at the LHC

    NASA Astrophysics Data System (ADS)

    Jenkovszky, László; Orava, Risto; Salii, Andrii

    2013-04-01

    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.

  16. 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.

  17. Mode specificity for the dissociative chemisorption of H2O on Cu(111): a quantum dynamics study on an accurately fitted potential energy surface.

    PubMed

    Liu, Tianhui; Zhang, Zhaojun; Fu, Bina; Yang, Xueming; Zhang, Dong H

    2016-03-16

    The mode-specific dynamics for the dissociative chemisorption of H2O on Cu(111) is first investigated by seven-dimensional quantum dynamics calculations, based on an accurately fitted potential energy surface (PES) recently developed by neural network fitting to DFT energy points. It is indicated that excitations in all three vibrational modes have a significant impact on reactivity, which are more efficacious than increasing the translational energy in promoting the reaction, with the largest enhancement for the excitation in the asymmetric stretching mode. There is large discrepancy between the six-dimensional reactivities with fixed azimuthal angles and seven-dimensional results, revealing that the 6D "flat surface" model cannot accurately characterize the reaction dynamics. The azimuthal angle-averaging approach is validated for vibrational excited states of the reactant, where the 7D mode-specific probability can be well reproduced by averaging the 6D azimuthal angle-fixed probabilities over 18 angles. PMID:26941197

  18. Accurate thermochemistry for larger molecules : gaussian-2 theory with bond separation energies.

    SciTech Connect

    Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.

    1997-04-22

    Gaussian-2 (G2) theory is combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. For a test set of 40 molecules composed of H, C, O, and N, our method yields enthalpies of formation, {Delta}H{sub f}{sup 0}(298 K), with a mean absolute deviation from experiment of only 0.5 kcal/mol. This is an improvement of a factor of three over the deviation of 1.5 kcal/mol seen in standard G2 theory.

  19. 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.

  20. Energy and critical ionic-bond parameter of a 3D large-radius bipolaron

    SciTech Connect

    Lakhno, V. D.

    2010-05-15

    A theory of a strong-coupling large-radius bipolaron has been developed. The possibility of the formation of 3D bipolarons in high-temperature superconductors is discussed. For the bipolaron energy, the lowest variational estimate has been obtained at {alpha} > 8, where {alpha} is the electron-phonon coupling constant. The critical ionic-bond parameter {eta}{sub c} = {epsilon}{sub {infinity}/{epsilon}0}, where {epsilon}{sub {infinity}} and {epsilon}{sub 0} are the high-frequency and static dielectric constants, has been found to be {eta}{sub c} = 0.2496.

  1. 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.

  2. 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.

  3. The heats of formation of some C2H5O + isomers, relevant bond energies in ethanol and PA(CH3CHO)

    NASA Astrophysics Data System (ADS)

    Ruscic, B.; Berkowitz, J.

    1994-12-01

    The ionization potentials of the transient species CH3CH2O, CH3CHOH, and CH2CH2OH (generated by the F+ethanol reactions) are measured by photoionization mass spectrometry: I.P.(CD3CD2O)=10.290.08 eV (tentative), I.P.(CH3CHOH)<6.85 eV, and I.P.(CD2CH2OH) ?8.350.06 eV. The latter results in a cation of uncertain structure. These reactions also generate vinyl alcohol (adiabatic I.P.=9.330.01 eV) and acetaldehyde. A redetermined appearance potential of CH3CHOH+ from ethanol enables one to infer the proton affinity of acetaldehyde to be ?183.80.2 kcal/mol and an ? (C-H) bond energy in ethanol ?91.1 kcal/mol (0 K). The appearance potential of m/e=45 ion from bromoethanol is interpreted as formation of a C2H5O+ isomer having the oxirane structure, with ?Hf00 of 173.9 kcal/mol, consistent with earlier alternative measurements. A second increase in the m/e=45 ion yield curve from ethanol is interpreted as formation of this same isomer. This interpretation, and an alternative cycle, lead to a ? (C-H) bond energy in ethanol of 982 kcal/mol. The implication of the current results to the dynamics of dissociation of ethanol cations is discussed.

  4. 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.

  5. Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

    NASA Astrophysics Data System (ADS)

    Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Wang, Yangang; Hupalo, Myron; McDougall, Dan; Tringides, Michael; Ho, Kaiming

    2013-12-01

    The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H2 molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H2 molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

  6. Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

    SciTech Connect

    Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Hupalo, Myron; Wang, Yangang; Supercomputing Center of Computer Network Information Center, CAS, Beijing 100190 ; McDougall, Dan; Tringides, Michael; Ho, Kaiming; Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011

    2013-12-14

    The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H{sub 2} molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H{sub 2} molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

  7. Distinguishing Bonds.

    PubMed

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

    The energy change per electron in a chemical or physical transformation, ΔE/n, may be expressed as Δχ̅ + Δ(VNN + ω)/n, where Δχ̅ is the average electron binding energy, a generalized electronegativity, ΔVNN is the change in nuclear repulsions, and Δω is the change in multielectron interactions in the process considered. The last term can be obtained by the difference from experimental or theoretical estimates of the first terms. Previously obtained consequences of this energy partitioning are extended here to a different analysis of bonding in a great variety of diatomics, including more or less polar ones. Arguments are presented for associating the average change in electron binding energy with covalence, and the change in multielectron interactions with electron transfer, either to, out, or within a molecule. A new descriptor Q, essentially the scaled difference between the Δχ̅ and Δ(VNN + ω)/n terms, when plotted versus the bond energy, separates nicely a wide variety of bonding types, covalent, covalent but more correlated, polar and increasingly ionic, metallogenic, electrostatic, charge-shift bonds, and dispersion interactions. Also, Q itself shows a set of interesting relations with the correlation energy of a bond. PMID:26910496

  8. Empirical valence bond models for reactive potential energy surfaces: A parallel multilevel genetic program approach

    NASA Astrophysics Data System (ADS)

    Bellucci, Michael A.; Coker, David F.

    2011-07-01

    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.

  9. 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.

  10. A quantum mechanics-molecular mechanics study of dissociative electron transfer: The methylchloride radical anion in aqueous solution

    NASA Astrophysics Data System (ADS)

    Soriano, Alejandro; Silla, Estanislao; Tuñón, Iñaki

    2002-04-01

    The dissociative electron transfer reaction CH3Cl+e-→CH3•+Cl- in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem (a methylchloride molecule plus an electron) is described using density functional theory while the solvent (300 water molecules) is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force (PMF) for the carbon-chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Marcus' relationship, originally developed for electron transfer processes not involving bond breaking. We also investigated dynamical aspects by means of 60 dissociative trajectories started with the addition of an extra electron to different configurations of a methylchloride molecule in solution. The PMF shows the existence of a very flat region, in which the system is trapped during some finite time if the quantum subsystem quickly losses its excess kinetic energy transferring it to the solvent molecules. One of the most important factors determining the effectiveness of this energy transfer seems to be the existence of close contacts (hydrogen bonds) between the solute and the solvent.

  11. Electron-impact dissociation and ionization of NH+ and ND+

    NASA Astrophysics Data System (ADS)

    Lecointre, J.; Belic, D. S.; Jureta, J. J.; Cherkani-Hassani, S.; Defrance, P.

    2012-11-01

    Electron-impact dissociation and ionization of NH+ and ND+ ions leading to formation of D+, N+ and N2+ products have been measured by applying the animated electron-ion beam method in the energy range from respective thresholds up to 2.5 keV. Absolute cross sections are determined separately for dissociative excitation (DE), dissociative ionization (DI) and for asymmetric dissociative ionization (ADI) processes.

  12. Wavepacket theory of collisional dissociation in molecules

    SciTech Connect

    Kulander, K.

    1980-01-01

    An explicit integration scheme is used to solve the time dependent Schroedinger equation for wavepackets which model collisions in the collinear H + H/sub 2/ system. A realistic LEPS-type potential energy surface is used. Collision energies considered are above the dissociation threshold and probabilities for collision induced dissociation are reported. Also quantum mechanical state-to-state transition probabilities are generated. These results are compared to extensive classical trajectory calculations performed on this same system. The time evolution of the wavepacket densities is studied to understand the dynamics of the collinear collisional dissociation process.

  13. Using beryllium bonds to change halogen bonds from traditional to chlorine-shared to ion-pair bonds.

    PubMed

    Alkorta, Ibon; Elguero, José; Mó, Otilia; Yáñez, Manuel; Del Bene, Janet E

    2015-01-21

    Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the structures, binding energies, and bonding characteristics of binary complexes HFBe:FCl, R2Be:FCl, and FCl:N-base, and of ternary complexes HFBe:FCl:N-base and R2Be:FCl:N-base for R = H, F, Cl; N-base = NH3, NHCH2, NCH. Dramatic synergistic cooperative effects have been found between the Be···F beryllium bonds and the Cl···N halogen bonds in ternary complexes. The Cl···N traditional halogen bonds and the Be···F beryllium bonds in binary complexes become significantly stronger in ternary complexes, while the F-Cl bond weakens. Charge-transfer from F to the empty p(σ) orbital of Be leads to a bending of the XYBe molecule and a change in the hybridization of Be, which in the limit becomes sp(2). As a function of the intrinsic basicity of the nitrogen base and the intrinsic acidity of the Be derivative, the halogen-bond type evolves from traditional to chlorine-shared to ion-pair bonds. The mechanism by which an ion-pair complex is formed is similar to that involved in the dissociative proton attachment process. EOM-CCSD spin-spin coupling constants (1X)J(Cl-N) across the halogen bond in these complexes also provide evidence of the same evolution of the halogen-bond type. PMID:25486548

  14. [Dissociative symptoms and sleep].

    PubMed

    Giesbrecht, T; Merckelbach, H

    2006-01-01

    There is a widespread view among psychiatrists that dissociative experiences such as depersonalisation, derealisation, absorption, and psychogenic amnesia have a traumatic etiology. This view is subjected to a critical evaluation. We also discuss an alternative interpretation namely that dissociative experiences are caused by a labile sleep-wake rhythm. We evaluated this alternative view in two exploratory studies. In study 1 we looked at the relationship between the Dissociative Experience Scale (DES) and the Iowa Sleep Experiences Survey (ISES) and in study 2, we checked this relationship when the response bias was controlled for. Dissociative experiences (measured with the DES) correlated with the ISES. The correlation between DES and ISES remained completely intact even when we controlledfor response bias. Our findings show that dissociative symptoms are associated with typical sleep experiences such as nightmares and strange dreams. The association is not the by-product of the positive response bias which generally characterises persons with dissociative symptoms. PMID:16956084

  15. Electronic structure, charge transfer and bonding in intermetallics using EELS and density functional theory[Electron Energy Loss Spectroscopy

    SciTech Connect

    Humphreys, C.J.; Botton, G.A.; Pankhurst, D.A.; Keast, V.J.; Temmerman, W.M.

    1999-07-01

    Electron energy loss spectroscopy and density functional theory have been used to show that there is a covalent component to the bonding in NiAl, CoAl and FeAl, between the transition metal atom and Al. There is no charge transfer and no ionic component to the bonding in NiAl and probably not in CoAl and FeAl. The bonding is non-stoichiometric NiAl is studied. Preliminary results are given for a {Sigma}{sub 3} boundary in NiAl.

  16. The Pairwise Correlated Generalized Valence Bond Model of Electronic Structure I; The Estimation of Pair Energies from Orbital Overlaps

    PubMed Central

    Petersson, G. A.

    1974-01-01

    A new method for the accurate a priori calculation of atomic and molecular energies is proposed. The new method agrees with experiment to within less than 1 kcal/mole in all cases examined thus far, and is applicable to excited states and to transition states for chemical reactions. Since the new method corrects the results of generalized valence bond calculations for the effects of electron pair correlations, we call the new method the pairwise correlated generalized valence bond method. PMID:16592172

  17. Threshold collision-induced dissociation of diatomic molecules: A case study of the energetics and dynamics of O{sub 2}{sup -} collisions with Ar and Xe

    SciTech Connect

    Ahu Akin, F.; Ree, Jongbaik; Ervin, Kent M.; Hyung, Kyu Shin

    2005-08-08

    The energetics and dynamics of collision-induced dissociation of O{sub 2}{sup -} with Ar and Xe targets are studied experimentally using guided ion-beam tandem mass spectrometry. The cross sections and the collision dynamics are modeled theoretically by classical trajectory calculations. Experimental apparent threshold energies are 2.1 and 1.1 eV in excess of the thermochemical O{sub 2}{sup -} bond dissociation energy for argon and xenon, respectively. Classical trajectory calculations confirm the observed threshold behavior and the dependence of cross sections on the relative kinetic energy. Representative trajectories reveal that the bond dissociation takes place on a short time scale of about 50 fs in strong direct collisions. Collision-induced dissociation is found to be remarkably restricted to the perpendicular approach of Ar/Xe to the molecular axis of O{sub 2}{sup -}, while collinear collisions do not result in dissociation. The higher collisional energy-transfer efficiency of xenon compared with argon is attributed to both mass and polarizability effects.

  18. Tripartite efflux pumps: energy is required for dissociation, but not assembly or opening of the outer membrane channel of the pump

    PubMed Central

    Janganan, Thamarai K; Bavro, Vassiliy N; Zhang, Li; Borges-Walmsley, Maria Inês; Walmsley, Adrian R

    2013-01-01

    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. PMID:23565750

  19. Effect of aging on surface chemical bonds of PTFE irradiated by low energy Ti ion

    NASA Astrophysics Data System (ADS)

    Zhang, Jizhong; Zhang, Xiaoji; Zhou, Hongyu

    2003-01-01

    Polytetrafluoroethylene (PTFE) was irradiated by low energy titanium ion in a metal vapor vacuum arc (MEVVA) implanter. The samples were irradiated with 80 keV Ti ion with fluences from 5×10 15 to 5×10 17 Ti/cm 2, respectively. Transportation of Ion in Matters (TRIM) code was employed to simulate Ti ion irradiation. The as-irradiated samples were investigated by ESCA, SEM and wettability. As increasing ion fluence, various chemical bonds and irradiation-damaged surfaces were observed. The water droplet contact angel of PTFE samples increased gradually with ion fluence. All the as-irradiated PTFE samples were aged in air for 1 year. After aging the surface-restructuring behavior was observed on the surfaces of the samples irradiated with ion fluence equal to or less than 5×10 16 Ti/cm 2, which resulted in decrease of the droplet contact angle of these samples. The surface roughness change of the aged samples, which were measured by atomic force microscopy (AFM), was consistent with the droplet contact angle change. The experimental results revealed that Ti ion fluence closely affected the surface chemical bond, morphology and wettability, as well as the aging stability of the as-irradiated PTFE samples.

  20. On the mean kinetic energy of the proton in strong hydrogen bonded systems.

    PubMed

    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. PMID:26851916

  1. Zero-kinetic-energy photoelectron spectroscopy of the hydrogen-bonded phenol-water complex

    NASA Astrophysics Data System (ADS)

    Dopfer, Otto; Reiser, Georg; Müller-Dethlefs, Klaus; Schlag, Edward W.; Colson, Steven D.

    1994-07-01

    Two-photon, two-color (1+1') zero-kinetic-energy (ZEKE) photoelectron spectra are presented for the 1:1 phenol-water complex, a prototype system for hydrogen bonding between an aromatic molecule and a simple solvent. ZEKE spectra via different (intermolecular) vibrational intermediate S1 levels of the fully protonated complex (C6H5OH-H2O, h3) as well as the ZEKE spectrum via the vibrationless S1 state of the threefold deuterated complex (C6H5OD-D2O, d3) have been recorded. The spectra are rich in structure, which is mainly attributable to intermolecular vibrations of the ionic complex. Progressions of the intermolecular stretch vibration (240 cm-1) in combination with different intermolecular and intramolecular vibrational levels are the dominant feature of all ZEKE spectra obtained and indicate a large change in the complex geometry along the hydrogen-bond coordinate on ionization. Comparison between the spectrum of the d3 complex and the spectra via different intermediate intermolecular levels of the h3 complex has allowed a more detailed analysis of the intermolecular features compared to previously reported results. Finally, the vibrational assignments obtained are compared with ab initio results for the phenol-water cation reported in the following paper in this issue.

  2. 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.

  3. Protein collapse driven against solvation free energy without H-bonds.

    PubMed

    Karandur, Deepti; Harris, Robert C; Pettitt, B Montgomery

    2016-01-01

    Proteins collapse and fold because intramolecular interactions and solvent entropy, which favor collapse, outweigh solute-solvent interactions that favor expansion. Since the protein backbone actively participates in protein folding and some intrinsically disordered proteins are glycine rich, oligoglycines are good models to study the protein backbone as it collapses, both during conformational changes in disordered proteins and during folding. The solvation free energies of short glycine oligomers become increasingly favorable as chain length increases. In contrast, the solubility limits of glycine oligomers decrease with increasing chain length, indicating that peptide-peptide, and potentially solvent-solvent interactions, overcome peptide-solvent interactions to favor aggregation at finite concentrations of glycine oligomers. We have recently shown that hydrogen- (H-) bonds do not contribute significantly to the concentration-based aggregation of pentaglycines but that dipole-dipole (CO) interactions between the amide groups on the backbone do. Here we demonstrate for the collapse of oligoglycines ranging in length from 15 to 25 residues similarly that H-bonds do not contribute significantly to collapse but that CO dipole interactions do. These results illustrate that some intrapeptide interactions that determine the solubility limit of short glycine oligomers are similar to those that drive the collapse of longer glycine peptides. PMID:26174309

  4. Collision-induced dissociation of transition metal-oxide ions: dynamics of VO+ collision with Xe.

    PubMed

    Ree, J; Kim, Y H; Shin, H K

    2006-02-21

    The collision-induced dissociation of VO(+) by Xe has been studied by the use of classical dynamics procedures on London-Eyring-Polanyi-Sato potential-energy surfaces in the collision energy range of 5.0-30 eV. The dissociation threshold behavior and the dependence of reaction cross sections on the collision energy closely follow the observed data with the threshold energy of 6.00 eV. The principal reaction pathway is VO(+) + Xe --> V(+)+ O + Xe and the minor pathway is VO(+) + Xe--> VXe(+) + O. At higher collision energies (E > 8.0 eV), the former reaction preferentially occurs near the O-V(+)...Xe collinear and perpendicular alignments, but the latter only occurs near the perpendicular alignment. At lower energies close to the threshold, the reactions are found to occur near the collinear configuration. No reaction occurs in the collinear alignment V(+)-O...Xe. The high and low energy-transfer efficiencies of the collinear alignments O-V(+)...Xe and V(+)-O...Xe are attributed to the effects of mass distribution. The activation of the VO(+) bond toward the dissociation threshold occurs through a translation-to-vibration energy transfer in a strong collision on a time scale of about 50 fs. PMID:16497036

  5. Dynamic strength of molecular adhesion bonds.

    PubMed Central

    Evans, E; Ritchie, K

    1997-01-01

    In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale of molecular motions. Using results from a simulation of biotin-avidin bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., this issue), we describe how Brownian dynamics can help bridge the gap between molecular dynamics and probe tests. Images FIGURE 2 PMID:9083660

  6. Hydrogen dissociation below 1 K

    NASA Astrophysics Data System (ADS)

    Helffrich, J.; Maley, M.; Krusius, M.; Wheatley, J. C.

    1987-03-01

    We report on an investigation of hydrogen dissociation at dilution refrigerator temperatures. The objective of this study is to develop a low-temperature hydrogen atom source for experiments on spin-polarized atomic hydrogen. We find that, in a discharge tube coated with a solid H2 layer and a superfluid He film, hydrogen dissociation is mediated by a glow discharge supported by He vapor. The He discharge provides the energetic particles needed for removing H atoms from the solid H2 coating. In order to strike a He discharge, the He vapor pressure has to correspond to a wall temperature of 0.60 0.75 K. The best results are obtained close to the low-temperature threshold for ignition, or at even lower temperatures if the rf discharge pulse is preceded by a heat pulse adjusted to flash-evaporate the required initial He density. Hydrogen atom yields of 1013 H/discharge pulse are typical, and scale with the pulsed rf energy as long as the discharge volume is not overheated and remains in good thermal contact with its cooling jacket. In these conditions the H flux from the dissociator is proportional to the average rf power with a dissociation efficiency of ˜3%. With a dilution refrigerator circulation of 0.3 mmole/sec of3He, H fluxes of 5×1013 H/sec are obtained in steady-state discharge conditions.

  7. Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Lin, Ming-Fu; Neumark, Daniel M.; Gessner, Oliver; Leone, Stephen R.

    2014-02-01

    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH2=CHBr, are probed using femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy. Strong-field ionization is initiated with an intense femtosecond, near infrared (NIR, 775 nm) laser field. Femtosecond XUV pulses covering the photon energy range of 50-72 eV probe the subsequent dynamics by measuring the time-dependent spectroscopic features associated with transitions of the Br (3d) inner-shell electrons to vacancies in molecular and atomic valence orbitals. Spectral signatures are observed for the depletion of neutral C2H3Br, the formation of C2H3Br+ ions in their ground ({tilde X}) and first excited (tilde A) states, the production of C2H3Br++ ions, and the appearance of neutral Br (2P3/2) atoms by dissociative ionization. The formation of free Br (2P3/2) atoms occurs on a timescale of 330 ± 150 fs. The ionic tilde A state exhibits a time-dependent XUV absorption energy shift of ˜0.4 eV within the time window of the atomic Br formation. The yield of Br atoms correlates with the yield of parent ions in the tilde A state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C2H3Br+ (tilde A) ions undergoes intramolecular vibrational energy redistribution followed by the C-Br bond dissociation. The C2H3Br+ ({tilde X}) products and the majority of the C2H3Br++ ions are relatively stable due to a deeper potential well and a high dissociation barrier, respectively. The results offer powerful new insights about orbital-specific electronic processes in high field ionization, coupled vibrational relaxation and dissociation dynamics, and the correlation of valence hole-state location and dissociation in polyatomic molecules, all probed simultaneously by ultrafast table-top XUV spectroscopy.

  8. Ionization and dissociation dynamics of vinyl bromide probed by femtosecond extreme ultraviolet transient absorption spectroscopy.

    PubMed

    Lin, Ming-Fu; Neumark, Daniel M; Gessner, Oliver; Leone, Stephen R

    2014-02-14

    Strong-field induced ionization and dissociation dynamics of vinyl bromide, CH2=CHBr, are probed using femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy. Strong-field ionization is initiated with an intense femtosecond, near infrared (NIR, 775 nm) laser field. Femtosecond XUV pulses covering the photon energy range of 50-72 eV probe the subsequent dynamics by measuring the time-dependent spectroscopic features associated with transitions of the Br (3d) inner-shell electrons to vacancies in molecular and atomic valence orbitals. Spectral signatures are observed for the depletion of neutral C2H3Br, the formation of C2H3Br(+) ions in their ground (X̃) and first excited (Ã) states, the production of C2H3Br(++) ions, and the appearance of neutral Br ((2)P3/2) atoms by dissociative ionization. The formation of free Br ((2)P3/2) atoms occurs on a timescale of 330 ± 150 fs. The ionic à state exhibits a time-dependent XUV absorption energy shift of ∼0.4 eV within the time window of the atomic Br formation. The yield of Br atoms correlates with the yield of parent ions in the à state as a function of NIR peak intensity. The observations suggest that a fraction of vibrationally excited C2H3Br(+) (Ã) ions undergoes intramolecular vibrational energy redistribution followed by the C-Br bond dissociation. The C2H3Br(+) (X̃) products and the majority of the C2H3Br(++) ions are relatively stable due to a deeper potential well and a high dissociation barrier, respectively. The results offer powerful new insights about orbital-specific electronic processes in high field ionization, coupled vibrational relaxation and dissociation dynamics, and the correlation of valence hole-state location and dissociation in polyatomic molecules, all probed simultaneously by ultrafast table-top XUV spectroscopy. PMID:24527919

  9. The vibrational dynamics of 3D HOCl above dissociation

    SciTech Connect

    Lin, Yi-Der; Reichl, L. E.; Jung, Christof

    2015-03-28

    We explore the classical vibrational dynamics of the HOCl molecule for energies above the dissociation energy of the molecule. Above dissociation, we find that the classical dynamics is dominated by an invariant manifold which appears to stabilize two periodic orbits at energies significantly above the dissociation energy. These stable periodic orbits can hold a large number of quantum states and likely can support a significant quasibound state of the molecule, well above the dissociation energy. The classical dynamics and the lifetime of quantum states on the invariant manifold are determined.

  10. Collision induced dissociation study of azobenzene and its derivatives: computational and experimental results

    NASA Astrophysics Data System (ADS)

    Rezaee, Mohammadreza; Compton, Robert

    2015-03-01

    Experimental and computational investigation have been performed in order to study the bond dissociation energy of azobenzene and its derivatives using collision induced dissociation method as well as other energy and structural characteristics. The results have been verified by comparing with results obtained from computational quantum chemistry. We used different density functional methods as well as the Möller-Plesset perturbation theory and the coupled cluster methods to explore geometric, electronic and the spectral properties of the sample molecules. Geometries were calculated and optimized using the 6-311 + + G(2d,2p) basis set and the B3LYP level of theory and these optimized structures have been subjected to the frequency calculations to obtain thermochemical properties by means of different density functional, Möller-Plesset, and coupled cluster theories to obtain a high accuracy estimation of the bond dissociation energy value. The results from experiments and the results obtained from computational thermochemistry are in close agreement. Physics and Astronomy Department

  11. Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation

    SciTech Connect

    Zhang, Haizhen; Yang, Feng; Qian, Weijun; Brown, Roslyn N.; Wang, Yuexi; Merkley, Eric D.; Park, Jea H.; Monroe, Matthew E.; Purvine, Samuel O.; Moore, Ronald J.; Shi, Liang; Fredrickson, Jim K.; Pasa-Tolic, Ljiljana; Smith, Richard D.; Lipton, Mary S.

    2011-10-01

    c-type cytochromes play essential roles in many biological activities of both prokaryotic and eukaryotic cells, including electron transfer, enzyme catalysis and induction of apoptosis. We report a novel enrichment strategy for identifying c-type heme-containing peptides that uses non-activated IMAC resin. The strategy demonstrated at least seven-fold enrichment for heme-containing peptides digested from a cytochrome c protein standard, and quantitative linear performance was also assessed for heme-containing peptide enrichment. Heme-containing peptides extracted from the periplasmic fraction of Shewanella oneidensis MR-1 were further identified using higher-energy collisional dissociation tandem mass spectrometry. The results demonstrated the applicability of this enrichment strategy to identify c-type heme-containing peptides from a highly complex biological sample, and at the same time, confirmed the periplasmic localization of heme-containing proteins during suboxic respiration activities of S. oneidensis MR-1.

  12. Dissociative Photoionization of Diethyl Ether.

    PubMed

    Voronova, Krisztina; Mozaffari Easter, Chrissa M; Covert, Kyle J; Bodi, Andras; Hemberger, Patrick; Sztáray, Bálint

    2015-10-29

    The dissociative photoionization of internal energy selected diethyl ether ions was investigated by imaging photoelectron photoion coincidence spectroscopy. In a large, 5 eV energy range Et2O(+) cations decay by two parallel and three sequential dissociative photoionization channels, which can be modeled well using statistical theory. The 0 K appearance energies of the CH3CHOCH2CH3(+) (H-loss, m/z = 73) and CH3CH2O═CH2(+) (methyl-loss, m/z = 59) fragment ions were determined to be 10.419 ± 0.015 and 10.484 ± 0.008 eV, respectively. The reemergence of the hydrogen-loss ion above 11 eV is attributed to transition-state (TS) switching, in which the second, outer TS is rate-determining at high internal energies. At 11.81 ± 0.05 eV, a secondary fragment of the CH3CHOCH2CH3(+) (m/z = 73) ion, protonated acetaldehyde, CH3CH═OH(+) (m/z = 45) appears. On the basis of the known thermochemical onset of this fragment, a reverse barrier of 325 meV was found. Two more sequential dissociation reactions were examined, namely, ethylene and formaldehyde losses from the methyl-loss daughter ion. The 0 K appearance energies of 11.85 ± 0.07 and 12.20 ± 0.08 eV, respectively, indicate no reverse barrier in these processes. The statistical model of the dissociative photoionization can also be used to predict the fractional ion abundances in threshold photoionization at large temperatures, which could be of use in, for example, combustion diagnostics. PMID:26444101

  13. Dynamics of dissociative photodetachment in cluster anions: O4- and O2--H2O

    NASA Astrophysics Data System (ADS)

    Continetti, Robert E.; Sherwood, Christopher R.; Garner, Mark C.; Hanold, Karl A.; Strong, Karen M.

    1995-09-01

    A preliminary report is presented on experiments using fast ion-beam translational energy spectroscopy to study dissociative photodetachment and photodissociation dynamics in the small cluster ions O4- and O2-(DOT)(H2O). Translational energy and angular distributions of coincident molecular fragments were recorded from the photodestruction of O4- and O2-(DOT)(H2O) at 523, 349, and 262 nm. At each wavelength, the O4- results confirm the existence of at least two distinct channels: dissociative photodetachment (O4- + h(nu) yields O2 + O2 + e-) and photodissociation (O4- + h(nu) yields O2 + O2-). Observation of strongly anisotropic angular distributions shows that dissociation occurs on the time-scale of molecular rotation in both processes. The photodissociation of O4- at 523 nm gives a new value for the O2-O2- bond energy, DO equals 0.39 +/- 0.05 eV. In O2-(DOT)(H2O), a single dissociative photodetachment channel (O2-(DOT)(H2O) + h(nu) yields O2 + H2O + e-) is observed at all wavelengths. Angular distributions from this process are slightly anisotropic and exhibit a small wavelength dependence.

  14. Dissociative recombination and dissociative excitation of 4HeH+: Absolute cross sections and mechanisms

    NASA Astrophysics Data System (ADS)

    Strömholm, C.; Semaniak, J.; Rosén, S.; Danared, H.; Datz, S.; van der Zande, W.; Larsson, M.

    1996-10-01

    Absolute cross sections have been determined for the dissociative recombination and dissociative excitation of 4HeH+ for electron energies below 40 eV. The dissociative recombination cross section is in semiquantitative agreement with recent theoretical results by Sarpal, Tennyson, and Morgan [J. Phys. B 27, 5943 (1994)] and Guberman [Phys. Rev. A 49, R4277 (1994); in XIXth International Conference on the Physics of Electronic and Atomic Collisions, Whistler, Canada, AIP Conf. Proc. No. 360, edited by L. J. Dube, J. B. A. Mitchell, J. W. McConkey, and C. E. Brion (AIP, New York, 1995), p. 307]. The calculated resonant structure below a collision energy of 1 eV was not fully reproduced by the experiment. The quantum states of the dissociative recombination products at 0 eV collision energy have been determined; ground-state helium and excited hydrogen atoms (n=2) are dominantly formed, in agreement with recent predictions by Guberman. The dissociative excitation has an onset around 10 eV and follows the shape of the dissociative recombination cross section, illustrating that both processes start with the formation of doubly excited neutral states that lie in the ionization continuum as well as in the dissociation continuum. The dissociative excitation cross section is in quite good agreement with recent calculations by Orel and Kulander.

  15. Density functional study on positively charged six-coordinate FeO2 porphyrin complex for a trigger of O2 dissociation

    NASA Astrophysics Data System (ADS)

    Kitagawa, Naohiro; Obata, Masao; Oda, Tatsuki

    2016-01-01

    Properties on electronic structure in an Fe-porphyrin (FeP) complex with the proximal imidazole (Im) ligand, a model of active moiety of hemeprotein for analyzing bonding- and separating-processes of dioxygen molecule (O2), were studied by means of spin-polarized density functional theory. It was found that in the ionized model, the bonding stability of O2 was reduced by one order in energy compared with that of the neutral model, implying existence of the state having a large fluctuation between bonded and separated configurations. We proposed a microscopic scenario on O2 dissociation phenomenon in terms of spin-crossover and allosteric mechanism.

  16. Products of Dissociative Recombination in the Ionosphere

    NASA Technical Reports Server (NTRS)

    Cosby, Philip

    1996-01-01

    SRI International undertook a novel experimental measurement of the product states formed by dissociative ro-combination (DR) of C2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and ro-vibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates.

  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. Density function theory study of the adsorption and dissociation of carbon monoxide on tungsten nanoparticles.

    PubMed

    Weng, Meng-Hsiung; Ju, Shin-Pon; Chen, Hsin-Tsung; Chen, Hui-Lung; Lu, Jian-Ming; Lin, Ken-Huang; Lin, Jenn-Sen; Hsieh, Jin-Yuan; Yang, Hsi-Wen

    2013-02-01

    The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk. PMID:23646573

  19. Electronic structure and photoionization dissociation studies of chlorocarbonyl trifluoromethanesulfonate, CF3SO3C(O)Cl

    NASA Astrophysics Data System (ADS)

    Wang, XiaoPeng; Tong, ShengRui; Ge, MaoFa; Wang, WeiGang; Wang, DianXun

    2012-09-01

    Chlorocarbonyl trifluoromethanesulfonate, CF3SO3C(O)Cl, was prepared by heterogeneous reaction of gaseous ClC(O)SCl with CF3SO3Ag. The electronic structure and photoionization dissociation were investigated by HeI photoelectron spectroscopy (PES) and photoionization mass spectroscopy (PIMS). The assignments of the bands in the PES were reasonably supported by previous studies on analogous molecules, as well as the outer-valence Green's function (OVGF) calculations. The experimental first vertical ionization potential of CF3SO3C(O)Cl was determined to be 12.36 eV, which was assigned to the ionization mainly from the oxygen lone pair orbital. It shows three peaks: ClCO+ (63, 65), CF3+ (69) and CFSO2+ (133) in the spectrum of PIMS, with the dominant features being the ClCO+ and CF3+ peaks. According to the calculated bond dissociation energies, the dissociation process was also discussed.

  20. Dissociation kinetics of hydrogen-passivated (100) Si/SiO2 interface defects

    NASA Astrophysics Data System (ADS)

    Stathis, J. H.

    1995-06-01

    The activation energy for thermal dissociation of hydrogen from silicon dangling-bond defects (Pb centers) has been measured using both (111)- and (100)-oriented samples. The behavior of each of the three Pb varieties [P111b at the (111) interface, P100b0 and P100b1 at the (100) interface] is compared. For P111b, excellent agreement with previous results by Brower [Phys. Rev. B 42, 3444 (1990)] is obtained. The activation energies of the (100)-interface Pb centers are slightly higher, assuming the same vibrational frequency, and, unlike that of P111b, are affected by a postoxidation anneal.

  1. Dissociation of H2+ in intense femtosecond laser fields studied by coincidence three-dimensional momentum imaging

    NASA Astrophysics Data System (ADS)

    Wang, P. Q.; Sayler, A. M.; Carnes, K. D.; Xia, J. F.; Smith, M. A.; Esry, B. D.; Ben-Itzhak, I.

    2006-10-01

    The dissociation of H2+ in an intense laser field has been experimentally studied using femtosecond laser pulses at 790nm in the intensity range of 1013-1015W/cm2 . Kinematically complete measurements of both the ionic H+ and neutral H fragments dissociated from a vibrationally excited H2+ beam have been achieved by a coincidence three-dimensional momentum imaging system. Angular-resolved kinetic energy release spectra for a series of different intensity ranges have been obtained using the intensity-difference spectrum method, thus disentangling the problem caused by the intensity volume effect. Our results indicate that the dissociation dynamics are drastically different for “long” (135fs) and “short” (45fs) laser pulses at similar high laser intensities. Specifically, bond softening is found to be the main feature in long pulses, while above threshold dissociation is dominant in short pulses whose durations are comparable with the vibrational period of the molecule. Bond softening in short pulses appears at low kinetic energy release with a narrow angular distribution. The experimental results are well interpreted by solving the time-dependent Schrödinger equation in the Born-Oppenheimer representation without nuclear rotation.

  2. Ab Initio Investigation of O-H Dissociation from the Al-OH2 Complex Using Molecular Dynamics and Neural Network Fitting.

    PubMed

    Ho, Thi H; Pham-Tran, Nguyen-Nguyen; Kawazoe, Yoshiyuki; Le, Hung M

    2016-01-28

    The dissociation dynamics of the O-H bond in Al-OH2 is investigated on an approximated ab initio potential energy surface (PES). By adopting a dynamic sampling method, we obtain a database of 92 834 configurations. The potential energy for each point is calculated using MP2/6-311G (3df, 2p) calculations; then, a 60-neuron feed-forward neural network is utilized to fit the data to construct an analytic PES. The root-mean-square error (rmse) for the training set is reported as 0.0036 eV, while the rmse for the independent testing set is 0.0034 eV. Such excellent fitting accuracy indeed confirms the reliability of the constructed PES. Subsequently, quasi-classical molecular dynamics (MD) trajectories are performed on the constructed PES at various levels of vibrational excitation in the range of 1.03 to 2.23 eV to investigate the probability of O-H bond dissociation. The results indicate a linear relationship between reaction probability and internal energy, from which we can determine the minimum activation internal energy required for the dissociation as 0.62 eV. Moreover, the O-H bond rupture is shown to be highly correlated with the formation of Al-O bond. PMID:26741404

  3. 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.

  4. Butanethiol adsorption and dissociation on Ag (111): A periodic DFT study

    NASA Astrophysics Data System (ADS)

    Li, Aixiao; Piquemal, Jean-Philip; Richardi, Johannes; Calatayud, Monica

    2016-04-01

    The molecular and dissociative adsorption of butanethiol (C4H9SH) on regular Ag (111) surfaces has been studied by means of periodic ab initio density functional techniques. In molecular form, butanethiol is bound to the surface only by weak polarization-induced forces with the C-S axis tilted by 38° relative to the normal surface. The S atom occupies a position between a hollow fcc and a bridge site. In the dissociative adsorption process, the S-H bond breaks leading to butanethiolate. The S atom of the thiolate also occupies a threefold position, slightly displaced to a hollow fcc site compared to the thiol adsorption case. The C-S axis of the thiolate is tilted by about 37°. The calculated adsorption energies show that the butanethiol and butanethiolate have similar adsorption ability. The computed reaction pathway for the S-H dissociation gives an activation energy of 0.98 eV indicating that the thiolate formation from thiol, although not spontaneous at room temperature, might be feasible on silver surfaces. The dissociation process induces both adsorbate and surface polarization with a significant charge transfer from the substrate to the adsorbate.

  5. UV and 532 nm Photo-Dissociation of 2-Nitrotoluene: Observation of Electronically-Excited NO; Emission from Carbon (I); N2-NO Energy Transfer; and Stabilization of 2-Nitrotoluene-Ar Clusters

    NASA Astrophysics Data System (ADS)

    Diez-y-Riega, H.; Eilers, H.

    2012-07-01

    2-nitrotoluene is a taggant used in explosive compounds and also often used as a simulant for nitro-based high explosives. Various spectroscopic techniques focus on the detection of vibrationally excited NO as an indicator for the presence of explosives. We report on the photo-dissociation of 2-nitrotoluene using UV and 532 nm wavelengths. We not only observe vibrationally excited NO in its electronic ground state, but also vibrationally excited NO in its electronic excited state. The photo-dissociation of 2-nitrotoluene leads to the formation of atomic carbon and its emission, overlapping the NO emission, is observed. Energy transfer from laser-excited nitrogen to NO leads to NO emission with long lifetimes. Argon atoms stabilize 2-nitrotoluene molecules and delay their photo-dissociation.

  6. 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. PMID:26670708

  7. Nanoscale metals and semiconductors for the storage of solar energy in chemical bonds

    NASA Astrophysics Data System (ADS)

    Manthiram, Karthish

    The transduction of electrical energy into chemical bonds represents one potential strategy for storing energy derived from intermittent sources such as solar and wind. Driving the electrochemical reduction of carbon dioxide using light requires (1) developing light absorbers which convert photons into electron-hole pairs and (2) catalysts which utilize these electrons and holes to reduce carbon dioxide and oxidize water, respectively. For both the light absorbers and catalysts, the use of nanoscale particles is advantageous, as charge transport length scales are minimized in the case of nanoscale light absorbers and catalytic surface-area-to-volume ratio is maximized for nanoscale catalysts. In many cases, although semiconductors and metals in the form of thin films and foils are increasingly well-characterized as photoabsorbers and electrocatalysts for carbon dioxide reduction, respectively, the properties of their nanoscale counterparts remain poorly understood. This dissertation explores the nature of the light absorption mode of non-stoichiometric semiconductors which are utilized as light absorbers and the development of catalysts with enhanced stability, activity, and selectivity for carbon dioxide reduction. Chapter 1 provides