Rate coefficients for the reactions C2H with C2H4, C2H6, and H2 are measured over the temperature range 150?359 K using transient infrared laser absorption spectroscopy. The ethynyl radical is formed by photolysis of C2H2 with a pulsed excimer laser at 193 nm, and its transient absorption is monitored with a color center laser on the Q11(9) line of the A2Π?X2Σ transition at 3593.68 cm-1. Over the experimental temperature range 150?359 K the rate constants of C2H with C2H4, C2H6, and H2 can be fit to the Arrhenius expressions kC2H4 = (7.8 ± 0.6) × 10-11 exp[(134 ± 44)/T], kC2H6 = (3.5 ± 0.3) × 10-11 exp[(2.9 ± 16)/T], and kH2 = (1.2 ± 0.3) × 10-11 exp[(?998 ± 57)]/T cm3 molecule-1 s-1, respectively. The data for C2H with C2H4 and C2H6 indicate a negligible activation energy to product formation shown by the mild negative temperature dependence of both reactions. When the H2 data are plotted together with the most recent high-temperature results from 295 to 854 K, a slight curvature is observed. The H2 data can be fit to the non-Arrhenius form kH2 = 9.2 × 10-18T2.17±0.50 exp[(?478 ± 165)/T] cm3 molecule-1 s-1. The curvature in the Arrhenius plot is discussed in terms of both quantum mechanical tunneling of the H atom from H2 to the C2H radical and bending mode contributions to the partition function.
{"title":"Rate Coefficients of C2H with C2H4, C2H6, and H2 from 150 to 359 K","authors":"Brian J. Opansky, Stephen R. Leone","doi":"10.1021/jp9619604","DOIUrl":"https://doi.org/10.1021/jp9619604","url":null,"abstract":"<p >Rate coefficients for the reactions C<sub>2</sub>H with C<sub>2</sub>H<sub>4</sub>, C<sub>2</sub>H<sub>6</sub>, and H<sub>2</sub> are measured over the temperature range 150?359 K using transient infrared laser absorption spectroscopy. The ethynyl radical is formed by photolysis of C<sub>2</sub>H<sub>2</sub> with a pulsed excimer laser at 193 nm, and its transient absorption is monitored with a color center laser on the Q<sub>11</sub>(9) line of the A<sup>2</sup>Π?X<sup>2</sup>Σ transition at 3593.68 cm<sup>-1</sup>. Over the experimental temperature range 150?359 K the rate constants of C<sub>2</sub>H with C<sub>2</sub>H<sub>4</sub>, C<sub>2</sub>H<sub>6</sub>, and H<sub>2</sub> can be fit to the Arrhenius expressions <i>k</i><sub>C</sub><sub><sub>2</sub></sub><sub>H</sub><sub><sub>4</sub></sub> = (7.8 ± 0.6) × 10<sup>-11</sup> exp[(134 ± 44)/<i>T</i>], <i>k</i><sub>C</sub><sub><sub>2</sub></sub><sub>H</sub><sub><sub>6</sub></sub> = (3.5 ± 0.3) × 10<sup>-11</sup> exp[(2.9 ± 16)/<i>T</i>], and <i>k</i><sub>H</sub><sub><sub>2</sub></sub> = (1.2 ± 0.3) × 10<sup>-11</sup> exp[(?998 ± 57)]/<i>T</i> cm<sup>3</sup> molecule<sup>-1</sup> s<sup>-1</sup>, respectively. The data for C<sub>2</sub>H with C<sub>2</sub>H<sub>4</sub> and C<sub>2</sub>H<sub>6</sub> indicate a negligible activation energy to product formation shown by the mild negative temperature dependence of both reactions. When the H<sub>2</sub> data are plotted together with the most recent high-temperature results from 295 to 854 K, a slight curvature is observed. The H<sub>2</sub> data can be fit to the non-Arrhenius form <i>k</i><sub>H</sub><sub><sub>2</sub></sub> = 9.2 × 10<sup>-18</sup><i>T</i><sup>2.17±0.50</sup> exp[(?478 ± 165)/<i>T</i>] cm<sup>3</sup> molecule<sup>-1</sup> s<sup>-1</sup>. The curvature in the Arrhenius plot is discussed in terms of both quantum mechanical tunneling of the H atom from H<sub>2</sub> to the C<sub>2</sub>H radical and bending mode contributions to the partition function. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp9619604","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"308517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Masahiro Kawasaki, Kunihiro Suto, Yoshihiro Sato, Yutaka Matsumi, Richard Bersohn
The photodissociation dynamics of four chlorine-containing compounds was studied by the ion imaging technique. Two compounds, ClNO and (CH3)3COCl, exhibited strong anisotropy, and the kinetic energy distributions for Cl(2P3/2) and Cl*(2P1/2) were indistinguishable. For CCl4 and SOCl2 the kinetic energy distributions of Cl and Cl* were very different. In all cases most of the chlorine atoms were released in their ground 2P3/2 state. A general explanation is given based on these data and those of others. The process is described in terms of three states whose energies are in the following order:? the ground state, a state correlating with Cl*, and a state correlating with Cl. Sooner or later the Cl state must cross the Cl* state. If the crossing is sooner, i.e. in the Franck?Condon region, Cl and Cl* will have different translational energy distributions. If the crossing is later, i.e. at long distances, Cl and Cl* will have descended a repulsive surface and reached their asymptotic and nearly equal kinetic energies.
{"title":"Ion Imaging of the Photodissociation of Chlorine-Containing Molecules","authors":"Masahiro Kawasaki, Kunihiro Suto, Yoshihiro Sato, Yutaka Matsumi, Richard Bersohn","doi":"10.1021/jp9609343","DOIUrl":"https://doi.org/10.1021/jp9609343","url":null,"abstract":"<p >The photodissociation dynamics of four chlorine-containing compounds was studied by the ion imaging technique. Two compounds, ClNO and (CH<sub>3</sub>)<sub>3</sub>COCl, exhibited strong anisotropy, and the kinetic energy distributions for Cl(<sup>2</sup>P<sub>3/2</sub>) and Cl*(<sup>2</sup>P<sub>1/2</sub>) were indistinguishable. For CCl<sub>4</sub> and SOCl<sub>2</sub> the kinetic energy distributions of Cl and Cl* were very different. In all cases most of the chlorine atoms were released in their ground <sup>2</sup>P<sub>3/2</sub> state. A general explanation is given based on these data and those of others. The process is described in terms of three states whose energies are in the following order:? the ground state, a state correlating with Cl*, and a state correlating with Cl. Sooner or later the Cl state must cross the Cl* state. If the crossing is sooner, i.e. in the Franck?Condon region, Cl and Cl* will have different translational energy distributions. If the crossing is later, i.e. at long distances, Cl and Cl* will have descended a repulsive surface and reached their asymptotic and nearly equal kinetic energies. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp9609343","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"306861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Edward R. Lovejoy, David R. Hanson, L. Gregory Huey
The kinetics of the gas-phase reactions of SO3 with H2O and D2O were studied over the temperature range 250?360 K in N2 with a laminar flow reactor coupled to a chemical ionization mass spectrometer. The SO3 loss is second order in the water concentration, is independent of pressure (20?80 Torr N2, 300 K), and has a strong negative temperature dependence and a significant H/D isotope effect (kH2O ≈ 2kD2O). The yield of sulfuric acid is 1.0 ± 0.5 per SO3 consumed. These observations are consistent with the rapid association of SO3 and H2O to form the adduct H2OSO3 which reacts with water to produce sulfuric acid. The first-order rate coefficients for loss of SO3 by reaction with H2O and D2O are given by kI(s-1) = (2.26 ± 0.85) × 10-43T exp((6544 ± 106)/T)[H2O]2 and (9.45 ± 2.68) × 10-44T exp((6573 ± 82)/T)[D2O]2, where T ≡ K and [H2O, D2O] ≡ molecule cm-3. The errors are the uncertainty at the 95% confidence level for precision only. Analysis of the temperature dependence of the SO3 loss yields an upper limit for the H2O?SO3 bond enthalpy of 13 kcal mol-1.
{"title":"Kinetics and Products of the Gas-Phase Reaction of SO3 with Water","authors":"Edward R. Lovejoy, David R. Hanson, L. Gregory Huey","doi":"10.1021/jp962414d","DOIUrl":"https://doi.org/10.1021/jp962414d","url":null,"abstract":"<p >The kinetics of the gas-phase reactions of SO<sub>3</sub> with H<sub>2</sub>O and D<sub>2</sub>O were studied over the temperature range 250?360 K in N<sub>2</sub> with a laminar flow reactor coupled to a chemical ionization mass spectrometer. The SO<sub>3</sub> loss is second order in the water concentration, is independent of pressure (20?80 Torr N<sub>2</sub>, 300 K), and has a strong negative temperature dependence and a significant H/D isotope effect (<i>k</i><sub>H</sub><sub><sub>2</sub></sub><sub>O</sub> ≈ 2<i>k</i><sub>D</sub><sub><sub>2</sub></sub><sub>O</sub>). The yield of sulfuric acid is 1.0 ± 0.5 per SO<sub>3</sub> consumed. These observations are consistent with the rapid association of SO<sub>3</sub> and H<sub>2</sub>O to form the adduct H<sub>2</sub>OSO<sub>3</sub> which reacts with water to produce sulfuric acid. The first-order rate coefficients for loss of SO<sub>3</sub> by reaction with H<sub>2</sub>O and D<sub>2</sub>O are given by <i>k</i><sup>I</sup>(s<sup>-1</sup>) = (2.26 ± 0.85) × 10<sup>-43</sup><i>T</i> exp((6544 ± 106)/<i>T</i>)[H<sub>2</sub>O]<sup>2</sup> and (9.45 ± 2.68) × 10<sup>-44</sup><i>T</i> exp((6573 ± 82)/<i>T</i>)[D<sub>2</sub>O]<sup>2</sup>, where T ≡ K and [H<sub>2</sub>O, D<sub>2</sub>O] ≡ molecule cm<sup>-3</sup>. The errors are the uncertainty at the 95% confidence level for precision only. Analysis of the temperature dependence of the SO<sub>3</sub> loss yields an upper limit for the H<sub>2</sub>O?SO<sub>3</sub> bond enthalpy of 13 kcal mol<sup>-1</sup>. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp962414d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"308520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. M. A. Koedijk, R. Wannemacher, R. J. Silbey, S. Völker
Time-resolved spectral hole-burning experiments have been performed to probe the dynamics of the S1 ← S0 0?0 transition of bacteriochlorophyll-a at low concentration (1 × 10-5M) in four different glasses (2-methyltetrahydrofuran, protonated and deuterated ethanol, diethyl ether, and triethylamine) as a function of delay time td (from 10-6 to 103 s) and temperature T (1.2?4.2 K). It is shown that spectral diffusion, the broadening of the optical linewidth followed here over nine orders of magnitude in time, increases with temperature as T1.3±0.1 and strongly depends on the glass structure. The functional dependence, however, is not influenced by the specific glass. The variation of the “effective” homogeneous linewidth (Γ‘hom) with T and td is described by a function Γ‘hom(T,td) derived by modifying the standard model of two-level systems (TLS). This revised TLS model, in which the distribution functions of the TLS tunneling parameters are different from those in the standard model, takes into account the common origin of the dependence of Γ‘hom on td and T. It is shown that other hole-burning and photon-echo data reported in the literature can also be fitted by the same function Γ‘hom(T,td). In ethanol glass, the number of TLSs and the amount of spectral diffusion appear to be independent of the probe molecule.
{"title":"Spectral Diffusion in Organic Glasses: Time Dependence of Spectral Holes","authors":"J. M. A. Koedijk, R. Wannemacher, R. J. Silbey, S. Völker","doi":"10.1021/jp961464f","DOIUrl":"https://doi.org/10.1021/jp961464f","url":null,"abstract":"<p >Time-resolved spectral hole-burning experiments have been performed to probe the dynamics of the S<sub>1</sub> ← S<sub>0</sub> 0?0 transition of bacteriochlorophyll-<i>a</i> at low concentration (1 × 10<sup>-5</sup>M) in four different glasses (2-methyltetrahydrofuran, protonated and deuterated ethanol, diethyl ether, and triethylamine) as a function of delay time <i>t</i><sub>d</sub> (from 10<sup>-6</sup> to 10<sup>3</sup> s) and temperature <i>T</i> (1.2?4.2 K). It is shown that spectral diffusion, the broadening of the optical linewidth followed here over nine orders of magnitude in time, increases with temperature as <i>T</i><sup>1.3±0.1</sup> and strongly depends on the glass structure. The functional dependence, however, is not influenced by the specific glass. The variation of the “effective” homogeneous linewidth (Γ‘<sub>hom</sub>) with <i>T</i> and <i>t</i><sub>d</sub> is described by a function Γ‘<sub>hom</sub>(<i>T</i>,<i>t</i><sub>d</sub>) derived by modifying the standard model of two-level systems (TLS). This revised TLS model, in which the distribution functions of the TLS tunneling parameters are different from those in the standard model, takes into account the common origin of the dependence of Γ‘<sub>hom</sub> on <i>t</i><sub>d</sub> and <i>T</i>. It is shown that other hole-burning and photon-echo data reported in the literature can also be fitted by the same function Γ‘<sub>hom</sub>(<i>T</i>,<i>t</i><sub>d</sub>). In ethanol glass, the number of TLSs and the amount of spectral diffusion appear to be independent of the probe molecule. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp961464f","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"284945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The water-induced disproportionation of the electrogenerated superoxide ion (O2-) in acetonitrile, dimethylformamide, and dimethyl sulfoxide media containing various concentrations of water as a Br?nsted acid has been examined by UV?vis spectroscopy. Analysis of the kinetics as a function of O2- and water concentrations and of the measurement time demonstrated that the disproportionation of O2- by water in these media obeys a common mechanism:? O2- + H2O ? HO2? + OH- (k1, k-1) HO2? + O2- → HO2- + O2 (k2) (HO2?, hydroperoxyl radical; HO2-, hydrogen peroxide anion). The solvent dependence of the obtained kinetic parameters of (k1/k-1)k2, k1 and k-1/k2 is discussed in terms of the solvation of O2- and H2O as well as the effective acidities of H2O in different aprotic solvents.
{"title":"Water-Induced Disproportionation of Superoxide Ion in Aprotic Solvents","authors":"Yong Che, Manabu Tsushima, Futoshi Matsumoto, Takeyoshi Okajima, Koichi Tokuda, Takeo Ohsaka","doi":"10.1021/jp9625523","DOIUrl":"https://doi.org/10.1021/jp9625523","url":null,"abstract":"<p >The water-induced disproportionation of the electrogenerated superoxide ion (O<sub>2</sub><sup>-</sup>) in acetonitrile, dimethylformamide, and dimethyl sulfoxide media containing various concentrations of water as a Br?nsted acid has been examined by UV?vis spectroscopy. Analysis of the kinetics as a function of O<sub>2</sub><sup>-</sup> and water concentrations and of the measurement time demonstrated that the disproportionation of O<sub>2</sub><sup>-</sup> by water in these media obeys a common mechanism:? O<sub>2</sub><sup>-</sup> + H<sub>2</sub>O ? HO<sub>2</sub><sup>?</sup> + OH<sup>-</sup> (<i>k</i><sub>1</sub>, <i>k</i><sub>-1</sub>) HO<sub>2</sub><sup>?</sup> + O<sub>2</sub><sup>-</sup> → HO<sub>2</sub><sup>-</sup> + O<sub>2</sub> (<i>k</i><sub>2</sub>) (HO<sub>2</sub><sup>?</sup>, hydroperoxyl radical; HO<sub>2</sub><sup>-</sup>, hydrogen peroxide anion). The solvent dependence of the obtained kinetic parameters of (<i>k</i><sub>1</sub>/<i>k</i><sub>-1</sub>)<i>k</i><sub>2</sub>, <i>k</i><sub>1</sub> and <i>k</i><sub>-1</sub>/<i>k</i><sub>2</sub> is discussed in terms of the solvation of O<sub>2</sub><sup>-</sup> and H<sub>2</sub>O as well as the effective acidities of H<sub>2</sub>O in different aprotic solvents. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp9625523","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"284948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mn2+-doped CdS nanocrystals (1?2 nm in size) dispersed in organic?inorganic silica xerogels are prepared by combining a controlled precipitation of nanocrystals in inverted micelles, a separation as a pure capped cluster powder, and a dispersion in hydrolyzed silicon alkoxide. ESR study identified two Mn2+ sites, one bulklike, and another one which is attributed to ions located near the surface and which represents the main contribution. The average number of Mn2+ per particle is in the 0.2?0.8 range. The luminescence is characteristic of a Mn2+ internal transition, with energy and lifetime as in bulk materials. This bright emission (quantum yield of 7%) corresponds to an energy transfer from surface trapped carriers to Mn2+ ions.
{"title":"CdS:Mn Nanocrystals in Transparent Xerogel Matrices: Synthesis and Luminescence Properties","authors":"G. Counio, S. Esnouf, T. Gacoin, J.-P. Boilot","doi":"10.1021/jp961937i","DOIUrl":"https://doi.org/10.1021/jp961937i","url":null,"abstract":"<p >Mn<sup>2+</sup>-doped CdS nanocrystals (1?2 nm in size) dispersed in organic?inorganic silica xerogels are prepared by combining a controlled precipitation of nanocrystals in inverted micelles, a separation as a pure capped cluster powder, and a dispersion in hydrolyzed silicon alkoxide. ESR study identified two Mn<sup>2+</sup> sites, one bulklike, and another one which is attributed to ions located near the surface and which represents the main contribution. The average number of Mn<sup>2+</sup> per particle is in the 0.2?0.8 range. The luminescence is characteristic of a Mn<sup>2+</sup> internal transition, with energy and lifetime as in bulk materials. This bright emission (quantum yield of 7%) corresponds to an energy transfer from surface trapped carriers to Mn<sup>2+</sup> ions. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp961937i","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"306866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Szetsen S. Lee, Maynard J. Kong, Stacey F. Bent, Chao-Ming Chiang, S. M. Gates
Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) has been applied to characterize amorphous silicon monohydride films before and after reaction with deuterium atoms. The hydride films were grown by chemical vapor deposition on oxide-covered silicon substrates, and the data suggest that the film is terminated by a homogeneous monolayer of primarily dimerized silicon monohydride. Exposure of this film to atomic deuterium causes the replacement of silicon hydride with adsorbed deuterium. Only the monodeuteride is formed by reaction at 200 °C. Reaction at ?110 °C produces mono-, di-, and trideuteride, demonstrating that the isolation of insertion products is temperature-dependent.
{"title":"Infrared Study of the Reactions of Atomic Deuterium with Amorphous Silicon Monohydride","authors":"Szetsen S. Lee, Maynard J. Kong, Stacey F. Bent, Chao-Ming Chiang, S. M. Gates","doi":"10.1021/jp961928+","DOIUrl":"https://doi.org/10.1021/jp961928+","url":null,"abstract":"<p >Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) has been applied to characterize amorphous silicon monohydride films before and after reaction with deuterium atoms. The hydride films were grown by chemical vapor deposition on oxide-covered silicon substrates, and the data suggest that the film is terminated by a homogeneous monolayer of primarily dimerized silicon monohydride. Exposure of this film to atomic deuterium causes the replacement of silicon hydride with adsorbed deuterium. Only the monodeuteride is formed by reaction at 200 °C. Reaction at ?110 °C produces mono-, di-, and trideuteride, demonstrating that the isolation of insertion products is temperature-dependent. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp961928+","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"284953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We have extended Monte Carlo procedures for computing statistical averages over protonation states of a protein to include conformational states of the titrating amino acid side chains. This computational method couples side chain motion and protonation with changes in solution pH. Using a continuum electrostatic model for protein titration, we applied this sampling method to calculate titration curves for lysozyme, myoglobin, and hemoglobin. In addition to the X-ray conformation, each titrating site was allowed to reorient to a conformation with maximum solvent accessibility. For all proteins considered, inclusion of these additional conformations improved agreement with experimental measurements for both overall titration and individual pKas. The results suggest that well-solvated orientations of amino acid side chains are an important factor in determining proton binding characteristics of proteins.
{"title":"Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration","authors":"Paul Beroza, David A. Case","doi":"10.1021/jp9623709","DOIUrl":"https://doi.org/10.1021/jp9623709","url":null,"abstract":"<p >We have extended Monte Carlo procedures for computing statistical averages over protonation states of a protein to include conformational states of the titrating amino acid side chains. This computational method couples side chain motion and protonation with changes in solution pH. Using a continuum electrostatic model for protein titration, we applied this sampling method to calculate titration curves for lysozyme, myoglobin, and hemoglobin. In addition to the X-ray conformation, each titrating site was allowed to reorient to a conformation with maximum solvent accessibility. For all proteins considered, inclusion of these additional conformations improved agreement with experimental measurements for both overall titration and individual p<i>K</i><sub>a</sub>s. The results suggest that well-solvated orientations of amino acid side chains are an important factor in determining proton binding characteristics of proteins. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp9623709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"284954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
W. Li, G. S. Hsiao, D. Harris, R. M. Nyffenegger, J. A. Virtanen, R. M. Penner
Previously, the scanning tunneling microscope has been employed to deposit single nanoscopic silver structures from aqueous silver solutions onto the graphite basal plane surface. In this paper, the mechanism of this electrochemical lithography is elucidated. The deposition of metal occurs via a two-step mechanism following the application of a sample negative pulse to the graphite surface. First, within 5 μs of the application of a bias pulse having an amplitude greater than +4 V (tip positive), the formation of a shallow, circular pit in the surface is observed. If the pulse is sustained for longer durations, the reductive deposition of metal begins to occur at ~10 μs and the volume of the nascent silver nanostructure saturates at 30?50 μs. The resulting metal nanostructure has a disk geometry with typical dimensions of 200?400 ? in diameter and 20?50 ? in height. STM data coupled with electrochemical measurements and computer simulations of the deposition process demonstrate that the silver metal involved in nanostructure formation is initially present as an underpotentially deposited (UPD) monolayer of silver on the surface of the platinum STM tip. After application of a bias pulse, this adsorbed silver is oxidatively desorbed and silver ions migrate across the tip?sample gap and are deposited in the shallow nucleation site in the graphite surface. This adsorbed silver is susceptible to depletion when silver nanostructures are deposited in rapid succession from dilute silver electrolytes.
{"title":"Mechanistic Study of Silver Nanoparticle Deposition Directed with the Tip of a Scanning Tunneling Microscope in an Electrolytic Environment","authors":"W. Li, G. S. Hsiao, D. Harris, R. M. Nyffenegger, J. A. Virtanen, R. M. Penner","doi":"10.1021/jp962328d","DOIUrl":"https://doi.org/10.1021/jp962328d","url":null,"abstract":"<p >Previously, the scanning tunneling microscope has been employed to deposit single nanoscopic silver structures from aqueous silver solutions onto the graphite basal plane surface. In this paper, the mechanism of this electrochemical lithography is elucidated. The deposition of metal occurs via a two-step mechanism following the application of a sample negative pulse to the graphite surface. First, within 5 μs of the application of a bias pulse having an amplitude greater than +4 V (tip positive), the formation of a shallow, circular pit in the surface is observed. If the pulse is sustained for longer durations, the reductive deposition of metal begins to occur at ~10 μs and the volume of the nascent silver nanostructure saturates at 30?50 μs. The resulting metal nanostructure has a disk geometry with typical dimensions of 200?400 ? in diameter and 20?50 ? in height. STM data coupled with electrochemical measurements and computer simulations of the deposition process demonstrate that the silver metal involved in nanostructure formation is initially present as an underpotentially deposited (UPD) monolayer of silver on the surface of the platinum STM tip. After application of a bias pulse, this adsorbed silver is oxidatively desorbed and silver ions migrate across the tip?sample gap and are deposited in the shallow nucleation site in the graphite surface. This adsorbed silver is susceptible to depletion when silver nanostructures are deposited in rapid succession from dilute silver electrolytes. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp962328d","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"284957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christian A. Müller, Marek Maciejewski, René A. Koeppel, Reto Tschan, Alfons Baiker
The contribution of a redox mechanism involving lattice oxygen in the catalytic combustion of methane over PdO/ZrO2 catalysts, prepared from amorphous Pd?Zr alloys, has been studied by means of gas pulse methods, including a novel technique “pulse thermal analysis”, and using labeled catalysts containing Pd18O. Special emphasis was devoted to the influence of the isotope exchange (scrambling) of reactants and products, especially O2 and CO2, with the catalyst on the quantity of 18O-containing reaction products. Substantial amounts of H218O and C18O16O were detected during pulses of a reactant mixture consisting of methane and 16O2 in a ratio 1:4 at 300 and 500 °C. The effect of the oxygen exchange of molecular oxygen with the solid phase proved to be negligible due to its low extent. At 300 °C, at least 20% of the CO2 formed originated from the redox mechanism involving lattice oxygen. At 500 °C, oxygen exchange of CO2 with the catalyst became predominant and precluded determining reliably the proportion of CO2 formed by the redox process. The results indicate that a substantial part of methane is oxidized via a redox process. Consequently, this reaction has to be taken into account when interpreting the catalytic behavior of palladium-based catalysts and explaining the structure?activity relations previously observed.
{"title":"Role of Lattice Oxygen in the Combustion of Methane over PdO/ZrO2: Combined Pulse TG/DTA and MS Study with 18O-Labeled Catalyst","authors":"Christian A. Müller, Marek Maciejewski, René A. Koeppel, Reto Tschan, Alfons Baiker","doi":"10.1021/jp961903a","DOIUrl":"https://doi.org/10.1021/jp961903a","url":null,"abstract":"<p >The contribution of a redox mechanism involving lattice oxygen in the catalytic combustion of methane over PdO/ZrO<sub>2</sub> catalysts, prepared from amorphous Pd?Zr alloys, has been studied by means of gas pulse methods, including a novel technique “pulse thermal analysis”, and using labeled catalysts containing Pd<sup>18</sup>O. Special emphasis was devoted to the influence of the isotope exchange (scrambling) of reactants and products, especially O<sub>2</sub> and CO<sub>2</sub>, with the catalyst on the quantity of <sup>18</sup>O-containing reaction products. Substantial amounts of H<sub>2</sub><sup>18</sup>O and C<sup>18</sup>O<sup>16</sup>O were detected during pulses of a reactant mixture consisting of methane and <sup>16</sup>O<sub>2</sub> in a ratio 1:4 at 300 and 500 °C. The effect of the oxygen exchange of molecular oxygen with the solid phase proved to be negligible due to its low extent. At 300 °C, at least 20% of the CO<sub>2</sub> formed originated from the redox mechanism involving lattice oxygen. At 500 °C, oxygen exchange of CO<sub>2</sub> with the catalyst became predominant and precluded determining reliably the proportion of CO<sub>2</sub> formed by the redox process. The results indicate that a substantial part of methane is oxidized via a redox process. Consequently, this reaction has to be taken into account when interpreting the catalytic behavior of palladium-based catalysts and explaining the structure?activity relations previously observed. </p>","PeriodicalId":58,"journal":{"name":"The Journal of Physical Chemistry ","volume":null,"pages":null},"PeriodicalIF":2.781,"publicationDate":"1996-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1021/jp961903a","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"307036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}