Transition state theory | EPFL Graph Search

In chemistry, transition state theory (TST) explains the reaction rates of elementary chemical reactions. The theory assumes a special type of chemical equilibrium (quasi-equilibrium) between reactants and activated transition state complexes. TST is used primarily to understand qualitatively how chemical reactions take place. TST has been less successful in its original goal of calculating absolute reaction rate constants because the calculation of absolute reaction rates requires precise knowledge of potential energy surfaces, but it has been successful in calculating the standard enthalpy of activation (ΔH‡, also written Δ‡Hɵ), the standard entropy of activation (ΔS‡ or Δ‡Sɵ), and the standard Gibbs energy of activation (ΔG‡ or Δ‡Gɵ) for a particular reaction if its rate constant has been experimentally determined. (The ‡ notation refers to the value of interest at the transition state; ΔH‡ is the difference between the enthalpy of the transition state and that of the reactants.

Atmospheric heterogeneous reactions of chlorine and bromine containing molecules

Arnaud Aguzzi

This thesis deals with a laboratory study of heterogeneous reactions involving bromine and chlorine containing reservoir species on alkali salt substrates which are relevant to the marine boundary layer, and on ice substrates which are relevant to the lower stratosphere. The aim is to obtain reliable data on uptake coefficients γ and reaction mechanisms for the sake of extrapolation of results obtained in the laboratory to atmospheric conditions. The experiments have been performed in a Teflon coated Knudsen flow reactor equipped with a quadrupole mass spectrometer. The reactions of BrONO2 with solid alkali halides have been studied at ambient temperature. The initial uptake coefficients γ0 of BrONO2 on NaCl and KBr substrates are γ0 = 0.31 ± 0.10 and γ0 = 0.32 ± 0.09, respectively. For NaCl substrates BrCl, Br2 and HCl and for KBr both Br2 and HBr are observed as products. HCl and HBr result from the interaction of NaCl and KBr, respectively, with HNO3 generated in the hydrolysis of BrONO2 with H2O condensed on the salt sample. Using NaCl we observed Br2 which is formed from heterogeneous BrONO2 decomposition occurring on solid KBr samples. Halogen exchange reactions are competing with hydrolysis and decomposition which also take place on non-reactive salts (NaNO3, Na2SO4). A high rate of initial uptake (0.2 ≤ γ0 ≤ 0.4) and a Br2 yield on the order of 50 % are observed on non-reactive salts with a closed mass balance for Br2. The ClONO2-salt system has been reinvestigated. Experiments on NaCl, KBr (reactive salts) and on NaNO3 and Na2SO4 (non-reactive salts) have been performed. The hydrolysis of ClONO2 was not observable in contrast to heterogeneous decomposition which occurred on non-reactive salts with a Cl2 yield of (25 ± 5) %. Calculations have been performed using a 0-D box model in order to observe the effects of heterogeneous chemistry on sea salt in the marine boundary layer. Chlorine and bromine chemistry is activated by heterogeneous reactions occurring on NaCl and KBr which are the sole sources of chlorine and bromine in the model. Simulations performed with chlorine heterogeneous chemistry and gas phase chemistry indicate: 1) Denitrification of the troposphere (NOy converted to solid nitrates). 2) Increase of the oxidative capacity of the troposphere by the release of Cl atoms. When bromine chemistry is added to the model, the recombination reaction of NO2 with BrO leads to an increase of tropospheric denitrification through formation of BrONO2. Calculations show that at high [NOx], the most important bromine reservoir is BrONO2, while at low [NOx] HOBr is the most important bromine reservoir. The uptake of HNO3 on ice, solid sulfuric acid solutions and solid ternary solutions (STS) has been investigated at 180 to 211 K. The uptake coefficient γ decreases from 0.30 at 180 K to 0.06 at 211 K. The Arrhenius representation shows two distinct regimes. The first at low temperatures (180-190 K) shows a constant value γ of 0.3, whereas the second regime at T > 195 K corresponds to an activation energy of Ea = -7 ± 1 kcal/mol. At a fixed temperature, γ is independent of [HNO3] thus confirming a rate law first order in [HNO3]. The γ values of HNO3 on H2SO4/H2O solid solutions linearly decreases from 0.20 (0.10) at 10 wt % H2SO4 to 0.05 (0.03) at 98 wt % H2SO4 at 180 K (200K). The γ values of HNO3 with STS of H2SO4/HNO3/H2O is equal to 0.10 ± 0.03 in the temperature range 185-195 K at conditions where the composition of the interface was held constant at the given temperature by adding an external flow of H2O. Br2O hydrolysis on ice surfaces occurs rapidly in the chosen temperature range of 180 to 210 K. At a fixed temperature the uptake kinetics follow an apparent first order rate law in [Br2O]. The observed negative temperature dependence leads to an activation energy Ea for heterogeneous hydrolysis of -2.3 ± 0.6 kcal/mol. These facts point towards a complex reaction mechanism implying that the interaction of Br2O with ice is not an elementary reaction. BrONO2 hydrolysis has been measured on bulk (B), condensed (C) and single crystal (SC) ice in the temperature range 180-210 K. On all types of ice, HOBr and Br2O are observed as products. At a fixed temperature the rate law is first order in [BrONO2] with γ ≈ 0.3 at 180 K. The observed negative temperature dependence leads to an activation energy Ea for the hydrolysis of BrONO2 on pure ice of -2.0 ± 0.2, -2.1 ± 0.2 and -6.6 ± 0.3 kcal/mol on (C), (B) and (SC) ice, respectively, pointing towards different kinetics of BrONO2 on these different types of ice. Doping the ice samples with HBr leads to the formation of Br2, preceded by BrONO2 hydrolysis. The Arrhenius representation corresponds to an activation energy of Ea = -1.2 ± 0.2 kcal/mol. We investigated the structural properties of the near-surface region of various types of HX (X = Cl or Br) doped ice. Basically, we studied the time dependent [HX] in the interface region using the fast reaction titration XONO2 + HX → X2 + HNO3. These experiments reveal that HX is located near the surface of the substrate in a well defined region of thickness I. The HX molecules composing the interface are immediately available for the titration reaction, whatever the flow of XONO2. In the temperature range 190-200 K, we measured a value of IHCl = 43 ± 16, 250 ± 50 and 444 ± 120 nm for (SC), (C) and (B) ices, respectively and IHBr = 110 ± 15 nm on (C) ice at 205K. Finally, we assessed the bulk diffusion coefficient for HX, DHX by modeling our results according to Fick's laws of diffusion. We obtained values of DHCl = 4.5·10-15 - 1.0·10-12 cm2/s at 190 K and DHBr = (6.5 ± 3.0)·10-15 cm2/s at 205 K.

EPFL2001

The effect of molecular vibrations and surface structure on the chemisorption of methane on platinum

Marco Sacchi

In this thesis, I report state-resolved measurements of the chemisorption probability of CH4 on Pt(111) and Pt(110)-(1×2) for several rovibrationally excited states (2ν3, ν1+ν4, and 2ν2+ν4) in addition to the ground state. Measurements of the state resolved reactivity as function of the incident translational energy lead to state-resolved reactivity curves for each of the states under study. The relative efficacy of activating the dissociation reaction is obtained for each excited state by comparing the increase in reactivity observed upon excitation of a particular state to the effect of increasing the translational energy of CH4 in the ground state. The results provide clear evidence for mode specific reactivity with the highest efficacy for the stretch-bend combination (ν1+ν4), followed by the stretch overtone (2ν3) and the bend overtone state (2ν2+ν4). The results demonstrate that vibrational activation of CH4/Pt chemisorption process does not simply scale with the total internal energy of the incident CH4 molecule, which is a central assumption of the PC-MURT statistical model for dissociative chemisorption reactions developed by the group of Harrison [Ukraintsev et al., Chem. Phys., 1994. 101(2): p. 1564]. On the contrary, the qualitative predictions of the vibrationally adiabatic model proposed by Halonen et al. [J. Chem. Phys., 2001. 115(12): p. 5611] are in good agreement with our results. The higher efficacy of the ν1+ν4 state can also be rationalized by observing that, at the transition state, the breaking C-H bond is both stretched and bent from its equilibrium geometry, therefore I suggest that this state might have a significant projection on the reaction coordinate [Psofogiannakis et al., J. Phys. Chem. B, 2006. 110 : p. 24593 ; Anghel et al., Phys. Rev. B, 2005. 71 : p. 4]. Comparison between the state-resolved reactivity for CH4(2ν3) on Pt(111) and Ni(111) is used to obtain information about differences in barrier height and transition state location for the dissociation on the two different metals [Bisson et al., J. Phys. Chem., 2007. 111: p. 12679]. Finally, for the more corrugated Pt(110)-(1×2) surface, I determined the state-resolved sticking coefficients for different polar and azimuthal angles of incidence. Comparison between the reaction probability for incidence parallel and perpendicular to the missing rows of this surface shows shadowing effects that are consistent with predominant reactivity of the top layer Pt atoms.

EPFL2008

New methods for the investigation of RNA refolding by NMR spectroscopy

Philipp Wenter

A detailed characterization of the time scales and mechanisms by which RNA molecules change their folding structure upon binding of metabolites or during catalysis is important for the understanding of the different biological functions of RNA. The folding from an unfolded, denaturated state has been extensively studied, establishing hierarchical pathways, in which fast formation of secondary structural elements precedes the folding of tertiary elements. In contrast, only a few examples of time-resolved RNA refolding in the native state have been reported so far. Specifically, NMR spectroscopy has not yet been employed for the investigation of RNA refolding despite its intrinsic sensibility to dynamic structural changes. In the project presented here, new tools for the identification of RNA secondary structures and the quantification of RNA refolding processes by NMR spectroscopy have been developed and employed. Preparation of 15N-labeled phosphoramidites and their sequence-selective introduction into RNA sequences allowed a straightforward identification of base pairs and imino protons by HNN-COSY and 15N HSQC experiments, respectively. Synthesis and introduction of NPE-protected uridines and guanosines into bistable RNA sequences provided a powerful method for the photoinduced preparation of selected RNA folds far from equilibrium. When introduced into bistable RNA sequences they allow to disrupt selected base pairs, thereby destabilizing the associated secondary structures. As a consequence, one out of usually two coexisting fold could be prepared selectively in its caged form. Upon photolysis, the native sequence was released under physiological conditions with completely retained, preselected secondary structure arrangement. Refolding into the thermodynamic equilibrium was subsequently followed by real-time imino proton NMR spectroscopy, providing quantitative, time-resolved and structural information for the refolding processes of three bistable RNA sequences and a Mg2+-induced secondary and tertiary structure refolding. Depending on their topology, these RNA sequences refold either via a dissociative mechanism in which the disruption of existing base pairs precedes the formation of new ones or via an associative mechanism in which new base pairs are formed from initially unpaired sequence regions simultaneously to the detachement of existing base pairs. In the transition state approximately half of the base pairs are disrupted. The investigation of a bistable RNA sequence designed to undergo a topologically favored refolding processes was carried out by exchange sensitive NMR experiments. The introduction of sequence specific 15N-labeles into RNA sequences allowed the implementation of exchange sensitive 1D and 2D 1H/15N-heteronuclear NMR methods which were designed to map very slow exchange. We found that a 34mer RNA sequence exhibits two folds which exchange on the observable time scale (τobs = T1{15N}

EPFL2006