Thermochemical kinetics: does it still give insights?

This tutorial review revisits the subject of the seminal book written by Sidney Benson in 1968. A short summary of the nature of the subject is presented, including its place in the wider world of quantitative chemistry. A number of themes are selected to illustrate its previous and continuing usefulness in evaluating numerical values of important quantities, and probing ideas of reaction mechanism. These include strain enthalpies for biradical combination, chain reactions, why some reactions don't occur and the involvement of carbenes in hydrocarbon rearrangements.

Asymmetric [2,3]-rearrangement of glycine-derived allyl ammonium ylids

The first examples of highly enantioselective [2,3]-sigmatropic rearrangements of acyclic allylic ammonium ylids are reported. Thus, a range of N-{2‘-[(N‘-allyl-N‘,N‘-dialkyl)ammonium]}acetyl camphor sultams undergo rearrangement at 0 °C in DME solution with high diastereofacial control (up to 99:1 dr) to give allylglycines in generally high yield. The power of the method has been demonstrated in a rapid and efficient synthesis of (R)-allyl glycine.

A comparison of two time-domain analysis procedures in the determination of VO2 kinetics by pseudorandom binary sequence exercise testing

The purpose of this study was to apply and compare two time-domain analysis procedures in the determination of oxygen uptake (VO2) kinetics in response to a pseudorandom binary sequence (PRBS) exercise test. PRBS exercise tests have typically been analysed in the frequency domain. However, the complex interpretation of frequency responses may have limited the application of this procedure in both sporting and clinical contexts, where a single time measurement would facilitate subject comparison. The relative potential of both a mean response time (MRT) and a peak cross-correlation time (PCCT) was investigated. This study was divided into two parts: a test-retest reliability study (part A), in which 10 healthy male subjects completed two identical PRBS exercise tests, and a comparison of the VO2 kinetics of 12 elite endurance runners (ER) and 12 elite sprinters (SR; part B). In part A, 95% limits of agreement were calculated for comparison between MRT and PCCT. The results of part A showed no significant difference between test and retest as assessed by MRT [mean (SD) 42.2 (4.2) s and 43.8 (6.9) s] or by PCCT [21.8 (3.7) s and 22.7 (4.5) s]. Measurement error (%) was lower for MRT in comparison with PCCT (16% and 25%, respectively). In part B of the study, the VO2 kinetics of ER were significantly faster than those of SR, as assessed by MRT [33.4 (3.4) s and 39.9 (7.1) s, respectively; P<0.01] and PCCT [20.9 (3.8) s and 24.8 (4.5) s; P < 0.05]. It is possible that either analysis procedure could provide a single test measurement Of VO2 kinetics; however, the greater reliability of the MRT data suggests that this method has more potential for development in the assessment Of VO2 kinetics by PRBS exercise testing.

Mechanisms of alkylpyrazine formation in a potato model system containing added glycine

The use of glycine to limit acrylamide formation during the heating of a potato model system was also found to alter the relative proportions of alkylpyrazines. The addition of glycine increased the quantities of several alkylpyrazines, and labeling studies using [2-C-13]glycine showed that those alkylpyrazines which increased in the presence of glycine had at least one C-13-labeled methyl substituent derived from glycine. The distribution of C-13 within the pyrazines suggested two pathways by which glycine, and other amino acids, participate in alkylpyrazine formation, and showed the relative contribution of each pathway. Alkylpyrazines that involve glycine in both formation pathways displayed the largest relative increases with glycine addition. The study provided an insight into the sensitivity of alkylpyrazine formation to the amino acid composition in a heated food and demonstrated the importance of those amino acids that are able to contribute an alkyl substituent. This may aid in estimating the impact of amino acid addition on pyrazine formation, when amino acids are added to foods for acrylamide mitigation.

Effect of citric acid and glycine addition on acrylamide and flavor in a potato model system

Acrylamide levels in cooked/processed food can be reduced by treatment with citric acid or glycine. In a potato model system cooked at 180 degrees C for 10-60 min, these treatments affected the volatile profiles. Strecker aldehydes and alkylpyrazines, key flavor compounds of cooked potato, were monitored. Citric acid limited the generation of volatiles, particularly the alkylpyrazines. Glycine increased the total volatile yield by promoting the formation of certain alkylpyrazines, namely, 2,3-dimethylpyrazine, trimethylpyrazine, 2-ethyl-3,5-dimethylpyrazine, tetramethylpyrazine, and 2,5-diethyl-3- methylpyrazine. However, the formation of other pyrazines and Strecker aldehydes was suppressed. It was proposed that the opposing effects of these treatments on total volatile yield may be used to best advantage by employing a combined treatment at lower concentrations, especially as both treatments were found to have an additive effect in reducing acrylamide. This would minimize the impact on flavor but still achieve the desired reduction in acrylamide levels.

Modelling the uptake and growth kinetics of Penicillium glabrum in a tannic acid-containing solid-state fermentation for tannase production

A mathematical growth model for the batch solid-state fermentation process for fungal tannase production was developed and tested experimentally. The unstructured model describes the uptake and growth kinetics of Penicillium glabrum in an impregnated polyurethane foam substrate system. In general, good agreement between the experimental data and model simulations was obtained. Biomass, tannase and spore production are described by logistic kinetics with a time delay between biomass production and tannase and spore formation. Possible induction mechanisms for the latter are proposed. Hydrolysis of tannic acid, the main carbon source in the substrate system, is reasonably well described with Michaelis-Menten kinetics with time-varying enzyme concentration but a more complex reaction mechanism is suspected. The metabolism of gallic acid, a tannase-hydrolysis product of tannic acid, was shown to be growth limiting during the main growth phase. (c) 2004 Elsevier Ltd. All rights reserved.

Kinetics of high pressure facilitated starch gelatinisation in Thai glutinous rice

The combined effect of pressure and temperature on the rate of gelatinisation of starch present in Thai glutinous rice was investigated. Pressure was found to initiate gelatinisation when its value exceeded 200 MPa at ambient temperature. On the other hand, complete gelatinisation was observed at 500 and 600 MPa at 70 degrees C, when the rice was soaked in water under these conditions for 120 min. A first-order kinetic model describing the rate of gelatinisation was developed to estimate the values of the rate constants as a function of pressure and temperature in the range: 0.1-600 MPa and 20-70 degrees C. The model, based on the well-known Arrhenius and Eyring equations, assumed the form [GRAPHICS] The constants k(0), E-a, and Delta V were found to take values: 31.19 s(-1), 37.89 kJ mol(-1) and -9.98 cm(3) mol(-1), respectively. It was further noted that the extent of gelatinisation occurring at any time, temperature and pressure, could be exclusively correlated with the grain moisture content. (c) 2006 Elsevier Ltd. All rights reserved.

Wigner Transport models of the electron-phonon kinetics in quantum wires

Two quantum-kinetic models of ultrafast electron transport in quantum wires are derived from the generalized electron-phonon Wigner equation. The various assumptions and approximations allowing one to find closed equations for the reduced electron Wigner function are discussed with an emphasis on their physical relevance. The models correspond to the Levinson and Barker-Ferry equations, now generalized to account for a space-dependent evolution. They are applied to study the quantum effects in the dynamics of an initial packet of highly nonequilibrium carriers, locally generated in the wire. The properties of the two model equations are compared and analyzed.

Hydrogen bond-induced pair formation of glycine on the chiral Cu{531} surface

Enantio-specific interactions on intrinsically chiral or chirally modified surfaces can be identified experimentally via comparison of the adsorption geometries of similar nonchiral and chiral molecules. Information about the effects of substrate-related and in interactions on the adsorption geometry of glycine, the only natural nonchiral amino acid, is therefore important for identifying enantio-specific interactions of larger chiral amino acids. We have studied the long- and short-range adsorption geometry and bonding properties of glycine on the intrinsically chiral Cu{531} surface with low-energy electron diffraction, near-edge X-ray absorption One structure spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption. For coverages between 0.15 and 0.33 ML (saturated chemisorbed layer) and temperatures between 300 and 430 K, glycine molecules adsorb in two different azimuthal orientations, which are associated with adsorption sites on the {110} and {311} microfacets of Cu{531}. Both types of adsorption sites allow a triangular footprint with surface bonds through the two oxygen atoms and the nitrogen atom. The occupation of the two adsorption sites is equal for all coverages, which can be explained by pair formation due to similar site-specific adsorption energies and the possibility of forming hydrogen bonds between molecules on adjacent {110} and {311} sites. This is not the ease for alanine and points toward higher site specificity in the case of alanine, which is eventually responsible for the enantiomeric differences observed for the alanine system.

Multiplexed quantitative proteomics using differential metabolic 15N-labeling

There are several advantages of using metabolic labeling in quantitative proteomics. The early pooling of samples compared to post-labeling methods eliminates errors from different sample processing, protein extraction and enzymatic digestion. Metabolic labeling is also highly efficient and relatively inexpensive compared to commercial labeling reagents. However, methods for multiplexed quantitation in the MS-domain (or ‘non-isobaric’ methods), suffer from signal dilution at higher degrees of multiplexing, as the MS/MS signal for peptide identification is lower given the same amount of peptide loaded onto the column or injected into the mass spectrometer. This may partly be overcome by mixing the samples at non-uniform ratios, for instance by increasing the fraction of unlabeled proteins. We have developed an algorithm for arbitrary degrees of nonisobaric multiplexing for relative protein abundance measurements. We have used metabolic labeling with different levels of 15N, but the algorithm is in principle applicable to any isotope or combination of isotopes. Ion trap mass spectrometers are fast and suitable for LC-MS/MS and peptide identification. However, they cannot resolve overlapping isotopic envelopes from different peptides, which makes them less suitable for MS-based quantitation. Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry is less suitable for LC-MS/MS, but provides the resolving power required to resolve overlapping isotopic envelopes. We therefore combined ion trap LC-MS/MS for peptide identification with FTICR LC-MS for quantitation using chromatographic alignment. We applied the method in a heat shock study in a plant model system (A. thaliana) and compared the results with gene expression data from similar experiments in literature.

Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O'Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (Q(II)(G)) to the diamond (Q(II)(D)) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the Q(II)(D) phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (H-II) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

Gas-phase kinetics of chlorosilylene reactions II. ClSiH + C2H4: absolute rate measurements and quantum chemical and RRKM calculations for the prototype pi addition reaction

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, are carried out to obtain rate constants for its bimolecular reaction with ethene, C2H4, in the gas-phase. The reaction is studied over the pressure range 0.13-13.3 kPa (with added SF6) at five temperatures in the range 296-562 K. The second order rate constants, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1))=(-10.55 +/- 0.10) + (3.86 +/- 0.70) kJ mol(-1)/RT ln10. The Arrhenius parameters correspond to a loose transition state and the rate constant at room temperature is 43% of that for SiH2 + C2H4, showing that the deactivating effect of Cl-for-H substitution in the silylene is not large. Quantum chemical calculations of the potential energy surface for this reaction at the G3MP2//B3LYP level show that, as well as 1-chlorosilirane, ethylchlorosilylene is a viable product. The calculations reveal how the added effect of the Cl atom on the divalent state stabilisation of ClSiH influences the course of this reaction. RRKM calculations of the reaction pressure dependence suggest that ethylchlorosilylene should be the main product. The results are compared and contrasted with those of SiH2 and SiCl2 with C2H4.

Gas-phase kinetics of chlorosilylene reactions. I. ClSiH + Me3SiH: absolute rate measurements and theoretical calculations for prototype Si−H insertion reactions

Time-resolved studies of chlorosilylene, CISiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane, Me3SiH, in the gas phase. The reaction was studied at total pressures up to 100 torr (with and without added SF6) over the temperature range 297-407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-13.97 +/- 0.25) + (12.57 +/- 1.64) kJ mol(-1)/RT In 10. The Arrhenius parameters are consistent with a mechanism involving an intermediate complex, whose rearrangement is the rate-determining step. Quantum chemical calculations of the potential energy surface for this reaction and also the reactions of CISiH with SiH4 and the other methylsilanes support this conclusion. Comparisons of both experiment and theory with the analogous Si-H insertion processes of SiH2 and SiMe2 show that the main factor causing the lower reactivity of ClSiH is the secondary energy barrier. The calculations also show the existence of a novel intramolecular H-atom exchange process in the complex of ClSiH with MeSiH3.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations

Time-resolved kinetic studies of the reactions of silylene, SiH2, and dideutero-silylene, SiD2, generated by laser. ash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH3C CCH3. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(-1)/RTln10 log(k(D)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTln10 Additionally, pressure-dependent rate coefficients for the reaction of SiH2 with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC4H8 reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH2C(CH3)=C(CH3)-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH3CH=C(CH3)SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H - D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Direct time-resolved study of the kinetics of the reaction of silylene with phenylsilane in the gas phase. Does SiH2 react with the aromatic ring?

Laser flash photolysis studies of silylene, SiH2, generated by the 193 nm laser flash photolysis phenylsilane, PhSiH3, have been carried out to obtain rate constants for its bimolecular reaction with PhSiH3 itself, in the gas phase. The reaction was studied in SF6 (mostly at 10 Torr total pressure) over the temperature range 298-595 K. The rate constants (also found to be pressure independent) gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-9.92 +/- 0.04) + (3.31 +/- 0.27) kJ mol(-1)/RT ln 10 Similar investigations of the reaction of silylene with benzene, C6H6, (295-410 K) gave data suggestive of the fact that SiH2 might be reacting with photochemical products of C6H6 as well as with C6H6 itself. However, in the latter system, apparent rate constants were sufficiently low to indicate that in the reaction of SiH2 with PhSiH3 addition to the aromatic ring was unlikely to be in excess of 3% of the total. Quantum chemical calculations of the energy surface for SiH2 + C6H6 indicate that 7-silanorcaradiene and 7-silacycloheptatriene are possible products but that PhSiH3 formation is unlikely. RRKM calculations suggest that 7-silanorcaradiene should be the initial product but that it cannot be collisionally stabilized under experimental conditions