Struan H. Robertson

A theoretical analysis of the reaction between ethyl and molecular oxygen

Using a combination of electronic-structure theory, variational transition-state theory, and solutions to the time-dependent master equation, the authors have studied the kinetics of the title reaction theoretically over wide ranges of temperature and pressure. The agreement between theory and experiment is quite good. By comparing the theoretical and experimental results describing the kinetic behavior, they have been able to deduce a value for the C{sub 2}H{sub 5}-O{sub 2} bond energy of {approximately}34 kcal/mole and a value for the exit-channel transition-state energy of {minus}4.3 kcal/mole (measured from reactants). These numbers compare favorably with the electronic-structure theory predictions of 33.9 kcal/mole and {minus}3.0 kcal/mole, respectively. The master-equation solutions show three distinct temperature regimes for the reaction, discussed extensively in the paper. Above T {approx} 700 K, the reaction can be written as an elementary step, C{sub 2}H{sub 5} + O{sub 2} {leftrightarrow} C{sub 2}H{sub 4} + HO{sub 2}, with the rate coefficient, k(T) = 3.19 x 10{sup {minus}17} T{sup 1.02} exp(2035/RT) cm{sup 3}/molec.-sec., independent of pressure even though the intermediate collision complex may suffer a large number of collisions.

Interception of excited vibrational quantum states by o2 in atmospheric association reactions

Vibrating in a Crowd High-vacuum molecular beam studies can probe the roles of specific vibrations and rotations on molecular reactivity with remarkably fine resolution. Glowacki et al. (p. 1066; see the Perspective by Tyndall) now show, through a combination of spectroscopy and theoretical modeling, that oxidation of acetylene under effectively atmospheric conditions proceeds in part through vibrationally excited intermediates prior to collisional randomization. Vibrationally excited reaction intermediates play a bigger role under atmospheric conditions than previously suspected. Bimolecular reactions in Earth’s atmosphere are generally assumed to proceed between reactants whose internal quantum states are fully thermally relaxed. Here, we highlight a dramatic role for vibrationally excited bimolecular reactants in the oxidation of acetylene. The reaction proceeds by preliminary adduct formation between the alkyne and OH radical, with subsequent O2 addition. Using a detailed theoretical model, we show that the product-branching ratio is determined by the excited vibrational quantum-state distribution of the adduct at the moment it reacts with O2. Experimentally, we found that under the simulated atmospheric conditions O2 intercepts ~25% of the excited adducts before their vibrational quantum states have fully relaxed. Analogous interception of excited-state radicals by O2 is likely common to a range of atmospheric reactions that proceed through peroxy complexes.

Monte Carlo methods in Materials Studio

We survey the use of the Monte Carlo method within the Materials Studio application, which integrates a large number of modules for molecular simulation. Several of these modules work by generating configurations of a system at random, which can then be used to calculate averages of interest – for instance, interaction energies of contacting pairs of molecules (Blends module) and properties of a flexible polymer chain (Conformers). A different technique is used to sample an appropriate physical distribution (which in practice is that for the canonical ensemble) using the Metropolis or configurational bias method. This is done by the Sorption module (which calculates the thermodynamic properties of small molecules in a matrix) and Amorphous Cell (which constructs periodic simulation cells). Lastly, certain other modules use simulated annealing and related methods to optimise a function, with application to crystal structure prediction from molecular structure (Polymorph Predictor), to crystal structure prediction from X-ray powder diffraction data (Powder Solve) and to find preferential sites for adsorption (Adsorption Locator).

COMPASS II: extended coverage for polymer and drug-like molecule databases

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338–7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

Direct studies on the decomposition of the tert-butoxy radical and its reaction with NO

The first laser induced fluorescence (LIF) spectrum for the tert-butoxy radical is reported following radical generation by excimer laser photolysis of tert-butyl nitrite. The laser flash photolysis-LIF technique is used to measure the temperature dependence of the rate coefficient for the reaction with NO (T=200–390 K): which can be represented in either Arrhenius or AT-n format: and the tert-butoxy decomposition. Whilst the former reaction shows no pressure dependence (p=70–500 Torr of helium), the latter reaction is in the fall-off regime over the entire range of experimental conditions (T=303–393 K, p=13–600 Torr helium). The fall-off data were fitted using an inverse Laplace transformation/master equation model to give the following Arrhenius parameters: These Arrhenius parameters are significantly lower than previous indirect measurements or calculations and the atmospheric and mechanistic implications are discussed.Finally, reaction (3) was also studied by monitoring the temporal dependence of the NO LIF signal following the photolysis of tert-butylnitrite with no additional NO. The results are in good agreement with the tert-butoxy monitoring and allow for an estimation of the rate parameters for the tert-butoxy self reaction.

Analysis of the kinetics and yields of OH radical production from the CH3OCH2 + O2 reaction in the temperature range 195-650 K: an experimental and computational study.

The methoxymethyl radical, CH3OCH2, is an important intermediate in the low temperature combustion of dimethyl ether. The kinetics and yields of OH from the reaction of the methoxymethyl radical with O2 have been measured over the temperature and pressure ranges of 195-650 K and 5-500 Torr by detecting the hydroxyl radical using laser-induced fluorescence following the excimer laser photolysis (248 nm) of CH3OCH2Br. The reaction proceeds via the formation of an energized CH3OCH2O2 adduct, which either dissociates to OH + 2 H2CO or is collisionally stabilized by the buffer gas. At temperatures above 550 K, a secondary source of OH was observed consistent with thermal decomposition of stabilized CH3OCH2O2 radicals. In order to quantify OH production from the CH3OCH2 + O2 reaction, extensive relative and absolute OH yield measurements were performed over the same (T, P) conditions as the kinetic experiments. The reaction was studied at sufficiently low radical concentrations (∼10(11) cm(-3)) that secondary (radical + radical) reactions were unimportant and the rate coefficients could be extracted from simple bi- or triexponential analysis. Ab initio (CBS-GB3)/master equation calculations (using the program MESMER) of the CH3OCH2 + O2 system were also performed to better understand this combustion-related reaction as well as be able to extrapolate experimental results to higher temperatures and pressures. To obtain agreement with experimental results (both kinetics and yield data), energies of the key transition states were substantially reduced (by 20-40 kJ mol(-1)) from their ab initio values and the effect of hindered rotations in the CH3OCH2 and CH3OCH2OO intermediates were taken into account. The optimized master equation model was used to generate a set of pressure and temperature dependent rate coefficients for the component nine phenomenological reactions that describe the CH3OCH2 + O2 system, including four well-skipping reactions. The rate coefficients were fitted to Chebyshev polynomials over the temperature and density ranges 200 to 1000 K and 1 × 10(17) to 1 × 10(23) molecules cm(-3) respectively for both N2 and He bath gases. Comparisons with an existing autoignition mechanism show that the well-skipping reactions are important at a pressure of 1 bar but are not significant at 10 bar. The main differences derive from the calculated rate coefficient for the CH3OCH2OO → CH2OCH2OOH reaction, which leads to a faster rate of formation of O2CH2OCH2OOH.

Canonical flexible transition state theory revisited

A simple formula for the canonical flexible transition state theory expression for the thermal reaction rate constant is derived that is exact in the limit of the reaction path being well approximated by the distance between the centers of mass of the reactants. This formula evaluates classically the contribution to the rate constant from transitional degrees of freedom (those that evolve from free rotations in the limit of infinite separation of the reactants). As a result of this treatment, the formula contains the product of two factors: one that exclusively depends on the collision kinematics and one that exclusively depends on the potential energy surface that controls the transitional degrees of freedom. This second factor smoothly varies, in the classical limit, from harmonic oscillator to hindered rotor to free rotor partition functions as the potential energy surface varies from quadratic to sinusoidal to a constant in its dependence on the relative orientation angles of the fragments. An applica...

Forward and reverse rate coefficients in equilibrating isomerization reactions

Three models for the relaxation kinetics of a reversible unimolecular isomerization reaction are formulated and analyzed: a generalization of the simple Lindemann–Hinshelwood scheme, a detailed model with the strong collision approximation, and a master equation solution. For such systems the use of a classical relaxation analysis has been questioned. In each case it is found that the relaxation analysis does not give forward and reverse rate constants appropriate to the pure irreversible reactions, but that the rate constants so obtained can be interpreted in terms of irreversible schemes which allow for back reaction before collisional stabilization. The accuracy of this decomposition is linked with the applicability of the steady‐state approximation for the populations of the reactive states, as is demonstrated analytically under the strong collision approximation, and numerically with the full master equation. An alternative approach using perturbation theory is shown to be unacceptably inaccurate.

Reaction of CH radicals with methaneisotopomers

The kinetics of the reaction of methylidene [CH(D)] radicals with methane and [ 2 H 4 ]methane have been studied over the temperature range 290–772 K, using pulsed laser flash photolysis of bromoform to generate CH with observation of the resulting temporal CH profile by laser-induced fluorescence. The reactions are all fast [e.g. k 298,CH+CH4 =(9.79±0.37)× 10 -11 cm 3 molecule -1 s -1 ] and exhibit a negative temperature dependence which weakens above 500 K. The reactions can be represented over the experimental temperature range by the following parametrizations, where the error limits on the parameters correspond to ±1 standard deviation (SD): Deuteriation of the methylidene radical has little effect on the kinetics of the reaction, however, deuteriation of methane reduces the rate coefficient by ca. 30% over the entire temperature range. The results of reaction (2) are compared with previous determinations. The isotopic dependence of the reaction is incompatible with a Gorin model of a loose transition state. The suitability of reaction (2) as a calibration reaction, uniquely linking CH and H, is discussed.

Canonical flexible transition-state theory for generalized reaction paths

In previous work (J. Chem. Phys., 995, 103, 2917), simple yet exact formulae for the canonical flexible transition-state theory expression for the thermal reaction-rate constant were derived for all pairings of atomic, linear rigid top, and non-linear rigid top fragments when the distance between the centres of mass of the fragments serves as the reaction coordinate. In this paper, we derive the fundamental modifications required to generalize the reaction coordinate for all fragment-type pairings. That is, the hinge point about which each fragment rotates is no longer constrained to be the centre of mass of the fragment, being in general arbitrarily displaced from the fragment centre of mass. The generalized reaction coordinate is the line connecting the displaced hinge points. It is shown that only the kinetic energy associated with the internal relative motion of the two fragments is affected by a generalized reaction coordinate. The correction to this kinetic energy has a simple functional form whose evaluation for a given fragment-type pairing is straightforward. The ensuing formulae for the canonical rate constant will not be as simple as for the centres-of-mass reaction coordinate case, but are not more difficult to employ computationally. The new theory is applied to the simplest possible fragment-type pairing, atom–diatom, which serves to illustrate the essential features of the method and some of the implications of a generalized reaction coordinate.