David R. Glowacki

A combined experimental and theoretical study of the reaction between methylglyoxal and OH/OD radical: OH regeneration

Experimental studies have been conducted to determine the rate coefficient and mechanism of the reaction between methylglyoxal (CH(3)COCHO, MGLY) and the OH radical over a wide range of temperatures (233-500 K) and pressures (5-300 Torr). The rate coefficient is pressure independent with the following temperature dependence: k(3)(T) = (1.83 +/- 0.48) x 10(-12) exp((560 +/- 70)/T) cm(3) molecule(-1) s(-1) (95% uncertainties). Addition of O(2) to the system leads to recycling of OH. The mechanism was investigated by varying the experimental conditions ([O(2)], [MGLY], temperature and pressure), and by modelling based on a G3X potential energy surface, rovibrational prior distribution calculations and master equation RRKM calculations. The mechanism can be described as follows: Addition of oxygen to the system shows that process (4) is fast and that CH(3)COCO completely dissociates. The acetyl radical formed from reaction (4) reacts with oxygen to regenerate OH radicals (5a). However, a significant fraction of acetyl radical formed by reaction (R4) is sufficiently energised to dissociate further to CH(3) + CO (R4b). Little or no pressure quenching of reaction (R4b) was observed. The rate coefficient for OD + MGLY was measured as k(9)(T) = (9.4 +/- 2.4) x 10(-13) exp((780 +/- 70)/T) cm(3) molecule(-1) s(-1) over the temperature range 233-500 K. The reaction shows a noticeable inverse (k(H)/k(D) < 1) kinetic isotope effect below room temperature and a slight normal kinetic isotope effect (k(H)/k(D) > 1) at high temperature. The potential atmospheric implications of this work are discussed.

Temperature dependent kinetics (195-798 K) and H atom yields (298-498 K) from reactions of (1)CH(2) with acetylene, ethene, and propene.

The rate coefficients for the removal of the excited state of methylene, (1)CH(2) (a(1)A(1)), by acetylene, ethene, and propene have been studied over the temperature range 195-798 K by laser flash photolysis, with (1)CH(2) being monitored by laser-induced fluorescence. The rate coefficients of all three reactions exhibit a negative temperature dependence that can be parametrized as k((1)CH(2)+C(2)H(2)) = (3.06 +/- 0.11) x 10(-10) T ((-0.39+/-0.07)) cm(3) molecule(-1) s(-1), k((1)CH(2)+C(2)H(4)) = (2.10 +/- 0.18) x 10(-10) T ((-0.84+/-0.18)) cm(3) molecule(-1) s(-1), k((1)CH(2)+C(3)H(6)) = (3.21 +/- 0.02) x 10(-10) T ((-0.13+/-0.01)) cm(3) molecule(-1) s(-1), where the errors are statistical at the 2sigma level. Removal of (1)CH(2) occurs by chemical reaction and electronic relaxation to ground state triplet methylene. The H atom yields from the reactions of (1)CH(2) with acetylene, ethene, and propene have been determined by laser-induced fluorescence over the temperature range 298-498 K. For the reaction with propene, H atom yields are close to the detection limit, but for acetylene and ethene, the fraction of H atom production is approximately 0.88 and 0.71, respectively, at 298 K, rising to unity by 398 K, with the balance of the reaction with acetylene presumed to be electronic relaxation. Experimental constraints limit studies to a maximum of 1 Torr of bath gas; master equation calculations using an approach that allows treatment of intermediates with deep energy wells have been carried out to explore the role of collisional stabilization for the reaction of (1)CH(2) with acetylene. Stabilization is calculated to be insignificant under the experimental conditions, but does become significant at higher pressures. Between pressures of 100 and 1000 Torr, propyne and allene are formed in similar amounts with a slight preference for propyne. At higher pressures propyne formation becomes about a factor two greater than that of allene, and above 10(5) Torr (300 < T (K) < 600) cyclopropene formation starts to become significant. The implications of temperature-dependent (1)CH(2) relaxation on the roles of (1)CH(2) in chemical mechanisms for soot formation are discussed.

Design and performance of a throughput-matched, zero-geometric-loss, modified three objective multipass matrix system for FTIR spectrometry

The design of and initial results obtained from a multipass matrix system (MMS) for mid-infrared spectroscopy that operates in the Highly Instrumented Reactor for Atmospheric Chemistry (HIRAC) recently constructed in the School of Chemistry at the University of Leeds, is described. HIRAC is an evacuable, temperature variable, photochemical atmospheric reaction chamber. The MMS design is a modified Chernin cell, utilizing three objective mirrors and two field mirrors. In addition to providing the paraxial equations required for design of a throughput matched multipass cell and throughput matched transfer optics, advanced ray tracing simulations have been performed for the Chernin design described herein. The simulations indicate that, for this MMS, which features small off-axis angles and preserves perfectly the focal properties of the original White design, the paraxial equations are nearly exact, throughput losses due to astigmatism are insignificant, and the system has zero theoretical geometric loss. Measurements of the signal incident on the detector at different matrix arrangements confirm the ray trace results, suggesting that geometric loss in this system is insignificant. The MMS described herein provides adequate stability to permit measurements while the chamber mixing fans are on, gives very good detection limits for some representative species, and is easy to align.

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the proteins structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

O2(a1Δg) + Mg, Fe, and Ca: experimental kinetics and formulation of a weak collision, multiwell master equation with spin-hopping.

The first excited electronic state of molecular oxygen, O(2)(a(1)Δ(g)), is formed in the upper atmosphere by the photolysis of O(3). Its lifetime is over 70 min above 75 km, so that during the day its concentration is about 30 times greater than that of O(3). In order to explore its potential reactivity with atmospheric constituents produced by meteoric ablation, the reactions of Mg, Fe, and Ca with O(2)(a) were studied in a fast flow tube, where the metal atoms were produced either by thermal evaporation (Ca and Mg) or by pulsed laser ablation of a metal target (Fe), and detected by laser induced fluorescence spectroscopy. O(2)(a) was produced by bubbling a flow of Cl(2) through chilled alkaline H(2)O(2), and its absolute concentration determined from its optical emission at 1270 nm (O(2)(a(1)Δ(g) - X(3)Σ(g) (-)). The following results were obtained at 296 K: k(Mg + O(2)(a) + N(2) → MgO(2) + N(2)) = (1.8 ± 0.2) × 10(-30) cm(6) molecule(-2) s(-1); k(Fe + O(2)(a) → FeO + O) = (1.1 ± 0.1) × 10(-13) cm(3) molecule(-1) s(-1); k(Ca + O(2)(a) + N(2) → CaO(2) + N(2)) = (2.9 ± 0.2) × 10(-28) cm(6) molecule(-2) s(-1); and k(Ca + O(2)(a) → CaO + O) = (2.7 ± 1.0) × 10(-12) cm(3) molecule(-1) s(-1). The total uncertainty in these rate coefficients, which mostly arises from the systematic uncertainty in the O(2)(a) concentration, is estimated to be ±40%. Mg + O(2)(a) occurs exclusively by association on the singlet surface, producing MgO(2)((1)A(1)), with a pressure dependent rate coefficient. Fe + O(2)(a), on the other hand, shows pressure independent kinetics. FeO + O is produced with a probability of only ∼0.1%. There is no evidence for an association complex, suggesting that this reaction proceeds mostly by near-resonant electronic energy transfer to Fe(a(5)F) + O(2)(X). The reaction of Ca + O(2)(a) occurs in an intermediate regime with two competing pressure dependent channels: (1) a recombination to produce CaO(2)((1)A(1)), and (2) a singlet∕triplet non-adiabatic hopping channel leading to CaO + O((3)P). In order to interpret the Ca + O(2)(a) results, we utilized density functional theory along with multireference and explicitly correlated CCSD(T)-F12 electronic structure calculations to examine the lowest lying singlet and triplet surfaces. In addition to mapping stationary points, we used a genetic algorithm to locate minimum energy crossing points between the two surfaces. Simulations of the Ca + O(2)(a) kinetics were then carried out using a combination of both standard and non-adiabatic Rice-Ramsperger-Kassel-Marcus (RRKM) theory implemented within a weak collision, multiwell master equation model. In terms of atmospheric significance, only in the case of Ca does reaction with O(2)(a) compete with O(3) during the daytime between 85 and 110 km.

Remarkably Slow Rotation about a Single Bond between an sp3-Hybridised Carbon Atom and an Aromatic Ring without ortho Substituents

Look, no ortho substituents! A series of polycycles were prepared by using a three-component Joullié-Ugi reaction. The rate of rotation about the bond between a highly hindered bridgehead and a phenyl ring with no ortho substituents was measured, and was highly dependent on the substitution. Rotamer half-lives of up to 21 h at 298 K were observed (see figure). Rotamers resulting from this restricted rotation were isolated for the first time.A series of polycycles was prepared by using a three-component Joullié-Ugi reaction. The rate of rotation about the bond between a highly hindered bridgehead and a phenyl ring with no ortho substituents was measured by using, in general, variable-temperature HPLC. The rate of rotation was highly dependent on substitution and rotamer half-lives of up to 21 h at 298 K were observed. Insights into the effect of substitution on the rate of rotation were gleaned through electronic structure calculations on closely related derivatives. Rotamers resulting from restricted rotation about a bond between an sp(3)-hybridised carbon atom and a phenyl ring with no ortho substituents were isolated for the first time, and the equilibration of the separated rotamers was followed by using analytical HPLC. It was demonstrated, for the first time, that a highly hindered environment for the sp(3)-hybridised atom is sufficient for slow bond rotation about a single bond between sp(3)- and sp(2)-hybridised carbon atoms.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160u2009000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space

The problem of observing rare events is pervasive among the molecular dynamics community and an array of different types of methods are commonly used to accelerate these long time scale processes. Typically, rare event acceleration methods require an a priori specification of the event to be accelerated. In recent work, we have demonstrated the application of boxed molecular dynamics to energy space, as a way to accelerate rare events in the stochastic chemical master equation. Here we build upon this work and apply the boxed molecular dynamics algorithm to the energy space of a molecule in classical trajectory simulations. Through this new BXD in energy (BXDE) approach we demonstrate that generic rare events (in this case chemical reactions) may be accelerated by multiple orders of magnitude compared to unbiased simulations. Furthermore, we show that the ratios of products formed from the BXDE simulations are similar to those formed in unbiased simulations at the same temperature.