Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field.

Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.

Reaction dynamics. Vibrational relaxation and microsolvation of DF after F-atom reactions in polar solvents.

Solvent-solute interactions influence the mechanisms of chemical reactions in solution, but the response of the solvent is often slower than the reactive event. Here, we report that exothermic reactions of fluorine (F) atoms in d3-acetonitrile and d2-dichloromethane involve efficient energy flow to vibrational motion of the deuterium fluoride (DF) product that competes with dissipation of the energy to the solvent bath, despite strong solvent coupling. Transient infrared absorption spectroscopy and molecular dynamics simulations show that after DF forms its first hydrogen bond on a subpicosecond time scale, DF vibrational relaxation and further solvent restructuring occur over more than 10 picoseconds. Characteristic dynamics of gas-phase F-atom reactions with hydrogen-containing molecules persist in polar organic solvents, and the spectral evolution of the DF products serves as a probe of solvent reorganization induced by a chemical reaction.

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.

Reaction dynamics of CN radicals with tetrahydrofuran in liquid solutions.

Transient, broadband infra-red absorption spectroscopy with picosecond time resolution has been used to study the dynamics of reactions of CN radicals with tetrahydrofuran (THF) and d(8)-THF in liquid solutions ranging from neat THF to 0.5 M THF in chlorinated solvents (CDCl(3) and CD(2)Cl(2)). HCN and DCN products were monitored via their v(1) (C≡N stretching) and v(3) (C-H(D) stretching) vibrational absorption bands. Transient spectral features indicate formation of vibrationally excited HCN and DCN, and the onsets of absorption via the fundamental bands of HCN and DCN show short (5-15 ps) delays consistent with vibrational relaxation within the nascent reaction products. This interpretation is confirmed by non-equilibrium molecular dynamics simulations employing a newly derived analytic potential energy surface for the reaction in explicit THF solvent. The rate coefficient for reactive formation of HCN (as determined from measurements on both the 1(1)(0) and 3(1)(0) fundamental bands) decreases with increasing dilution of the THF in CDCl(3) or CD(2)Cl(2), showing pseudo-first order kinetic behaviour for THF concentrations in the range 0.5-4.5 M, and a bimolecular rate coefficient of (1.57 ± 0.12) × 10(10) M(-1) s(-1) is derived. Simultaneous analysis of time-dependent HCN 1(1)(0) and 3(1)(0) band intensities following reaction of CN with THF (3.0 M) in CD(2)Cl(2) suggests that C-H stretching mode excitation is favoured, and this deduction is supported by the computer simulations. The results extend our recent demonstration of nascent vibrational excitation of the products of bimolecular reactions in liquid solution to a different, and more strongly interacting class of organic solvents. They serve to reinforce the finding that dynamics (and thus the topology of the reactive potential energy surface) play an important role in determining the nascent product state distributions in condensed phase reactions.

Quasi-classical trajectory study of the dynamics of the Cl + CH4→ HCl + CH3 reaction.

We present an on-the-fly classical trajectory study of the Cl + CH(4)→ HCl + CH(3) reaction using a specific reaction parameter (SRP) AM1 Hamiltonian that was previously optimized for the Cl + ethane reaction [S. J. Greaves et al., J. Phys Chem A, 2008, 112, 9387]. The SRP-AM1 Hamiltonian is shown to be a good model for the potential energy surface of the title reaction. Calculated differential cross sections, obtained from trajectories propagated with the SRP-AM1 Hamiltonian compare favourably with experimental results for this system. Analysis of the vibrational modes of the methyl radical shows different scattering distributions for ground and vibrationally excited products.

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.