Temperature driven transformations of glycine molecules embedded in interstellar ice.

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

Atomistic simulations of the aggregation of small aromatic molecules in homogenous and heterogenous mixtures.

The relatively weak London dispersion forces are the only interactions that could cause aggregation between simple aromatic molecules. The use of molecular dynamics and high-level ab initio computer simulations has been used to describe the aggregation and interactions between molecular systems containing benzene, naphthalene and anthracene. Mixtures containing one type of molecule (homogenous) and more than one type of molecule (heterogenous) were considered. Our results indicate that as molecular weight increases so does the temperature at which aggregation will occur. In all simulations, the mechanism of aggregation is through small clusters coalescing into larger clusters. The structural analysis of the molecules within the clusters reveals that benzene will orient itself in T-shaped and parallel displaced configurations. Molecules of anthracene prefer to orient themselves in a similar manner to a bulk crystal with no T-shaped configuration observed. The aggregation of these aromatic molecules is discussed in the context of astrochemistry with particular reference to the dust formation region around stars.

Pressure dependent low temperature kinetics for CN + CH3CN: competition between chemical reaction and van der Waals complex formation.

The gas phase reaction between the CN radical and acetonitrile CH3CN was investigated experimentally, at low temperatures, with the CRESU apparatus and a slow flow reactor to explore the temperature dependence of its rate coefficient from 354 K down to 23 K. Whereas a standard Arrhenius behavior was found at T > 200 K, indicating the presence of an activation barrier, a dramatic increase in the rate coefficient by a factor of 130 was observed when the temperature was decreased from 168 to 123 K. The reaction was found to be pressure independent at 297 K unlike the experiments carried out at 52 and 132 K. The work was complemented by ab initio transition state theory based master equation calculations using reaction pathways investigated with highly accurate thermochemical protocols. The role of collisional stabilization of a CNCH3CN van der Waals complex and of tunneling induced H atom abstractions were also considered. The experimental pressure dependence at 52 and 132 K is well reproduced by the theoretical calculations provided that an anharmonic state density is considered for the van der Waals complex CH3CNCN and its Lennard-Jones radius is adjusted. Furthermore, these calculations indicate that the experimental observations correspond to the fall-off regime and that tunneling remains small in the low-pressure regime. Hence, the studied reaction is essentially an association process at very low temperature. Implications for the chemistry of interstellar clouds and Titan are discussed.

Rate constants and branching ratios for the reaction of CH radicals with NH3: a combined experimental and theoretical study.

The reaction between CH radicals and NH(3) molecules is known to be rapid down to at least 23 K {at which temperature k = (2.21 ± 0.17) × 10(-10) cm(3) molecule(-1) s(-1): Bocherel ; et al. J. Phys. Chem. 1996, 100, 3063}. However, there have been only limited theoretical investigations of this reaction and its products are not known. This paper reports (i) ab initio quantum chemical calculations on the energy paths that lead to various reaction products, (ii) calculations of the overall rate constant and branching ratios to different products using transition state and master equation methods, and (iii) an experimental determination of the H atom yield from the reaction. The ab initio calculations show that reaction occurs predominantly via the initial formation of a datively bound HC-NH(3) complex and reveal low energy pathways to three sets of reaction products: H(2)CNH + H, HCNH(2) + H, and CH(3) + NH. The transition state calculations indicate the roles of "outer" and "inner" transition states and yield rate constants between 20 and 320 K that are in moderate agreement with the experimental values. These calculations and those using the master equation approach show that the branching ratio for the most exothermic reaction, to H(2)CNH + H, is ca. 96% throughout the temperature range covered by the calculations, with those to HCNH(2) + H and CH(3) + NH being (4 ± 3)% and <0.3%, respectively. In the experiments, multiple photon dissociation of CHBr(3) was used to generate CH radicals and laser-induced fluorescence at 121.56 nm (VUV-LIF) was employed to observe H atoms. By comparing signals from CH + NH(3) with those from CH + CH(4), where the yield of H atoms is known to be unity, it is possible to estimate that the yield of H atoms from CH + NH(3) is equal to 0.89 ± 0.07 (2σ), in satisfactory agreement with the theoretical estimate.

Direct infrared absorption spectroscopy of benzene dimer.

The direct infrared (IR) absorption spectrum of benzene dimer formed in a free-jet expansion was recorded in the 3.3 µm region for the first time. This has led to the observation of the C-H stretching fundamental mode ν(13) (B(1u)), which is both IR and Raman forbidden in the monomer. Moreover, the IR forbidden and Raman allowed ν(7) (E(2g)) mode has been observed as well. These two modes were found to be red-shifted along with the IR allowed ν(20) (E(1u)) mode, as previously reported by Erlekam et al. [Erlekam; Frankowski; Meijer; Gert von Helden J. Chem. Phys.2006, 124, 171101], using ion-dip spectroscopy, contrary to the blue-shift predicted earlier by theoretical studies. The observation of the ν(13) band indicates that the symmetry is reduced in the dimer, confirming the T-shaped structure observed by Erlekam et al. Our experimental results have not provided any direct evidence for the presence of the parallel displaced geometry, the main objective of the present work, as predicted by theoretical calculations.

A theoretical analysis of the reaction between CN radicals and NH3.

The reaction between CN radicals and NH3 molecules has been studied experimentally over an unusually wide range of temperature (25-716 K). Below 295 K, the rate constant exhibits a strong negative dependence on temperature; that is, it increases sharply as the temperature is lowered. The present work analyses the kinetics of this reaction theoretically, both to explain this unusual temperature-dependence and to identify the major products of the reaction--which have not been well established by experiment. Quantum chemical calculations at the CCSD(T) theoretical level show that the minimum energy path for reaction proceeds: (a) first, via a potential well, which is 39.3 kJ mol(-1) below the energy of the separated reactants, when allowance is made for zero-point energies, corresponding to a quite strongly bound NC-NH3 complex, and (ii) then over a 'submerged' barrier with a crest 10.9 kJ mol(-1) below the energy of the reactants to the products HCN + NH2. These ab initio calculations also demonstrate that there is no low energy path to the products NCNH2 + H. The dynamics of the main reaction have been further investigated using the two transition state model of Klippenstein and co-workers, in which transition state theory is applied at the selected E, J microcanonical level. The rate constants calculated for temperatures between 25 and 200 K are in excellent agreement with the experimental values.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters.

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Interaction between n-Alkane Chains: Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.