Collision-induced state-changing rate coefficients for cyanogen backbones NCN 3Σ- and CNN 3Σ- in astrophysical environments.

We report quantum calculations involving the dynamics of rotational energy-transfer processes, by collision with He atoms in interstellar environments, of the title molecular species which share the presence of the CN backbone and are considered of importance in those environments. The latter structural feature is taken to be especially relevant for prebiotic chemistry and for its possible role in the processing of the heterocyclic rings of RNA and DNA nucleobases in the interstellar space. We carry out ab initio calculations of their interaction potentials with He atoms and further obtain the state-to-state rotationally inelastic cross sections and rate coefficients over the relevant range of temperatures. The similarities and differences between such species and other similar partners which have been already detected are analyzed and discussed for their significance on internal state populations in interstellar space for the two title molecular radicals.

Three-Body Collisions Driving the Ion-Molecule Reaction C2- + H2 at Low Temperatures.

We report on the three-body reaction rate of C2- with H2 producing C2H- studied in a cryogenic 16-pole radio frequency ion trap. The reaction was measured in the temperature range from 10 to 28 K, where it was found to only take place via three-body collisions. The experimentally determined termolecular rate coefficient follows the form of a·(T/T0)b with T0 = 20 K, where a = 8.2(3) × 10-30 cm6/s and b = -0.82(12) denotes the temperature dependence. We additionally performed accurate ab initio calculations of the forces between the interacting partners and carried out variational transition state theory calculations, including tunneling through the barrier along the minimum energy path. We show that, while a simple classical model can generally predict the temperature dependence, the variational transition state theoretical calculations, including accurate quantum interactions, can explain the dominance of three-body effects in the molecular reaction mechanism and can reproduce the experimentally determined reaction coefficients, linking them to a temperature-dependent coupling parameter for energy dissipation within the transition complex.

The CH-3Σ+ Anion: Inelastic Rate Coefficients from Collisions with He at Interstellar Conditions.

We present accurate ab initio calculations on several properties of a gas-phase system of interest in the interstellar medium (ISM), where the title molecular anion has been often surmised but not yet confirmed by observations. The CH-3Σ+ constitutes the smallest term in the series of longer anionic polyynes which have been observed in the ISM (e.g., C4H- and several others). Hence, its dynamical behavior in collision with He atoms, one of the most abundant atoms in that environment, can provide quantitative indicators on the changes which can occur in the rotational state population of the title anion when driven by this collision dynamics. We therefore report an accurate evaluation of the full potential energy surface (PES) which acts between the molecular anion in its ground vibrational state and the He atom. The relevant inelastic scattering cross sections and the corresponding inelastic rate coefficients are then computed within a quantum treatment of the collisions. We find that the fairly small values of the final inelastic rate coefficients indicate state-changing processes by collisions to be inefficient paths for modifying the rotational state populations of this anion and therefore to aid its possible observation from direct radiative emission in the microwave region.

Dimerization dynamics of carboxylic acids in helium nanodroplets.

The dimerization of molecules in helium nanodroplets is known to preferentially yield structures of higher energy than the global energy minimum structure for a number of quite different monomers. Here, we explore dimerization in this environment using an atomistic model within statistically converged molecular dynamics (MD) trajectories, treating the solvent implicitly through the use of a thermostat, or more explicitly by embedding one monomer in a He100 cluster. The focus is on the two simplest carboxylic acids, formic and acetic, both of which have been studied experimentally. While the global minimum structure, which comprises two CO⋯HO hydrogen bonds, is predicted to be the most abundant dimer in the absence of the helium solvent, this is no longer the case once helium atoms are included. The simulations confirm the importance of kinetic trapping effects and also shed light on the occurrence of specific dynamical effects, leading to the occasional formation of high-energy structures away from minima, such as saddle configurations. Theoretically predicted infrared spectra, based on the MD statistics, are in good agreement with the experimental spectra.

Collision-driven state-changing efficiency of different buffer gases in cold traps: He(1S), Ar(1S) and p-H2(1Σ) on trapped CN-(1Σ).

We employ potential energy surfaces (PES) from ab initio quantum chemistry methods to describe the interaction of the CN-(1Σ) molecule, one of the small anions often studied at low temperatures, with other possible gases which can be employed as buffer in cold ion traps: the He and Ar atoms and the p-H2 molecule. These PESs are used to calculate from quantum multichannel dynamics the corresponding state-changing rate constants between the populated rotational states of the anion, the latter being in its electronic and vibrational ground states. The different cross sections for the collision-driven quenching and excitation processes at low temperatures are compared and further used to model CN- cooling (de-excitation) efficiency under different trap conditions. The interplay of potential coupling strength and mass-scaling effects is discussed to explain the differences of behaviour among the buffer gases. The advantages of being able to perform collisional cooling at higher trap temperatures when using Ar and p-H2 as buffer gases are also discussed.

Vibrational quenching of CN- in collisions with He and Ar.

The vibrational quenching cross sections and corresponding low-temperature rate constants for the ν = 1 and ν = 2 states of CN-(1Σ+) colliding with He and Ar atoms have been computed ab initio using new three-dimensional potential energy surfaces. Little work has been carried out so far on low-energy vibrationally inelastic collisions for anions with neutral atoms. The cross sections and rates calculated at energies and temperatures relevant for both ion traps and astrochemical modeling are found by the present calculations to be even smaller than those of the similar C2 -/He and C2 -/Ar systems, which are in turn of the order of those existing for the collisions involving neutral diatom-atom systems. The implications of our finding in the present case mainly focus on the possible role of small computed rate constants in the dynamics of molecular cooling and the evolution of astrochemical modeling networks.

Energy Landscapes in Photochemical Dissociation of Small Peroxides.

Organic peroxides are known to have important roles in many chemical and biochemical processes such as intermediates in the oxidation of various hydrocarbons, as initiators of free-radical polymerization and cross-linking agents, etc. Consequently, the study of the organic peroxides and their radicals are of fundamental interest and importance. Although several reaction pathways after dissociation of organic peroxides have been successfully identified using time-resolved optical absorption spectroscopy, interpretation of the data can be complicated due to spectral overlap of parent molecules, intermediates, and products. Therefore, a reliable theoretical framework is necessary in case of complex or less studied systems. In this study, we investigated the plausible thermal dissociation pathways of diethyl peroxide, ditert butyl peroxide, and dicumyl peroxide by density functional theory with M06-2X hybrid functional and compared its results to coupled cluster single double and perturbative triple, CCSD(T), level energies. Our results indicate that methyl radical elimination is the main dissociation mechanism for all of the studied peroxides after O-O bond cleavage which has been also observed in experiments. The resulting relative energies of the M06-2X functional were found to have reasonable accuracy in comparison with the CCSD(T) method. We also show that time-dependent density functional theory (TD-DFT) with the M06-2X functional provides a suitable guide for interpretation of time-resolved optical absorption spectra of peroxides. The experimental transient absorption spectra of dicumyl peroxide are interpreted using the theoretically predicted pathways and transient radical species. Both results agree within experimental resolution and accuracy. We propose that the traditionally assigned visible absorption is not due to the cumuloxyl radical and the photodissociation of dicumyl peroxide involves other pathways with extremely short-lived radicals.

Collisional relaxation kinetics for ortho and para NH2- under photodetachment in cold ion traps.

The collisional cooling of the internal rotational states of the nonlinear anion NH2- (1A1), occurring at the low temperature of a cold ion trap under helium buffer gas cooling, is examined via quantum dynamics calculations and ion decay rate measurements. The calculations employ a novel ab initio potential energy surface that describes the interaction anisotropy and range of action between the molecular anions and the neutral He atoms. The state changing integral cross sections are employed to obtain the state-to-state rate coefficients, separately for the ortho- and the para-NH2- ions. These rates are in turn used to compute the state population evolution in the trap for both species, once photodetachment by a laser is initiated in the trap. The present work shows results for the combined losses of both species after the photodetachment laser is switched on and analyzes the differences of loss kinetics between the two hyperfine isomers.

NH2- in a cold ion trap with He buffer gas: Ab initio quantum modeling of the interaction potential and of state-changing multichannel dynamics.

We present an extensive range of accurate ab initio calculations, which map in detail the spatial electronic potential energy surface that describes the interaction between the molecular anion NH2- (1A1) in its ground electronic state and the He atom. The time-independent close-coupling method is employed to generate the corresponding rotationally inelastic cross sections, and then the state-changing rates over a range of temperatures from 10 to 30 K, which is expected to realistically represent the experimental trapping conditions for this ion in a radio frequency ion trap filled with helium buffer gas. The overall evolutionary kinetics of the rotational level population involving the molecular anion in the cold trap is also modelled during a photodetachment experiment and analyzed using the computed rates. The present results clearly indicate the possibility of selectively detecting differences in behavior between the ortho- and para-anions undergoing photodetachment in the trap.

Quantum features of a barely bound molecular dopant: Cs2(3Σu) in bosonic helium droplets of variable size.

We present in this work the study of small (4)He(N)-Cs(2)((3)Σ(u)) aggregates (2 ≤ N ≤ 30) through combined variational, diffusion Monte Carlo (DMC), and path integral Monte Carlo (PIMC) calculations. The full surface is modeled as an addition of He-Cs(2) interactions and He-He potentials. Given the negligible strength and large range of the He-Cs(2) interaction as compared with the one for He-He, a propensity of the helium atoms to pack themselves together, leaving outside the molecular dopant is to be expected. DMC calculations determine the onset of helium gathering at N = 3. To analyze energetic and structural properties as a function of N, PIMC calculations with no bosonic exchange, i.e., Boltzmann statistics, at low temperatures are carried out. At T = 0.1 K, although acceptable one-particle He-Cs(2) distributions are obtained, two-particle He-He distributions are not well described, indicating that the proper symmetry should be taken into account. PIMC distributions at T = 1 K already compare well with DMC ones and show minor exchange effects, although binding energies are still far from having converged in terms of the number of quantum beads. As N increases, the He-He PIMC pair correlation function shows a clear tendency to coincide with the experimental boson-liquid helium one at that temperature. It supports the picture of a helium droplet which carries the molecular impurity on its surface, as found earlier for other triplet dimers.

Structuring a quantum solvent around a weakly bound dopant: the He-Cs2(3Sigma(u)) complex.

The structure and energetics of (3,4)HeCs(2)((3)Sigma(u)) molecules are analyzed from first principles. Fixing the cesium dimer at its equilibrium distance, the electronic structure was determined through ab initio methods at the CCSD(T) level of theory using a large basis set to compute the interaction energies. At the T-shaped geometry, there is a shallow well with a depth of approximately 2 cm(-1) placed at R approximately 6.75 A, R being the distance from the center of mass of Cs(2) to He. That depth gradually decreases to approximately 0.75 cm(-1), while R increases to about 11.5 A at linear arrangements. A simple model of adding atom-atom Lennard-Jones potentials with well-depth and equilibrium distance parameters depending on the angular orientation was found to accurately reproduce the ab initio points. Using this analytical form, variational calculations at zero total angular momentum are performed, predicting a single bound level at approximately -0.106 (approximately -0.042) cm(-1) for the boson (fermion) species. Further calculations using Quantum Monte Carlo methods are carried out and found to be in good agreement with the variational ones. On the basis of the present results, such analytical expression could in turn be used to describe the structure and binding of larger complexes and therefore opens the possibility to further studies involving such aggregates.

Energetics and structures of charged helium clusters: comparing stabilities of dimer and trimer cationic cores.

We present accurate ab initio calculations of the most stable structures of He(n)(+) clusters in order to determine the more likely ionic core arrangements existing after reaching structural equilibrium of the clusters. Two potential energy surfaces are presented: one for the He(2)(+) and the other with the He(3)(+) linear ion, both interacting with one He atom. The two computed potentials are in turn employed within a classical structure optimization where the overall interaction forces are obtained within the sum-of-potentials approximation described in the main text. Because of the presence of many-body effects within the ionic core, we find that the arrangements with He(3)(+) as a core turn out to be energetically preferred, leading to the formation of He(3)(+)(He)(n-3) stable aggregates. Nanoscopic considerations about the relative stability of clusters with the two different cores are shown to give us new information on the dynamical processes observed in the impact ionization experiments of pure helium clusters and the importance of pre-equilibrium evaporation of the ionic dimers in the ionized clusters.

Isomeric Broadening of C60+ Electronic Excitation in Helium Droplets: Experiments Meet Theory.

Helium is considered an almost ideal tagging atom for cold messenger spectroscopy experiments. Although helium is bound very weakly to the ionic molecule of interest, helium tags can lead to shifts and broadenings that we recorded near 963.5 nm in the electronic excitation spectrum of C60+ solvated with up to 100 helium atoms. Dedicated quantum calculations indicate that the inhomogeneous broadening is due to different binding energies of helium to the pentagonal and hexagonal faces of C60+, their dependence on the electronic state, and the numerous isomeric structures that become available for intermediate coverage. Similar isomeric effects can be expected for optical spectra of most larger molecules surrounded by nonabsorbing weakly bound solvent molecules, a situation encountered in many messenger-tagging spectroscopy experiments.

A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for π-stacking interactions: dimers of benzene and planar C6.

A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for π-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C6 moieties. Møller-Plesset (MP2, SCS-MP2) and coupled cluster [CCSD(T)] calculations show that such generated basis sets provide an accurate description of π-stacking systems with favorable computation times compared to the standard augmented basis sets. The addition of these off-center functions eliminates the linear dependence of the augmented basis sets, which is one of the most encountered numerical problems during calculation of the oligomers of polyaromatic hydrocarbons (PAH). In this work, we present a comparative study of the general characteristics of the potential energy surfaces for the parallel stacked and T-shape conformations of benzene and planar C6 clusters, using a combination of cc-PVXZ and our optimized functions. We discuss properties, such as the depth and curvature of the potential functions, short and long distance behavior, and the frictional forces between two model monomers.

A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons.

In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol(-1) more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I2 + naphtalene dimer interaction is almost twice of that of I2 + naphtalene, showing the long range character of the interaction.

Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins.

We report a detailed analysis of the potential energy surface of N-acetyl-l-tryptophan-N-methylamide, (NATMA) both in the gas phase and in solution. The minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. The full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. The calculated energy maps correspond to the intrinsic conformational propensities of the individual NATMA molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. For this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. In native proteins, tryptophan conformations have strong preferences for the beta sheet, right-handed helix, tight turn, and bridge structures. The conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.

Phase-space invariants as indicators of the critical behavior of nanoaggregates.

A phase-space approach is proposed for molecular dynamics simulations, which serve as a bridge between detailed descriptions of microscopic world and macroscopic properties of matter. The introduction-aside from the angular momentum of spatial rotations-of other "hyperangular" momenta (the overall grand angular momentum of a cluster of particles and those describing the deformation and rearrangement modes) permits one to analyze different degrees of freedom and to extract, from simulation data, a kinetic energy partition in terms of phase-space invariants. Model calculations illustrate how these provide specific signatures of critical behavior, such as energy thresholds for openings of chaotic pathways in small clusters and for phase transitions in nanoaggregates.