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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 N H 2 − (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. [ABSTRACT FROM AUTHOR]

The potential energy surface of N-acetyl-L-tryptophan-N-methylamide (NATMA) is analyzed both in the gas phase and in solution, while the minima are identified using the density functional theory (DFT) with the 6-31 g(d) basis set. The results have concluded that, with two exceptions, the single residue DFT calculations have yielded minima that correspond to the populated regions of the native state values.

A robust method of identifying the sampling of the phase space in classical dynamical simulations is presented. The method provides an efficient way to detect structural changes, isomerizations, during the simulations even for those cases where the bond lengths may not show significant activity.

The relation between thermochromism in polythiophenes and the internal rotation was studied by density functional theory (DFT). It was found that the internal rotation alone was not sufficient to explain the mechanism of thermochromism.

Ab initio calculations can be used to investigate thermodynamical stability of all possible isomers of small oligomers of thiophene. Thermodynamical stability of small oligomers can distinguish various growth possibilities.

A study was conducted to analyze cyclobutadiene and benzocyclobutenes fused to o and p-quinone by computational techniques. The GIAO technique was utilized to determine absolute nuclear magnetic resonance (NMR) shielding values. The fused-ring system between cyclobutadiene and quinone were also examined. Experimental results indicated the preference of cyclobutadiene to fuse to benzene or to fuse to quinone. In addition, the 13C NMR chemical shift correlated with experimental data.

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. [ABSTRACT FROM AUTHOR]