A DFT study of the adsorption and surface enhanced Raman spectroscopy of pyridine on Au20, Ag20, and bimetallic Ag8Au12 clusters.

This work presents a theoretical detailed analysis of the surface-enhanced Raman spectroscopy (SERS) of the pyridine - Au20, pyridine - Ag20, and pyridine - Ag8Au12 model systems considering different symmetries of the clusters. In addition to the well-known Td geometry of this twenty atoms metal cluster, low energy structures have been analyzed (Cs and Cb). Density functional methodology with the use of PBE, PBE0, and scalar - relativistic pseudopotentials have been employed for the electronic structure calculations of these molecule-metal complexes. The projected state density analysis has shown a different behavior that distinguishes vertex (V) pyridine position from surface (S) adsorption site on both Td and Cs geometries. Adsorption of pyridine on the V position is always energetically favored as compared to S substitution. The chemical mechanism of enhancement has been analyzed through charge-transfer in the adsorption of pyridine to the metal cluster and charge-transfer excitations between both moieties. There is a close relationship between the amount of charge transfer from the pyridine molecule to the cluster and the SERS enhancements. The highest enhancement factors were obtained precisely for the Au20 cubic structure, where 102 order enhancements were calculated. A back - donation of charge triggers the highest enhancements obtained for this case. The bimetallic case also shows an improvement in the enhancements as compared to Td and Cs geometries. In addition, a direct relationship between resonant charge - transfer excitations in the 500-530 nm range and SERS enhancement have been obtained. Cs and cubic clusters show higher chemical enhancements than Td structures, thus representing a promise as SERS substrates.

Halogen bonding and rotational disorder in chlorine clathrate hydrate cages.

We present a detailed theoretical characterization of the structure and interactions in dichlorine clathrate hydrate cages. In the case of the dodecahedral cage, there is clear evidence of the presence of halogen bonding, whereas in the tetrakaidecahedral cage, the expected signatures are there but in a weaker form. Comparison is made with the available structural data from x-ray experiments, where the rotational motion of dichlorine has been taken into account through Monte Carlo simulations illustrating delocalization effects associated with sampling multiple minima, specifically for the larger cage. Finally, the intermolecular potentials have been calculated with local correlation methods, and energy decomposition analysis has been applied to shed light on the nature of the interactions.

Density Functional Study on the Fundamental and Valence Excited States of Dibromine in T, P, and H Clathrate Cages.

This work evaluates the performance of different DFT models in the accurate prediction of the guest-host intermolecular potentials for the ground and excited states of Br2 in the tetrakaidecahedral (T), pentakaidecahedral (P), and hexakaidecahedral (H) clathrate cages. Of a set of density functionals, we found that PBE0-D3 and wb97XD provide a physically sound and quantitatively correct description of the interaction and transition energies of low-lying valence excited states of Br2 inside these clathrate cages. The importance of correctly modeling dispersive interactions is also analyzed. This study provides the first detailed potential energy surface of the ground and excited states of Br2 in the largest H cage. Comparisons with the LCC2 method and experimental electronic shifts probe the reliability of PBE0-D3 and wb97XD to describe weak intermolecular forces in the ground and excited states.

Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling.

Isomerization kinetics of molecules in the gas phase naturally falls on the microcanonical ensemble of statistical mechanics, which for small systems might significantly differ from the more traditional canonical ensemble. In this work, we explore the examples of cis-trans isomerization in butane and bibenzyl and to what extent the fully atomistic rate constants in isolated molecules can be reproduced by coarse-graining the system into a lower dimensional potential of mean force (PMF) along a reaction coordinate of interest, the orthogonal degrees of freedom acting as a canonical bath in a Langevin description. Time independent microcanonical rate constants can be properly defined from appropriate state residence time correlation functions; however, the resulting rate constants acquire some time dependence upon canonical averaging of initial conditions. Stationary rate constants are recovered once the molecule is placed into a real condensed environment pertaining to the canonical ensemble. The effective one-dimensional kinetics along the PMF, based on appropriately chosen inertia and damping parameters, quantitatively reproduces the atomistic rate constants at short times but deviates systematically over long times owing to the neglect of some couplings between the system and the bath that are all intrinsically present in the atomistic treatment. In bibenzyl, where stronger temperature effects are noted than in butane, the effective Langevin dynamics along the PMF still performs well at short times, indicating the potential interest of this extremely simplified approach for sampling high-dimensional energy surfaces and evaluating reaction rate constants.

Nature of the valence excited states of bromine in the T and P clathrate cages.

The guest-host intermolecular potentials for the valence excited states of Br2 in the tetrakaidecahedral(T) and pentakaidecahedral(P) clathrate cages have been calculated using ab initio local correlation methods. We find that the excited states are more strongly bound than the corresponding ground states even in the small T cage where bromine has a tight fit. The angular dependence of the interaction energies is quite anisotropic; this reflects in the corresponding electronic shifts where regions of maxima for blue-shifts in the T cage indicate the presence of halogen bonding. We predict a large temperature dependence of the electronic shifts and compare absolute values with recent experimental studies. This stringent test indicates the reliability of local correlation treatments to describe weak intermolecular forces in ground and excited states.