Ab Initio and MM3 Studies of the Conformational Structures of Naphthalene Trimer: Comparison with Experiment

DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo

A complete scan of the potential-energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol(-1). The different behaviors of nonmethylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal mol(-1) relative to highly correlated ab initio theoretical calculations.

Stacked Clusters of Polycyclic Aromatic Hydrocarbon Molecules

Clusters of polycyclic aromatic hydrocarbon (PAH) molecules are modeled using explicit all-atom potentials using a rigid-body approximation. The considered range of PAHs goes from pyrene (C10H8) to circumcoronene (C54H18) and clusters containing between 2 and 32 molecules are investigated. In addition to the usual repulsion-dispersion interactions, electrostatic point-charge interactions are incorporated, as obtained from density functional theory calculations. The general electrostatic distribution in neutral or singly charged PAHs is reproduced well using a fluctuating-charges analysis, which provides an adequate description of the multipolar distribution. Global optimization is performed using a variety of methods, including basin-hopping and parallel tempering Monte Carlo. We find evidence that stacking the PAH molecules generally yields the most stable motif. A structural transition between one-dimensional stacks and three-dimensional shapes built from multiple stacks is observed at larger sizes, and the threshold for this transition increases with the size of the monomer. Larger aggregates seem to evolve toward the packing observed for benzene in bulk. Difficulties met in optimizing these clusters are analyzed in terms of the strong anisotropy of the molecules. We also discuss segregation in heterogeneous clusters and vibrational properties in the context of astrophysical observations.

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

The physical basis of nucleic acid base stacking in water

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.