Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.

Molecular dynamics (MD) simulations for RNA tetramers r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against H-H NOESY distances and scalar couplings to test effects of RNA torsion parametrizations. Four different starting structures were used for r(AAAA), r(CAAU), and r(GACC), while five starting structures were used for r(UUUU). On the basis of X-ray structures, criteria are reported for quantifying stacking.

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU).

Locked Nucleic Acids (LNAs) are RNA analogues with an O2'-C4' methylene bridge which locks the sugar into a C3'-endo conformation. This enhances hybridization to DNA and RNA, making LNAs useful in microarrays and potential therapeutics. Here, the LNA, L(CAAU), provides a simplified benchmark for testing the ability of molecular dynamics (MD) to approximate nucleic acid properties.

A pragmatic recipe for the treatment of hindered rotations in the vibrational averaging of molecular properties.

A computational protocol for the treatment of hindered rotations in the vibrational averaging of molecular properties is described. As examples, the specific rotations [alpha]D of (R)-methyloxirane, (1S)-methylnorbornanone, and (S)-epichlorohydrin and the spin-spin coupling constant J(HD) for [Ir(Cp)(PMe3)H2]+ are investigated. For each of the four molecules, the relaxed and unrelaxed potential energy surfaces along the rotational coordinate of interest are used to solve the nuclear Schrödinger equation using a pseudospectral method.

Vibrational corrections to magneto-optical rotation: a computational study.

Vibrational corrections to the Verdet constants of nine molecules (H2, N2, CO, H2O, CH4, benzene, toluene, p-xylene, and o-xylene) were calculated with pure density functional theory (DFT), hybrid DFT, and an approximate coupled-cluster theory. Comparisons are made for the accuracy of the vibrational averages among different methods and with respect to experimental data where available. It is found that vibrational corrections to magneto-optical rotation can be as large as 10% of the equilibrium value.

Temperature dependence of the optical rotation in six bicyclic organic molecules calculated by vibrational averaging.

The vibrational corrections and the temperature dependence of the specific rotation of six rigid organic molecules (alpha-pinene, beta-pinene, cis-pinane, camphene, camphor, and fenchone) were calculated at three wavelengths using hybrid time-dependent density functional theory (TDDFT). A technique for calculating the temperature dependence of the vibrational average of a molecular property has been applied to obtain the specific rotation of the molecules as a function of temperature. For cases in which accurate equilibrium optical rotations can be obtained as a "base value," and for which there is little effect from solvation, accurate predictions of the trends in the temperature-dependence of the specific rotations can be calculated.

Temperature dependence of the optical rotation of fenchone calculated by vibrational averaging.

On the basis of vibrational averaging, the temperature dependence of the optical rotation for fenchone has been calculated using TDDFT with the B3LYP hybrid functional at three wavelengths. The results show that very good agreement is obtained between theory and experiment. It is concluded that temperature-dependent vibrational effects are likely to account for much of the observed temperature dependence in optical rotation exhibited by rigid organic molecules in case there is only a weak temperature-dependent interaction with the solvent.

Zero-point corrections and temperature dependence of HD spin-spin coupling constants of heavy metal hydride and dihydrogen complexes calculated by vibrational averaging.

Vibrational corrections (zero-point and temperature dependent) of the H-D spin-spin coupling constant J(HD) for six transition metal hydride and dihydrogen complexes have been computed from a vibrational average of J(HD) as a function of temperature. Effective (vibrationally averaged) H-D distances have also been determined. The very strong temperature dependence of J(HD) for one of the complexes, [Ir(dmpm)Cp*H2]2 + (dmpm = bis(dimethylphosphino)methane) can be modeled simply by the Boltzmann average of the zero-point vibrationally averaged JHD of two isomers.

Magnitude of zero-point vibrational corrections to optical rotation in rigid organic molecules: a time-dependent density functional study.

The zero-point vibrational corrections (ZPVCs) to the optical rotation of 22 rigid organic molecules have been calculated using time-dependent density functional theory with the B3LYP hybrid functional. We outline an implementation for calculating ZPVCs that can be applied with a variety of quantum chemistry programs and methods. It is shown that the ZPVCs to optical rotation have a wide range of values and can be quite significant depending on the molecule.

Aerobic oxidation of methyl p-tolyl sulfide catalyzed by a remarkably labile heteroscorpionate RuII-aqua complex, fac-[RuII(H2O)(dpp)(tppm)]2+.

fac-[RuII(Cl)(dpp)(L3)]+ (L3 = tris(pyrid-2-yl)methoxymethane (tpmm) = [1A]+ and tris(pyrid-2-yl)pentoxymethane (tppm) = [1B]+ and dpp = di(pyrazol-1-yl)propane) rapidly undergo ligand substitution with water to form fac-[RuII(H2O)(dpp)(L3)]2+ (L3 = tpmm = [2A]2+ and tppm = [2B]2+). In the structure of [2A]2+, the distorted octahedral arrangement of ligands around Ru is evident by a long Ru(1)-O(40) of 2.172(3) A and a large angle O(40)-Ru(1)-N(51) of 96.