Search

Classical molecular dynamics (MD) simulations are useful for characterizing the structure and dynamics of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field is widely used and has well-defined bond length, bond angle, partial charge, and van der Waals parameters for all the common amino acids and nucleotides, but it lacks parameters for many of the modifications found in nucleic acids and proteins. Presently there are 107 known naturally occurring modifications that play important roles in RNA stability, folding, and other functions. Modified nucleotides are found in almost all transfer RNAs, ribosomal RNAs of both the small and large subunits, and in many other functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known to be present in RNA. The methodology used for deriving the modified nucleotide parameters is consistent with the methods used to develop the Cornell et al. force field. These parameters will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.

A new method for constructing empirical valence bond potential energy surfaces for reactions is presented. Building on the generalized Gaussian approach of Chang−Miller, V122(q) is represented by a Gaussian times a polynomial at the transition state and generalized to handle any number of data points on the potential energy surface. The method is applied to two model surfaces and the HCN isomerization reaction. The applications demonstrate that the present method overcomes the divergence problems encountered in some other approaches. The use of Cartesian versus internal or redundant internal coordinates is discussed.

The gas-phase reactions involved in the radical mechanism for zinc oxide chemical vapor deposition have been examined by ab initio and density functional calculations. Geometries of reactants, transition structures, intermediate complexes, and products have been optimized with B3LYP/6-31G(d), and energetics have been computed with B3LYP/6-311+G(d,p), CCSD(T)/6-311+G(d,p), and MP2/ 6-311+G(3df,2p) levels of theory. The latter two were combined to give a G2(MP2)-like estimate of the enthalpy and free energy. Initiation reactions involve the thermal dissociation of diethyl zinc. The second bond dissociation of diethyl zinc is calculated to be significantly smaller than experimental estimates. The first step in the propagation reactions is ethyl radical abstracting a hydrogen from water to form hydroxyl radical. This has the highest barrier of the reaction sequence and would appear to be the rate-limiting step. The addition of hydroxyl radical to diethyl zinc proceeds without a barrier producing ethyl zinc hydroxide and regenerates ethyl radical. A similar set of propagation reactions converts ethyl zinc hydroxide to zinc dihydroxide. Additional propagation reactions involving oxyzinc radicals were also investigated. The gas-phase intermediates can react further to produce linear and cyclic oligomers. Comparison of the gas-phase reactions in the radical and closed shell mechanisms for zinc oxide chemical vapor deposition shows that the barrier heights for the rate-limiting steps are very similar.

Tris(8-hydroxyquinoline)aluminum(iii), AlQ3, is used in organic light-emitting diodes (OLEDs) as an electron-transport material and emitting layer. The reaction of AlQ3 with trace H2O has been implicated as a major failure pathway for AlQ3-based OLEDs. Hybrid density functional calculations have been carried out to characterize the hydrolysis of AlQ3. The thermochemical and atomistic details for this important reaction are reported for both the neutral and oxidized AlQ3/AlQ3systems. In support of experimental conclusions, the neutral hydrolysis reaction pathway is found to be a thermally activated process, having a classical barrier height of 24.2 kcal mol−1. First-principles infrared and electronic absorption spectra are compared to further characterize AlQ3 and the hydrolysis pathway product, AlQ2OH. The activation energy for the cationic AlQ3 hydrolysis pathway is found to be 8.5 kcal mol−1lower than for the neutral reaction, which is significant since it suggests a role for charge imbalance in promoting chemical failure modes in OLED devices.

A direct dynamics technique, using energies, forces and second derivatives calculated at the UHF/6–31G* level of theory, was used to investigate product energy distributions of the F+C2H4→C2H3F+H collision reaction. The shifting and broadening of the product translational energy distribution as the system moves from the exit-channel barrier to the products was studied. Since properties associated with the rupturing C···H bond are similar for the C2H5‡ and C2H4F‡ exit-channel barriers, and integration of the C2H5‡→C2H4+H reaction is approximately 2.5 times faster than the C2H4F‡→C2H3F+H reaction, trajectories of the former reaction were propagated to gain insight into the exit-channel dynamics. Ensemble averaged results for C2H5‡ dissociation are well described by a model based on isotropic exit-channel dynamics which assumes that the product relative translational distribution arises from the centrifugal potential and relative translational energy distributions at the exit-channel barrier plus the exit-channel potential release. The width of the product translational energy distribution is sensitive to overall rotational angular momentum and its partitioning between C2H4···H‡ orbital angular momentum and C2H4‡ rotational angular momentum. The simulated product translational energy distribution for the C2H4F‡→C2H3F+H reaction is broadened by relative translation–vibrational couplings in the exit-channel and is similar to the distribution used to fit crossed molecular beam data. Approximately 50% of the available energy is in product relative translation, which also agrees with experiment. RRKM calculations indicate that a second reaction mechanism, involving 1–2 hydrogen migration prior to C···H bond fission, does not significantly contribute to C2H3F+H product formation.