Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations.

Background: Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite [α-Fe(OOH)]. Ab initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Several exchange correlation functionals were employed (PBE96, PBE96 + Grimme, and PBE0) in the simulations of a (3 × 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a = 30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).

QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer.

The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment).

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g.

Ion association in AlCl3 aqueous solutions from constrained first-principles molecular dynamics.

The Car-Parrinello-based molecular dynamics (CPMD) method was used to investigate the ion-pairing behavior between Cl(-) and Al(3+) ions in an aqueous AlCl(3) solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, with the internuclear separation (r(Al-Cl)) between the Al(3+) ion and one of the Cl(-) ions held constant. The calculated potential of mean force (PMF) of the Al(3+)-Cl(-) ion pair shows a global minimum at r(Al-Cl) = 2.

Near-Quantitative Agreement of Model-Free DFT-MD Predictions with XAFS Observations of the Hydration Structure of Highly Charged Transition-Metal Ions.

First-principles dynamics simulations (DFT, PBE96, and PBE0) and electron scattering calculations (FEFF9) provide near-quantitative agreement with new and existing XAFS measurements for a series of transition-metal ions interacting with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This analysis does not require either the development of empirical interparticle interaction potentials or structural models of hydration.

Parallel implementation of Γ-point pseudopotential plane-wave DFT with exact exchange.

Semi-local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self-interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid-DFT, e.

Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations.

Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn(2+) ion (T approximately 300 K, rho approximately 1 gm/cm(3)) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules ( approximately 15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.).

Vertical ionization potentials of nucleobases in a fully solvated DNA environment.

Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.

First principles simulation of the bonding, vibrational, and electronic properties of the hydration shells of the high-spin Fe(3+) ion in aqueous solutions.

Results of parameter-free first principles simulations of a spin up 3d(5) Fe(3+) ion hydrated in an aqueous solution (64 waters, 30 ps, 300 K) are reported. The first hydration shell associated with the first maximum of the radial distribution function, g(FeO)(r), at d(Fe-O(I)) = 2.11-2.

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction.

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism.

Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations.

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data.

Structure and dynamics of the hydration shells of the Al3+ ion.

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis.

The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations.

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration.