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In path integral molecular dynamics, efficient sampling of the phase space is not guaranteed due to the stiff harmonic part of the action arising from the quantum kinetic energy. This problem has been eliminated by incorporating a sufficient number of thermostats into the dynamical scheme and by introducing a transformation of the path ‘‘bead’’ variables. In this paper, an efficient Car–Parrinello path integral molecular dynamics algorithm, sufficiently general to include the use of ultrasoft pseudopotentials is introduced. Difficulties encountered when combining thermostats and transformations of the Cartesian ‘‘bead’’ coordinates with the generalized orthonormality condition are circumvented by employing a constrained nonorthogonal orbital method. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The essential ideas underlying ab initio path integral molecular dynamics and its efficient numerical implementation are discussed. In this approach the nuclei are treated as quantum particles within the path integral formulation of quantum statistical mechanics. The electronic degrees of freedom are treated explicitly based on state-of-the-art electronic structure theory. This renders ab initio simulations of quantum systems possible without recourse to model potentials. A combined extended Lagrangian for both quantum nuclei and electrons defines a dynamical system and yields molecular dynamics trajectories that can be analyzed to obtain quantum statistical expectation values of time-independent operators. The methodology can be applied to a wide range of fields addressing problems in molecular and condensed matter chemistry and physics. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The first ab initio molecular dynamics simulation of a Gd(III)-based contrast agent in explicit aqueous solution at ambient conditions as used in the actual magnetic resonance imaging of human bodies is presented. The description of the structure of this chelate complex is considerably improved with respect to typical force fields and ab initio calculations in continuum solvent models if the open 4f shell of Gd is included explicitly. The solvation-shell structure is revealed to be anionic and includes a rather short hydrogen bond donated by the hydroxypropyl arm. [ABSTRACT FROM AUTHOR]

On the basis of ab initio Gibbs ensemble Monte Carlo simulations, we map the liquid-vapor phase diagram of water described by the RPBE density functional supplemented by D3 dispersion corrections and estimate the critical point by density extrapolation. Knowing the approximate location of the critical point, two sets of ab initio molecular dynamics simulations at gas-like and liquid-like densities deep in the supercritical phase of water are carried out where particular attention is payed to ergodic sampling in view of large correlation lengths and long correlation times. Structural, H-bonding, and dipolar properties of RPBE-D3 water are analyzed along the liquid-vapor coexistence curve upon moving toward the critical point and compared to those in the supercritical state. The properties of high-density supercritical water are astonishingly similar to those of the liquid on the coexistence curve under subcritical conditions at comparable density. Upon decomposing the molecular dipole moments into purely configurational and electronic polarization/charge-transfer contributions, it is demonstrated that the latter play a decreasing role in liquid water upon approaching the critical point on the coexistence curve. Moreover, these many-body effects are systematically suppressed in supercritical water due to the significantly reduced H-bonding network. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics (MD) simulations of the amino acid, glycine at the water/pyrite interface, which can be carried out at the Iron-Sulfur World (ISW) is used for understanding the pyrite assisted peptide bond formation, which is the adsorption of GLY on the pyrite surface and its possible activation. It is seen that the GLY easily desorbs from a pyrite/water interface through hydrogen-bond assistance.

We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics (AIMD) simulations. Overall we find that the polarizable force field shows promising agreement with AIMD data for both glycine and valine in water. This includes the THz spectral assignments and the mode-specific spectral decomposition into intramolecular solute motions as well as distinct solute–water cross-correlation modes some of which cannot be captured by non-polarizable force fields that rely on fixed partial charges. This bodes well for future studies for simulating and decomposing the THz spectra for larger solutes such as proteins or polymers for which AIMD studies are presently intractable. Furthermore, we believe that the current study on rather simple aqueous solutions offers a way to systematically investigate the importance of charge transfer, nuclear quantum effects, and the validity of computationally practical density functionals, all of which are needed to fully quantitatively capture complex dynamical motions in the condensed phase. [ABSTRACT FROM AUTHOR]

The quinizarin chemisorbed on the basal-plane (0001) surface of alpha-Al2O3 is perpendicular on the surface and forms chelate bonds with surface aluminum atoms at exposed sites. This was observed ab initio calculations. The results also shows that the electronic characteristics due to long-range surface effects cannot explain the improved spectral hole-burning properties of chemisorbed quinizarin.