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The properties of N-methylacetamide along a cis-trans isomerization pathway reported by twisting about the C(O)-N bond are investigated at finite temperature both in vacuo and in explicit water solvent. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is analyzed to understand the changes in peptide 'partial-double' bond character [C(O)-N] as isomerization takes place.

A study was conducted to investigate the isothermal-isobaric molecular dynamics methods in system subject to holonomic constraints with the goal of devising equations of motion in which the scaling is performed on atomic positions. The result demonstrates that the Kneller-Mulders equations generate an isothermal-isobaric ensemble distribution only for systems with nonzero total force.

The dielectric and piezoelectric behavior of 70Pb(Mg1/3Nb2/3)O3-30PbTiO3 (70PMN-30PT) thin films was studied as a function of lateral scaling. Dense PMN-PT films 300–360 nm in thickness were prepared by chemical solution deposition using a 2-methoxyethanol solvent. These phase pure and strongly {001} oriented films exhibited dielectric constants exceeding 1400 and loss tangents of approximately 0.01. The films showed slim hysteresis loops with remanent polarizations of about 8 μC/cm2 and breakdown fields over 1500 kV/cm. Fully clamped films exhibited large signal strains of 1%, with a d33,f coefficient of 90 pm/V. PMN-PT films were patterned down to 200 nm in spatial scale with nearly vertical sidewalls via reactive ion etching. Upon lateral scaling, which produced partially declamped films, there was an increase in both small and large signal dielectric properties, including a doubling of the relative permittivity in structures with width-to-thickness aspect ratios of 0.7. In addition, declamping resulted in a counterclockwise rotation of the hysteresis loops, increasing the remanent polarization to 13.5 μC/cm2. Rayleigh analysis, Preisach modeling, and the relative permittivity as a function of temperature were also measured and further indicated changes in the domain wall mobility and intrinsic response of the laterally scaled PMN-PT. [ABSTRACT FROM AUTHOR]

In the effort to develop atomistic models capable of accurately describing nanoscale systems with complex interfaces, it has become clear that simple treatments with rigid charge distributions and dispersion coefficients selected to generate bulk properties are insufficient to predict important physical properties. The quantum Drude oscillator model, a system of one-electron pseudoatoms whose “pseudoelectrons” are harmonically bound to their respective “pseudonuclei,” is capable of treating many-body polarization and dispersion interactions in molecular systems on an equal footing due to the ability of the pseudoatoms to mimic the long-range interactions that characterize real materials. Using imaginary time path integration, the Drude oscillator model can, in principle, be solved in computer operation counts that scale linearly with the number of atoms in the system. In practice, however, standard expressions for the energy and pressure, including the commonly used virial estimator, have extremely large variances that require untenably long simulation times to generate converged averages. In this paper, low-variance estimators for the internal energy are derived, in which the large zero-point energy of the oscillators does not contribute to the variance. The new estimators are applicable to any system of harmonic oscillators coupled to one another (or to the environment) via an arbitrary set of anharmonic interactions. The variance of the new estimators is found to be much smaller than standard estimators in three example problems, a one-dimensional anharmonic oscillator and quantum Drude models of the xenon dimer and solid (fcc) xenon, respectively, yielding 2–3 orders of magnitude improvement in computational efficiency. [ABSTRACT FROM AUTHOR]

There are many atomic scale systems in materials, chemistry, and biology that can be effectively modeled as finite in two of the physical spatial dimensions and periodically replicated in the third including nanoscale metallic and semiconducting wires, carbon nanotubes, and DNA. However, it is difficult to design techniques to treat long range forces in these systems without truncation or recourse to slowly convergent supercells or computationally inefficient Poisson solvers. In this paper, a rigorous reciprocal space based formalism which permits long range forces on wires to be evaluated simply and easily via a small modification of existing methods for three dimensional periodicity is derived. The formalism is applied to determine long range interactions both between point particles using an Ewald-like approach and the continuous charge distributions that appear in electronic structure calculations. In this way, both empirical force field calculations and, for example, plane-wave based density functional theory computations on wires can be performed easily. The methodology is tested on model and realistic systems including a lithium doped carbon nanotube. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper (Paper I) and a companion paper (Paper II), novel new algorithms and applications of the isokinetic ensemble as generated by Gauss' principle of least constraint, pioneered for use with molecular dynamics 20 years ago, are presented for biophysical, path integral, and Car-Parrinello based ab initio molecular dynamics. In Paper I, a new "extended system" version of the isokinetic equations of motion that overcomes the ergodicity problems inherent in the standard approach, is developed using a new theory of non-Hamiltonian phase space analysis [M. E. Tuckerman et al., Europhys. Lett. 45, 149 (1999); J. Chem. Phys. 115, 1678 (2001)]. Reversible multiple time step integrations schemes for the isokinetic methods, first presented by Zhang [J. Chem. Phys. 106, 6102 (1997)] are reviewed. Next, holonomic constraints are incorporated into the isokinetic methodology for use in fast efficient biomolecular simulation studies. Model and realistic examples are presented in order to evaluate, critically, the performance of the new isokinetic molecular dynamic schemes. Comparisons are made to the, now standard, canonical dynamics method, Nosé-Hoover chain dynamics [G. J. Martyna et al., J. Chem. Phys. 97, 2635 (1992)]. The new isokinetic techniques are found to yield more efficient sampling than the Nosé-Hoover chain method in both path integral molecular dynamics and biophysical molecular dynamics calculations. In Paper II, the use of isokinetic methods in Car-Parrinello based ab initio molecular dynamics calculations is presented. [ABSTRACT FROM AUTHOR]

In this paper (Paper II), the isokinetic dynamics scheme described in Paper I is combined with the plane-wave based Car-Parrinello (CP) ab initio molecular dynamics (MD) method [R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)] to enable the efficient study of chemical reactions and metallic systems. The Car-Parrinello approach employs "on the fly" electronic structure calculations as a means of generating accurate internuclear forces for use in a molecular dynamics simulation. This is accomplished by the introduction of an extended Lagrangian that contains the electronic orbitals as fictitious dynamical variables (often expressed directly in terms of the expansion coefficients of the orbitals in a particular basis set). Thus, rather than quench the expansion coefficients to obtain the ground state energy and nuclear forces at every time step, the orbitals are "propagated" under conditions that allow them to fluctuate rapidly around their global minimum and, hence, generate an accurate approximation to the nuclear forces as the simulation proceeds. Indeed, the CP technique requires the dynamics of the orbitals to be both fast compared to the nuclear degrees of freedom while keeping the fictitious kinetic energy that allows them to be propagated dynamically as small as possible. While these conditions can be easy to achieve in many types of systems, in metals and highly exothermic chemical reactions difficulties arise. (Note, the CP dynamics of metals is incorrect because the nuclear motion does not occur on the ground state electronic surface but it can, nonetheless, provide useful information.) In order to alleviate these difficulties the isokinetic methods of Paper I are applied to derive isokinetic CP equations of motion. The efficacy of the new isokinetic CPMD method is demonstrated on model and realistic systems. The latter include, metallic systems, liquid aluminum, a small silicon sample, the 2 × 1 reconstruction of the silicon 100... [ABSTRACT FROM AUTHOR]

A new formalism designed to treat long range interactions on surfaces, systems which are infinitely replicated in two spatial directions but have finite extent in the third, is developed. The new formalism is based in reciprocal space and, thus, permits the facile extension of standard plane-wave based density functional theory, Ewald summation, and smooth particle-mesh Ewald methods to handle surfaces efficiently. The method is tested on both model (body centered cubic lattices) and realistic problems (an ice surface with a defect and the 2 x 1 surface reconstruction of silicon) and found to be accurate, efficient, and a marked improvement on existing formulations in speed, accuracy, and utility. [ABSTRACT FROM AUTHOR]

A study performed classical molecular dynamics simulations of aqueous N-methylacetamide (NMA) is conducted across a concentration range at 308 K. Results reveal that with increases in NMA concentration water molecules become progressively more isolated, forming dimers and trimers hydrogen-bonded to NMA.

An important goal of physical chemistry and structural features in neat liquid water is to develop a detailed understanding of its structure for explaining water's unusual temperature-dependent properties, which have far-reaching consequences for life. The most prevalent structures in liquid water are thermally disordered clusters derived from the hexagonal ice lattice.

The effect of water solvent on protein function is elucidated by the measurement of the radial and angular dependence of the solvation shell structure of NMA(aq). The feasibility and the isomerization of a peptide fragment is experimentally and theoretically studied.

Presents molecular dynamics algorithms for path integrals at constant pressure that can generate averages in the quantum mechanical canonical ensemble. Background in the formulation of the algorithms; Effective parallelization schemes for distributed memory computers; Evaluation of the proposed methods on a model and in real time.

Presents a reciprocal space based formalism for treating long range forces in clusters. Incorporation of the formalism into plane-wave based density function theory calculations, Ewald summation calculations and smooth particle-mesh Ewald calculations to yield accurate and numerically efficient descriptions of long range interactions in cluster systems.

A new fourth order predictor–corrector integration scheme is presented. The unique feature of the new algorithm and what distinguishes it from a Gear predictor–corrector is that the method is derived from the Trotter decomposition of a specially formulated evolution operator and as such, is both symplectic and reversible. In addition, the method retains the useful property of Gear methods that only one force evaluation per time step is required. The new integrator is tested on a harmonic plus quartic oscillator and the Henon–Heiles system. Comparisons are made to the second order velocity Verlet integrator, the true fourth order Yoshida/Suzuki schemes and fourth order Gear. In all cases, the new method works well, giving energy conservation and trajectories of much better quality than velocity Verlet and of comparable quality to the results of the true fourth order schemes for the same computational cost as velocity Verlet. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Modularly invariant equations of motion are derived that generate the isothermal–isobaric ensemble as their phase space averages. Isotropic volume fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two motions are considered. The resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase. [ABSTRACT FROM AUTHOR]

Metal–ammonia solutions are examined from the insulating to the conducting regime using three different microscopic models. In model I, the ammonia molecules are treated via a classical point charge model and the cations as a positive neutralizing background. In model II, the ammonia solvent is made fully polarizable and the cations are again, treated as a positive background. Finally, in model III, the solvent is taken to be fully polarizable and the ions, here lithium, are explicitly included. At T=260 K, the following picture emerges of the electronic states as a function of metal/electron concentration: The dilute solution behaves like an electrolyte in which the electrons exist as polarons, on average spherical states localized in solvent cavities, far from the counterions. At 1 mole percent metal (MPM), the electrons spin pair, forming peanut-shaped species called bipolarons. At slightly higher concentration, 2 MPM, the electronic states oscillate (moderated by solvent fluctuations) between dimers of bipolarons and connected tubular states. At 9 MPM, a good liquid metal is formed in which the electron density forms tubular extended states. These observations are in good agreement with experiment. The quantitative differences between the three models are discussed. In general, the effects of solvent polarizability are found to be rather small. However, the explicit inclusion of the cations is found to slightly increase the metallic character of the solution at 9 MPM. [ABSTRACT FROM AUTHOR]

Quantum mechanical studies of a lithium impurity in solid para-hydrogen and ortho-deuterium have been performed using the path integral formulation of statistical mechanics. Since an isolated lithium atom is much larger than the host molecules, trapping sites consisting of from one to six vacancies have been investigated. Interestingly, all of the sites are comparable in energy. This is due to the large compressibility of para-hydrogen and ortho-deuterium solids, which permits the lattice to relax to comfortably accommodate the impurity. The inhomogeneously broadened dipole spectrum of the lithium impurity in the various sites was calculated using the radial fast Fourier transform Lanczos method and compared to experiments by Fajardo [J. Chem. Phys. 98, 110 (1993)]. Based on the present calculations, lithium atoms appear to occupy preferentially a three-vacancy trapping site in para-hydrogen while in ortho-deuterium a four-vacancy trapping site seems to be favored. Complementary variational Einstein model calculations predict that the four-vacancy trapping site is favorable in both para-hydrogen and in ortho-deuterium. [ABSTRACT FROM AUTHOR]