Simon W. de Leeuw

Diffusion of Li-ions in rutile. An ab initio study

Ab initio calculations of lithium diffusion into titanium dioxide in the form of rutile are presented. An analysis of the site preference for intercalation and diffusion pathways of Li-ions is performed. The expansion of the host structure on Li-insertion is found to contribute to the enhanced diffusion of Li-ions along the tetragonal c direction. At the same time, a large distortion of the rutile framework makes Li diffusion in the ab planes prohibitively slow. Anisotropy of Li diffusion is used to explain the observed electrochemical behaviour of rutile. Computed diffusion coefficients were found in excellent agreement with the measured values.

Proton transport along water chains in an electric field

Proton transport along water chains is thought to be essential for the translocation of protons over large distances in proteins. In this paper the real-time nonequilibrium quantum dynamics of proton transport along chains of three or four water molecules is simulated using the multiconfigurational molecular dynamics with quantum transitions method. A linearly increasing external electric field is applied to the water chain to model the field exerted by a protein, and restraints are applied to the oxygen atoms to model the structural constraints of the protein. The simulations indicate that fluctuating electric fields and structural constraints strongly affect the dynamics of proton transport along water chains. In addition, quantum mechanical effects such as hydrogen tunneling and nonadiabatic transitions play an important role under certain nonequilibrium conditions.

Molecular-dynamics simulations of Coulombic systems on distributed-memory MIMD machines

Abstract Parallel algorithms are designed for molecular-dynamics simulations of bulk systems with Coulomb forces. The conditionally convergent series for the 1/ r interaction is treated by the Ewald method of summation. One of the algorithms involves the equipartition of an N -particle system into p subsystems of N/p particles each, with a one-to-one mapping between subsystems and p processors. The other algorithm is based on the spatial decomposition of the volume of a system into p equal parts which are geometrically mapped onto processors. The performance of these algorithms is tested on the in-house 8 node Intel iPSC/860 system. Execution times for these algorithms are comparable, and in both cases the computation time dominates the communication time. For a 64 000 particle one-component charged plasma in three dimensions, the execution time for a single molecular-dynamics time step is 27.4 s. Execution times increase linearly with an increase in the size of the system and they are inversely proportional to the number of processors. Parallel efficiencies of these algorithms are close to 0.85.

Open circuit voltage profile for Li-intercalation in rutile and anatase from first principles

Ab initio calculations of lithium intercalation into rutile- and anatase structured titanium dioxide are presented. An analysis of self-ordering at different depths of discharge is performed. The open circuit voltage profile is calculated. It reproduces and explains the characteristic features of experimental discharge curves.

A new phase of lithiated titania predicted from first principles

A new phase of Li-intercalated rutile-structured titania, LixTiO2 for x=0.75, is predicted on the basis of first principles calculations. The existence of this phase has been noted in X-ray diffraction measurements but its structure has not previously been determined. The new phase has important consequences for the performance of LixTiO2 as a battery cathode material. On the basis of the computed energetics of phases at x=0.75, 0.5 and 0.25 phases, and a careful comparison of the computed and measured diffraction data, a two phase model of intercalation for 0.25<x<0.75 is proposed. It is suggested that nucleation of the new x=0.75 phases results from kinetic restrictions under operating conditions. The structural features of the new phase and their manifestation in X-ray diffraction are discussed. The transformation of the new phase to an hexagonal phase at x=0.8 is analysed and its role in cathode degradation discussed.

Statistical mechanics of two-dimensional coulomb systems

Abstract The statistical mechanics of systems acting via two-dimensional charge-charge and dipole-dipole interactions is studied in periodic boundary conditions. The two-dimensional lattice theta-function transformation is obtained and the sum shown to contain a polarization correction to the Ewald sum, analogous to that found in three dimensions. Using a different approach, these sums are evaluated in closed form, for bodies of arbitrary shape. The methodology for the computer simulation of two dimensional dielectrics is discussed and the two-dimensional analogue of a generalized Kirkwood-Clausius-Mosotti-Debye formula derived.

Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

The relative stability of homochiral (D,D or L,L) and heterochiral (D,L or L,D) dipeptides may have been a decisive factor in the evolutionary propagation of a symmetry-breaking event leading to the present-day predominance of L-amino acids in natural proteins. Kinetic resolution in the solid-phase peptide synthesis of blocked dialanine suggests the activation free energy difference of formation of (D,D or L,L)- and (D,L or L,D)-dialanine to be 0.22 kJ mol−1 in favour of the formation of the homochiral dipeptide. Computer simulation studies were performed on water-solvated dialanine, applying a thermodynamic integration protocol using the GROMOS force field. Five different pathways and three force-field parameter sets have been used to assess the possibility of a computational prediction of the chiral preference. Inversion of the configuration around either one of the Cα-atoms by changing the improper dihedral angle with concomitant relaxation of the bond angles, leads to an excellent reproduction of the experimental result.

Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling.

We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to approximately 7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.

Structural deformations in lithium doped titanium dioxide

Density functional simulations of lithium intercalation into rutile structured titanium dioxide are presented. Full relaxation of structures for a wide range of insertion concentrations is used to identify the thermodynamically most stable configurations. The host lattice is found to undergo large deformations upon Li-insertion which can be related to the excitation of soft vibrational modes. The dominant screening interaction is found to be due to these elastic distortions of the lattice rather than to dielectric screening.

Ion clustering in molecular dynamics simulations of sodium iodide solutions

Model systems of sodium iodide dissolved in dimethyl ether or 1,2-dimethoxyethane (glyme) were studied in order to investigate the structural and dynamic properties of ionic solutions in small and polymeric ethers. Full molecular dynamics simulations were performed at a range of different salt concentrations. An algorithm was designed which assigns ions to clusters and then calculates all the terms which contribute to ionic conductivity. In dilute solutions, free ions are the most common ionic species, followed by ion pairs. As the concentration increases, pairs become the most common species, with significant concentrations of clusters with 3 through 6 ions. Changing the solvent from dimethyl ether to glyme significantly decreases the ion clustering due to the chelate effect in which the two oxygens on a solvent stabilize an associated cation. The conductivity in stable systems is shown to be primarily the result of the movement of free ions and the relative movement of ions within neutral pairs. The Nernst-Einstein relation, commonly used in the discussion of polymer electrolytes, is shown to be inadequate to quantitatively describe conductivity in the model systems.