The free-energy barrier to hydride transfer across a dipalladium complex.

We use density-functional theory molecular dynamics (DFT-MD) simulations to determine the hydride transfer coordinate between palladium centres of the crystallographically observed terminal hydride locations, Pd-Pd-H, originally postulated for the solution dynamics of the complex bis-NHC dipalladium hydride [{(MesIm)2CH2}2Pd2H][PF6], and then calculate the free-energy along this coordinate. We estimate the transfer barrier-height to be about 20 kcal mol(-1) with a hydride transfer rate in the order of seconds at room temperature. We validate our DFT-MD modelling using inelastic neutron scattering which reveals anharmonicity of the hydride environment that is so pronounced that there is complete failure of the harmonic model for the hydride ligand. The simulations are extended to high temperature to bring the H-transfer to a rate that is accessible to the simulation technique.

Temperature dependence of alkali-metal rattling dynamics in the ß-pyrochlores, AOs2O6 (A = K, Rb, Cs), from MD simulation.

We investigate the temperature response of the alkali-metal rattling modes in ß-pyrochlores, AOs2O6 (A = K, Rb, Cs), from the results of ab initio molecular dynamics (MD) simulations performed at 20 K, 100 K and 300 K. Our results show that the temperature response of the T1u mode is clearly different from that of the T2g mode for all three pyrochlores. In this regard, two features are of particular note for both K and Rb; (1) the T1u mode exhibits a distinctly stronger softening response with decreasing temperature compared to the T2g mode, and (2) the T1u mode becomes stronger and sharper with decreasing temperature. These two findings suggest that the T1u mode is significantly more anharmonic and sensitive to the cage dynamics than the T2g mode. Examination of the local potentials around the alkali-metal atoms reveals that K has the flattest and most anharmonic potential at all temperatures while Cs exhibits the narrowest potential. The temperature dependence of the local potentials reveals that, for K, the potential at a higher temperature is not a simple extrapolation to higher energy of that at a lower temperature. Instead, we find significant reconstruction of the potential at different temperatures. Finally, we explore the temperature response of the coupling between the alkali metals and find a complex temperature dependence which suggests that the origin of the coupling may be more complex than a pure Coulomb interaction. We also find an unexpected increase in the static disorder of the system at low temperatures for the K and Rb pyrochlores.

Molecular dynamics evidence for alkali-metal rattling in the ß-pyrochlores, AOs2O6 (A = K, Rb, Cs).

We have used ab initio molecular dynamics simulations validated against inelastic neutron scattering data to study alkali-metal dynamics in the ß-pyrochlore osmates AOs2O6 (A=K, Rb, Cs) at 300 K to gain insight into the microscopic nature of rattling dynamics in these materials. Our results provide new evidence at the microscopic level for rattling dynamics: (1) the elemental magnitude spectra calculated from the MD show a striking dominance by the alkali metals at low energies indicating weak coupling to the cage, (2) the atomic root-mean-square displacements for the alkali metals are significantly larger than for the other atoms, e.g., 25% and 150% larger than O and Os, respectively, in KOs2O6, and (3) motions of the alkali metals are weakly correlated to the dynamics in their immediate environment, e.g. K in KOs2O6 is 6 times less sensitive to its local environment than Os, indicating weak bonding of the K. There is broadening of the elemental spectra of the alkali metals from Cs to K corresponding to a similar broadening of the local potential around these atoms as determined from potential of mean-force calculations. This feature of the spectra is partly explained by the well-known increase in the relative cage volume with decreasing atomic size of the alkali metal. We find that for the smallest rattler in this series (K) the larger relative cage volume allows this atom freedom to explore a large space inside the cage leading to vibration at a broader range of frequencies, hence a broader spectrum. Thus, since K is considered the best rattler in this series, these findings suggest that a significant feature of a good rattler is the ability to vibrate at several different but closely spaced frequencies.

Dynamical transition in a large globular protein: Macroscopic properties and glass transition.

Hydrated soy-proteins display different macroscopic properties below and above approximately 25% moisture. This is relevant to the food industry in terms of processing and handling. Quasi-elastic neutron spectroscopy of a large globular soy-protein, glycinin, reveals that a similar moisture-content dependence exists for the microscopic dynamics as well. We find evidence of a transition analogous to those found in smaller proteins, when investigated as a function of temperature, at the so-called dynamical transition. In contrast, the glass transition seems to be unrelated. Small proteins are good model systems for the much larger proteins because the relaxation characteristics are rather similar despite the change in scale. For dry samples, which do not show the dynamical transition, the dynamics of the methyl group is probably the most important contribution to the QENS spectra, however a simple rotational model is not able to explain the data. Our results indicate that the dynamics that occurs above the transition temperature is unrelated to that at lower temperatures and that the transition is not simply related to the relaxation rate falling within the spectral window of the spectrometer.

Dispersive kinetics in discotic liquid crystals.

The dynamics of the discotic liquid-crystalline system, hexakis (n-hexyloxy) triphenylene (HAT6), is considered in the frame of the phenomenological model for rate processes proposed by Berlin. It describes the evolution of the system in the presence of the long-time scale correlations in the system, and we compare this with experimental quasielastic neutron scattering of the molecular assembly of HAT6 in the columnar phase. We interpret the parameters of this model in terms of nonextensive thermodynamics in which rare events in the local fast dynamics of some parts of the system control the slower dynamics of the larger molecular entity and lead to a fractional diffusion equation. The importance of these rare local events to the overall dynamics of the system is linked to the entropic index, this being obtained from the data within the model approach. Analysis of the waiting-time dependence from momentum transfer reveals a Lévy distribution of jump lengths, which allows us to construct the van Hove correlation function for discotic liquid-crystalline system.

Atomistic model of DNA: phonons and base-pair opening.

A fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, approximately 12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA.

Phonon driven proton transfer in crystals with short strong hydrogen bonds.

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.

Intermolecular interactions in solid benzene.

The lattice dynamics and molecular vibrations of benzene and deuterated benzene crystals are calculated from force constants derived from density-functional theory (DFT) calculations and compared with measured inelastic neutron-scattering spectra. A very small change (0.5%) in lattice parameter is required to obtain real lattice-mode frequencies across the Brillouin zone. There is a strong coupling between wagging and breathing modes away from the zone center. This coupling and sensitivity to cell size arises from two basic interactions. Firstly, comparatively strong interactions that hold the benzene molecules together in layers. These include an intermolecular interaction in which H atoms of one molecule link to the center of the aromatic ring of a neighboring molecule. The layers are held to each other by weaker interactions, which also have components that hold molecules together within a layer. Small changes in the lattice parameters change this second type of interaction and account for the changes to the lattice dynamics. The calculations also reveal a small auxetic effect in that elongation of the crystal along the b axis leads to an increase in internal pressure in the ac plane, that is, elongation in the b direction induces expansion in the a and c directions.

Dynamics and lithium binding energies of polyelectrolytes based on functionalized poly(para-phenylene terephthalamide).

Polyelectrolyte materials are an interesting class of electrolytes for use in fuel cell and battery applications. Poly(para-phenylene terephthalamide) (PPTA, Kevlar) is a liquid crystalline polymer that, when sulfonated, is a polyelectrolyte that exhibits moderate ion conductivity at elevated temperatures. In this work, quasi-elastic neutron scattering (QENS) experiments were performed to gain insight into the effect of the presence of lithium counterions on the chain dynamics in the material. It was found that the addition of lithium ions decreases the dynamics of the chains. Additionally, the binding of lithium ions to the sulfonic acids groups was investigated by density functional theory (DFT) calculations. It was found that the local surroundings of the sulfonic acid group have very little effect on the lithium-ion binding energy. Binding energies for a variety of different systems were all calculated to be around 150 kcal/mol. The DFT calculations also show the existence of a structure in which a single lithium ion interacts with two sulfonic acid moieties on different chains. The formation of such "electrostatic cross-links" is believed to be the source of the increased tendency to aggregate and the reduced dynamics in the presence of lithium ions.

How van der Waals bonds orient molecules in zeolites.

We show that weak bonds are responsible for the way a molecule is held in a zeolite, and for its reactivity.

Quantitative atom-atom potentials from rotational tunneling: their extraction and their use.

Rotational tunneling of small molecular groups has been the subject of considerable theoretical and experimental activity for several decades. Much of this activity has been driven by the promise of exploiting the extreme sensitivity of quantum tunneling to interatomic potentials, but until recently, there was no straightforward means by which quantitative information about these potentials could be extracted. This review explains how a quantitative method, suitable for general application, was developed. It then goes on to show how this has been used to understand tunneling systems for which no previous satisfactory explanation had been found. The application of the methodology, and its results, to other disciplines is discussed.

Inelastic neutron-scattering study of the proton transfer dynamics in polyglycine I at 20 K.

Inelastic neutron-scattering (INS) spectra of three isotopic derivatives of polyglycine I (-COCH2NH-)n, (-COCD2NH-)n, and (-COCH2ND-)n at 20 K are presented from 30 to 4000 cm(-1). The band frequencies are compared to those observed in the infrared and Raman. Assignments in terms of group vibrations are proposed. These mostly resemble previous assignment schemes, except for the amide bands. The INS intensities reveal that the proton dynamics for the (N)H proton are totally different from those proposed previously. They are independent of the molecular frame and the valence bond approach is not consistent with observation. A phenomenological approach is proposed in terms of localized modes. The calculated intensities reveal that the (N)H stretching mode has two components at approximately 1377 and 1553 cm(-1). This is a dramatic change compared to all former assignments at approximately 3280 cm(-1) based on infrared and Raman data. These proton-dynamics are associated with a weakening of the NH bond due to the ionic character of the hydrogen bond (N(delta-)...H+...O(delta'-)) and proton transfer. The infrared and Raman spectra are re-examined and a new assignment scheme is proposed for the amide bands; the amide A and B bands are re-assigned to the overtones of the stretching modes. A symmetric double-minimum potential for the proton is consistent with all the observations.

A new look at proton transfer dynamics along the hydrogen bonds in amides and peptides.

Vibrational spectroscopy with inelastic neutron scattering can provide spectra that are more detailed and easier to interpret than optical spectra. The spectral intensity depends on energy transfer and kinetic momentum transfer, allowing determination of the potential function. Experiments reveal that the proton involved in intermolecular hydrogen bonding in N-methylacetamide and polyglycine I vibrates almost independently. An ionic representation (N(delta-)...H(+)...O(delta-)) of the hydrogen bond is more realistic than the normally accepted covalent model (NH...O). For polyglycine I, the proton experiences a local, symmetric double-minimum potential arising from dynamic exchange between the amide-like (CONH) and imidol-like (HOCN) forms of the peptide unit.