Chemical Physics

A new strategy for global geometry optimization of clusters is presented. Important features are a restriction of search space to favorable nearest-neighbor distance ranges, a suitable cluster growth representation with diminished correlations, and easy transferability of the results to larger clusters. The strengths and possible limitations of the method are demonstrated for Si10 using an empirical potential.

Tight-binding molecular dynamics simulated annealing technique is employed to search for the ground state geometries of silicon clusters containing 11-17 atoms. These studies revealed that layer formation is the dominant growth pattern in all these clusters. Fullerene-like precursor structures consisting of fused pentagon rings are also observed. The atoms in all these clusters exhibit pronounced preference for residing on the surface.

The angular intensity distribution of He beams scattered from compact clusters and from diffusion limited aggregates, epitaxially grown on metal surfaces, is investigated theoretically. The purpose is twofold: to distinguish compact cluster structures from diffusion limited aggregates, and to find observable {\em signatures} that can characterize the compact clusters at the atomic level of detail. To simplify the collision dynamics, the study is carried out in the framework of the sudden approximation, which assumes that momentum changes perpendicular to the surface are large compared with momentum transfer due to surface corrugation. The diffusion limited aggregates on which the scattering calculations were done, were generated by kinetic Monte Carlo simulations. It is demonstrated, by focusing on the example of compact Pt Heptamers, that signatures of structure of compact clusters may indeed be extracted from the scattering distribution. These signatures enable both an experimental distinction between diffusion limited aggregates and compact clusters, and a determination of the cluster structure. The characteristics comprising the signatures are, to varying degrees, the Rainbow, Fraunhofer, specular and constructive interference peaks, all seen in the intensity distribution. It is also shown, how the distribution of adsorbate heights above the metal surface can be obtained by an analysis of the specular peak attenuation. The results contribute to establishing He scattering as a powerful tool in the investigation of surface disorder and epitaxial growth on surfaces, alongside with STM.

Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.

We report here on experimental and numerical studies of the influence of surfactants on mineral gel synthesis. The modification of the gel structure when the ratios water-precursor and water-surfactant vary is brought to the fore by fractal dimension measures. A property of {\em polydispersity of the initial hydrolysis} is proposed to explain these results, and is successfuly tested through numerical experiments of three dimensional chemically limited aggregation.

The structure of an aqueous solution of sodium chloride at a planar electrode is investigated by integral equation techniques. With the central force water model the aqueous electrolyte is modelled as a mixture of sodium and chloride ions and partially charged hydrogen and oxygen atoms interacting via effective spherically symmetric pair potentials. The bulk correlation functions are obtained from the Ornstein-Zernike equation. With the Wertheim-Lovett-Mou-Buff equation we have calculated the density profiles at the uncharged and charged electrode. Steric interactions between the differently sized ions and the ice-like water structure near the electrode dominates the ionic distribution. This model electrolyte also responds differently to opposite charges on the electrode.

Recent molecular simulation and integral equation results alkali-halide ion pair potentials-of-mean-force in water are discussed. Dielectric model calculations are implemented to check that these models produce that characteristic structure of contact and solvent-separated minima for oppositely charged ions in water under physiological thermodynamic conditions. Comparison of the dielectric model results with the most current molecular level information indicates that the dielectric model does not, however, provide an accurate description of these potentials-of-mean-force. We note that linear dielectric models correspond to modelistic implementations of second-order thermodynamic perturbation theory for the excess chemical potential of a distinguished solute molecule. Therefore, the molecular theory corresponding to the dielectric models is second-order thermodynamic perturbation theory for that excess chemical potential. The second-order, or fluctuation, term raises a technical computational issue of treatment of long-ranged interactions similar to the one which arises in calculation of the dielectric constant of the solvent. It is contended that the most important step for further development of dielectric models would be a separate assessment of the first-order perturbative term (equivalently the {\it potential at zero charge} ) which vanishes in the dielectric models but is generally nonzero. Parameterization of radii and molecular volumes should then be based of the second-order perturbative term alone. Illustrative initial calculations are presented and discussed.

Representing polyether-salt systems by chains of interacting coordination shells, defined by the cation and by its nearest ligands, we derive the interaction potential between closest shells -- the inter-shells potential -- in terms of two-electron polarization effects. Values are presented for monovalent-based crystalline poly(ethylene oxide), PEO, electrolytes. For the eutectic composition PEO 12 EuBr 3 , the inter-shells energy is evaluated also by relating the empirical value of the nearest-ligands local-field potential with the variation of the Eu 3+ concentration. Both methods give the same results.

The solution of the Ornstein-Zernike equation with various closure approximations is studied. This problem is rewritten as an integral equation that can be solved iteratively on a grid. The convergence of the fixed point iterations is relatively slow. We consider transformations of the sequence of solution vectors using non-linear sequence transformations, so-called vector extrapolation processes. An example is the vector J transformation. The transformed vector sequences turn out to converge considerably faster than the original sequences.

Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good and poor folding sequences. The good (fast folding) sequences have sharp well-defined thermodynamic transitions while the slow folding sequences have broad ones. We find two independent transitions: a collapse transition to compact states and a folding transition from compact states to the native state. The collapse transition is second order-like, while folding is first order. The system is also studied as a function of the energy parameters. In particular, as the average energetic drive toward compactness is reduced, the two transitions approach each other. At zero average drive, collapse and folding occur almost simultaneously; i.e., the chain collapses directly into the native state. At a specific value of this energy drive the folding temperature falls below the glass point, indicating that the chain is now trapped in local minimum. By varying one parameter in this simple model, we obtain a diverse array of behaviors which may be useful in understanding the different folding properties of various proteins.