Interface between platinum(111) and liquid isopropanol (2-propanol): a model for molecular dynamics studies

A molecular dynamics model and its parametrization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programed desorption experiment [Surf. Sci. 395, 248 (1998)]. The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl "brush." This brush then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atom distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence the mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions.     

Treatment of electrostatic interactions in simulations of the interface between transition metal surfaces and organic matter: the discrete classical model and the reaction-field dielectric method

A more efficient molecular dynamics model is devised to study the interface between platinum(111) and liquid isopropanol. The faster reaction-field dielectric method (RFD) is investigated as the alternative to the very accurate discrete classical model (DCM) (M. W. Finnis, Surf. Sci., 1991, 241, 61) to account for the electrostatic interactions at the interface. Differences in static and dynamic properties of the interface are examined. The mass-density and number-density distributions showed only a little sensitivity towards the choice of the method. The orientational structure revealed notable but still small quantitative changes for highly-polarized parts of the isopropanol molecules if the RFD is used instead of the DCM. The general qualitative picture is still preserved. The simulations of the platinum(111)/isopropanol interface with the DCM or the Ewald summation were carried out for longer times than in our previous contribution (K. B. Tarmyshov and F. Müller-Plathe, J. Chem. Phys., 2007, 126, 74702). The analysis disclosed that the influence of chemical or electrostatic interactions at the interface on the relative orientation of the neighbouring hydroxyl groups, which are adsorbed on the surface, is notably smaller than reported before. Overall, the reaction-field dielectric method can be used to study the properties of the interface between transition metals and organic matter, if there appears a chemical bond of 10 kT or higher between the surface and adsorbate molecules or their parts.     

Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP

The atomistic molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.     

Short-term changes in delta(13)C and delta(15)N signatures of water discharged from grazed grasslands

The composition of dissolved organic matter (DOM) in a soil is the product of a variety of soil processes. Changes in the composition of DOM in water discharged from soil should, therefore, give an important insight into modifications in these soil processes. We hypothesise that these processes in soils, under different grassland management regimes, would be affected to different extents by the short-term disturbance of a storm event and that evidence of this could be detected in delta(13)C and delta(15)N signatures in drainage and surface runoff waters. During a storm event we collected discharge waters from 1 ha grassland lysimeters, with or without artificial drainage, which received contrasting fertiliser inputs, and delta(13)C and delta(15)N signatures were determined. Changes in (13)C enrichment during the storm event were clearly identifiable, as were differences between plots for (13)C and (15)N, illustrating that this technique has potential to be a useful tool for identifying and investigating short- and long-term changes in soil organic matter dynamics. Copyright 1999 John Wiley & Sons, Ltd.     

Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study

MD studies of liquid isopropyl alcohol and melts of short poly(vinyl alcohol) (PVA) oligomers are described. The specific volume was found to depend inversely on the number N of repeat units. If the chain length is enhanced, the viscosity of the PVA melt increases and the peaks in the radial distribution function become sharper. Additional peaks that appear in melts of PVA chains are of pure intramolecular origin. The calculated radius of gyration was found to depend on the number of formula units via . The orientation correlation functions showed that all molecular vectors of PVA melts with chain lengths N = 1, 2, 3 relax completely within a few nanoseconds. The relaxation times for the O H bond vector as obtained via the Kohlrausch‐Williams‐Watts expression showed an exponential dependence on the number of repeat units.

     

Magnetic behavior of the oxide spinels: Li0.5Fe2.5−2x Al x Cr x O4

In order to study the effect of substitution of Fe³⁺ by Al³⁺ and Cr³⁺ in Li_0.5Fe_2.5O₄ on its structural and magnetic properties, the spinel system Li_0.5Al _x Cr _x Fe_2.5?2x O₄ (x=0.0, 0.2, 0.4, 0.5, 0.6 and 0.8) has been characterized by X-ray diffraction, high field magnetization, low field ac susceptibility and ⁵⁷Fe Mossbauer spectroscopy. Contrary to the earlier reports, about 50% of Al³⁺ is found to occupy the tetrahedral sites. The system exhibits canted spin structure and a central paramagnetic doublet was found superimposed on magnetic sextet in the Mössbauer spectra (x>0.5).     

Ion binding to cucurbit[6]uril: structure and dynamics

Molecular dynamics simulations are used to study the microscopic structure and dynamics of cations bound to cucurbit[6]uril (CB[6]) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183 M for the salts and 0.0184 M for CB[6]. The cations bind only to CB[6] carbonyl oxygens. They are never found inside the CB[6] cavity. Complexes with Na(+) and K(+) mostly involve one cation, whereas with Ca(2+) single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. When bound to CB[6], sodium and potassium cations jump mainly between nearest or second-nearest neighbors. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB[6] oxygen. A few water molecules (zero to four) can occupy the CB[6] cavity, which is limited by the CB[6] oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cation activity as "lids" over the CB[6] portal cannot, however, be identified. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells.