Head-group atoms

Figure 1.5. Plan view of Cu(lll)/CH3S- pseudo-(lOO) reconstruction assuming a commensurate [ 4 ] registry of the overlayer and substrate. The methylthiolate species are represented by the S head-group atoms alone, shown as the darkest spheres. The Cu atoms of the reconstructed pseudo-(lOO) layer are shown more darkly shaded than those of the underlying substrate. For clarity the reconstructed overlayer has been omitted from the lower right-hand side of the diagram, exposing the outermost unreconstructed Cu(l 11) layer.

A from any lipid head group atom were considered to be bound, and any water more than 4 A away from all lipid head groups was considered to be bulk. Because the bound/bulk status of waters can change during the course of a simulation, the nonbonded atom list was updated every picosecond. Of the 553 waters used in the simulation, on average there were only 160 bulk waters. The velocity autocorrelation functions (VAF), the mean square displacements (MSD), and the orientational correlational functions (OCF) for the bound and bulk waters were calculated. VAFs were calculated as ... 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

The functional reaction center contains two quinone molecules. One of these, Qb (Figure 12.15), is loosely bound and can be lost during purification. The reason for the difference in the strength of binding between Qa and Qb is unknown, but as we will see later, it probably reflects a functional asymmetry in the molecule as a whole. Qa is positioned between the Fe atom and one of the pheophytin molecules (Figure 12.15). The polar-head group is outside the membrane, bound to a loop region, whereas the hydrophobic tail is... 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

Further experimentation may lead to a homogeneous sample however, it does appear that the amine head group does not have as strong an affinity for the silver atoms as the mercapto group. The dodecyl alcohol ligand was a poor ligand for creation of silver particles and only large particles were produced that were either too... 

Some of the more commonly used types of collector are listed in Table 1. Many of these contain sulfur atoms in their polar head groups and are used in the recovery of base metals from their... 

Figure 1 (Plate 1). A molecular view of a small section of a flat lipid bilayer generated by molecular dynamics simulations. The bilayers are composed of l-stearoyl-2-docosa-hexaenoyl-5M-g]ycero-3-phosphatidylcholine lipids, i.e. the sn 1 chain is 18 C atoms long and the sn2 chain has 22 carbons, including six cis double bonds. The hydrophobic core is in the centre of the picture, and the hydrated head-group regions are both on top and bottom of the view graph. The head group is zwitterionic and no salt has been added. From [102], Reproduced by permission of the American Physical Society. Copyright (2003)...

Figure 5. Profiles across the bilayer of the total lipid density of DPPC, the water density and the densities of certain lipid groups as obtained from MD simulations by Berger et al. [58]. The profiles are found by taking the time average over the last 300 ps of the simulation. The densities for the lipid head-group components are only shown on one side for clarity. The origin of the z-axis is arbitrarily positioned on the left of the bilayer. On the y-axis, the atom density in atoms per nm3 is given. Redrawn from [58] by permission of the Biophysical Society...

Figure 6. V ariation of the orientational order parameter 5 along the hydrocarbon chains of the lipids of DMPC lipid bilayers, according to MD simulations of Berger et al. [58]. The line is drawn to guide the eye. The spheres are experimental values obtained by Seelig and Seelig [59] using 2H-NMR spectroscopy. (Numbering of C-atoms from the head group to the CH3 terminal group). Redrawn from [58] by permission of the Biophysical Society...

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