Molecular surface gradients

To display properties on molecular surfaces, two different approaches are applied. One method assigns color codes to each grid point of the surface. The grid points are connected to lines chicken-wire) or to surfaces (solid sphere) and then the color values are interpolated onto a color gradient [200]. The second method projects colored textures onto the surface [202, 203] and is mostly used to display such properties as electrostatic potentials, polarizability, hydrophobidty, and spin density. 

The linear solvent strength (LSS) model combined with QSRR calculations has been applied for the prediction of retention in gradient RP-HPLC. It was established that total dipole moment (jd), electron excess charge of the most negatively charged atom (<5Mm) and water-accessible molecular surface area (Awas) exert the highest impact on the retention ... 

Fig. 38 (Upper panel) Scanning force microscopy images of gold nanoparticles (diameter 17 nm) adsorbed along a surface-anchored poly(acryl amide) brush with a molecular weight gradient (Edge of each image = 1 p.m). (Lower panel) Dry thickness of poly(acryl amide) on the substrate before particle attachment (right, ) and particle number density profile (left, ). (Reproduced with permission from [140])...

H. Li and J. H. Jensen, Improving the accuracy and efficiency of geometry optimizations with the polarizable continuum model new energy gradients and molecular surface tessellation, J. Comput. Chem., 25 (2004) 1449-1462. 

The corresponding three-dimensional grid plots for the S-values [derived according to Eq. (5)] of these two polypeptides as the temperature and j/ values were systematically varied are shown in Fig. 26a-d. In each case, the S values for polypeptides 1 and 2 were derived by regression analysis methods from the gradient of the experimental plots of log k, vemus i/> at the specified j/ and T values with the regression eoefficients >0.9985. In turn, the S value of a peptide or protein in the presence of an RPC sorbent can be related [16,20,211,212] to extrathermodynamic parameters, such as the accessible molecular surface area, A/l, ui, through the expression... 

R. J. Wawak, K. D. Gibson, and H. A. Scheraga, Gradient discontinuities in calculations involving molecular surface area. J. Math. Chem. IS, 207 232 (1994). 

Pulay P 1977 Direct use of the gradients for investigating molecular energy surfaces Appiications of Eiectronic Structure Theory ed H F Schaefer III (New York Plenum) p 153... 

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