Atomic surface area

H-bond donor/acceptor atoms) Surface area of atoms with partial + [20]... 

Examples of combined descriptors using products are the contributions SA , largely used in -> CPSA descriptors, where q and 5A are partial charges and atomic surface areas [Bakken and Jurs, 1999a]. 

The second parameter is the surface fraction of hydrophobic carbon atoms Sf, calculated analogously to Wq - instead of atom counts, their CPK atomic surface areas from optimized geometries of compounds (in charged forms at neutral pH) are used. 

Labute, P. (2008) The generalized Born/ volume integral implicit solvent model estimation of the free energy of hydration using London dispersion instead of atomic surface area./. Comput. Chem. 29, 1693-1698. 

SA—positively charged solvent-accessible atomic surface area... 

Each catalyst atom surface area (cm ) 4nr2 3.14E-12... 

While a number of surface area approximation techniques have been proposed, the methods which currently gain the most attention are those of Lee and Richards, Hermann, and Pearlman. In these three algorithms, atomic surface areas are determined by cutting a molecule s individual spheres into fiat slices, as with Lee and Richards, or lunes, as described by Hermann and Pearlman. The overlap between spheres is calculated and the nonocluded areas are summed to yield the surface area associated with a molecule. 

Finally, in the case of solids, there is the difficulty that surface atoms and molecules differ in their properties from one location to another. The discussion in Section VII-4 made clear the variety of surface heterogeneities possible in the case of a solid. Those measurements that depend on the state of surface atoms or molecules will generally be influenced differently by such heterogeneities. Different methods of measuring surface area will thus often not only give different absolute values, but may also give different relative values for a series of solids. 

We have considered briefly the important macroscopic description of a solid adsorbent, namely, its speciflc surface area, its possible fractal nature, and if porous, its pore size distribution. In addition, it is important to know as much as possible about the microscopic structure of the surface, and contemporary surface spectroscopic and diffraction techniques, discussed in Chapter VIII, provide a good deal of such information (see also Refs. 55 and 56 for short general reviews, and the monograph by Somoijai [57]). Scanning tunneling microscopy (STM) and atomic force microscopy (AFT) are now widely used to obtain the structure of surfaces and of adsorbed layers on a molecular scale (see Chapter VIII, Section XVIII-2B, and Ref. 58). On a less informative and more statistical basis are site energy distributions (Section XVII-14) there is also the somewhat laige-scale type of structure due to surface imperfections and dislocations (Section VII-4D and Fig. XVIII-14). 

The MEP at the molecular surface has been used for many QSAR and QSPR applications. Quantum mechanically calculated MEPs are more detailed and accurate at the important areas of the surface than those derived from net atomic charges and are therefore usually preferable [Ij. However, any of the techniques based on MEPs calculated from net atomic charges can be used for full quantum mechanical calculations, and vice versa. The best-known descriptors based on the statistics of the MEP at the molecular surface are those introduced by Murray and Politzer [44]. These were originally formulated for DFT calculations using an isodensity surface. They have also been used very extensively with semi-empirical MO techniques and solvent-accessible surfaces [1, 2]. The charged polar surface area (CPSA) descriptors proposed by Stanton and Jurs [45] are also based on charges derived from semi-empirical MO calculations. 

Prediction of various physicochemical properties such as solubihty, lipophhicity log P, pfQ, number of H-donor and acceptor atoms, number of rotatable bonds, polar surface area), drug-likeness, lead-likeness, and pharmacokinetic properties (ADMET profile). These properties can be applied as a filter in the prescreening step in virtual screening. 

The PCM algorithm is as follows. First, the cavity siuface is determined from the van der Waals radii of the atoms. That fraction of each atom s van der Waals sphere which contributes to the cavity is then divided into a nmnber of small surface elements of calculable surface area. The simplest way to to this is to define a local polar coordinate frame at tlie centre of each atom s van der Waals sphere and to use fixed increments of AO and A(p to give rectangular surface elements (Figure 11.22). The surface can also be divided using tessellation methods [Paschual-Ahuir d al. 1987]. An initial value of the point charge for each surface element is then calculated from the electric field gradient due to the solute alone ... 

Hasel W, T F Hendrickson and W C Still 1988. A Rapid Approximation to the Solvent Accessibh Surface Areas of Atoms. Tetrahedron Computer hAethodology 1 103-116. 

The solvent accessible surface area (SASA) method is built around the assumption that the greatest amount of interaction with the solvent is in the area very close to the solute molecule. This is accounted for by determining a surface area for each atom or group of atoms that is in contact with the solvent. The free energy of solvation AG° is then computed by... 

GAPT (generalized atomic polar tensor) a charge calculation method GB/SA (generalized Born/surface area) method for computing solvation effects... 

As noted earlier m this section branched alkanes have lower boiling points than their unbranched isomers Isomers have of course the same number of atoms and elec Irons but a molecule of a branched alkane has a smaller surface area than an unbranched one The extended shape of an unbranched alkane permits more points of contact for mtermolecular associations Compare the boiling points of pentane and its isomers... 

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