Surface, molecular solvent-accessible

The following models describe those definitions of molecular surfaces that are most widely used. The van dcr Waals surface, the solvent-accessible surface, and the Connolly surface (sec below) based on Richards definitions play a major role [182],... 

They are the partial positive surface area PPSAi), the total charge weighted positive surface area PPSA2) and the atomic charge weighted positive surface area (PPSAj), divided by the total molecular solvent-accessible surface area (SA-SA), i.e. 

Let SAd and SAa be the solvent accessible surface areas of hydrogen-bonding donors (d) and acceptors (a), respectively, and Qa the corresponding partial atomic charges, SASA the molecular solvent-accessible surface area the HB-CPSA descriptors are then defined as follows (note that the two different symbols encountered in the literature for some are considered as synonymous). 

Connoiiy surface area - molecular surface (O solvent-accessible molecular surface) constant interval reciprocal indices -> distance matrix constant and near-constant variables variable reduction constitutional descriptors... 

Steric descriptors and/or -> size descriptors representing the volume of a molecule. The volume of a molecule can be derived from experimental observation such as the volume of the unit cell in crystals or the molar volume of a solution or from theoretical calculations. In fact, analytical and numerical approaches have been proposed for the calculation of molecular volume where the measure depends directly on the definition of - molecular surface-, -> van der Waals volume and -> solvent-excluded volume are two volume descriptors based on van der Waals surface and solvent-accessible surface, respectively. 

Connolly surface area —> molecular surface (0 solvent-accessible molecular surface)... 

Depending on the application, models of molecular surfaces arc used to express molecular orbitals, clcaronic densities, van dor Waals radii, or other forms of display. An important definition of a molecular surface was laid down by Richards [182] with the solvent-accessible envelope. Normally the representation is a cloud of points, reticules (meshes or chicken-wire), or solid envelopes. The transparency of solid surfaces may also be indicated (Figure 2-116). 

Tn general, the. solvent-accessible surface (SAS) represents a specific class of surfaces, including the Connolly surface. Specifically, the SAS stands for a quite discrete model of a surface, which is based on the work of Lee and Richards [182. They were interested in the interactions between protein and solvent molecules that determine the hydrophobicity and the folding of the proteins. In order to obtain the surface of the molecule, which the solvent can access, a probe sphere rolls over the van der Waals surface (equivalent to the Connolly surface). The trace of the center of the probe sphere determines the solvent-accessible surjace, often called the accessible swface or the Lee and Richards surface (Figure 2-120). Simultaneously, the trajectory generated between the probe and the van der Waals surface is defined as the molecular or Connolly surface. 

Figure 2-120. The center ofthe rolling probe sphere defines the solvent-accessible surface during movement of the probe over the van der Waals surface. Thus, the molecular surface is expanded by the radius of the solvent molecule,...

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. 

Richmond T J 1984. Solvent Accessible Surface Area and Excluded Volume in Proteins. Journal oj Molecular Biology 178 63-88. 

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