3D property

Thus, we have defined V , the contribution of atom i to the approximate VSA of a molecule. This contribution is reasonably accurate and has the advantage that it can be calculated using just connection table information and much more rapidly than the 3D VSA contribution. The approximate molecular VSA is very much a 2-ViD descriptor it is (highly correlated to) a conformation independent 3D property that requires only 2D connection information. 

Other measures of properties in 3D, such as Molecular Lipophilicity Potential (MLPot) and Molecular Hydrogen Bond Potential (MHBP), have been used to characterize 3D properties. They are defined for points on a molecular surface created around the molecule and calculated from the summation of contributions from the substructural fragments making up the molecule weighted by the distance function. The hydrogen bond potentials include an angle-dependent function. 

Lui, D., Jiang, H., Chen, K. and Ji, R. Anew approach to design virtual combinatorial library with genetic algorithm based on 3D property. J. Chem. Inf. Comput. Sci., 1998,38, 233-242. 

Ferrocene and some of its derivatives are well suited for the formation of CT complexes and offer an entry into solid state organometallic chemistry. Because such CT complexes contain radical species, the consideration of their physical properties is of fundamental importance and now constitutes an interdisciplinary research field. The systematic study of the magnetic properties of CT complexes of, notably, decamethylferrocene, by the Miller Epstein group has led to the discovery of bulk ferromagnetic molecular materials and to new insights into the mechanisms of magnetic coupling. Such results have shown that ID materials, as most CT complexes are, can display 3D properties if the molecular components are matched... 

Most commonly applied descriptors for the development of Fa models have different 2D and 3D properties. These are physicochemical, topological, electro-statical, or geometrical. Several different software programs for the calculation of these descriptors are available, which are rapid and allow several hundreds of descriptors to be calculated. Typical descriptors are discussed in detail in Section 14.2. 

The descriptors of the molecular structures that are used in QSAR include physical and electronic properties, fragment compositions, as well as calculated properties of the three-dimensional (3D) structures of the compounds. The 3D properties include scalar parameters like solvent-accessible surface area, or hydro-phobic surface area. They also include field-type reductions of the structure that represent steric interactions, electrostatic potentials, hydrogen-bonding potential, hydrophobic interactions, and so on. 

Descriptors can be divided into whole molecule properties, descriptors that can be calculated from the 2D graph of a structure, and descriptors that are based on 3D properties of molecules. 

The entire 3D property function P(r) can be represented by an infinite family of IPCOs, by taking one such surface G a) for each value of the contour parameter a, throughout the entire range a in a< ainiax- The minimum and maximum values Amin and flmax of the contour threshold a depend on the property P and the actual molecular system studied. 

One may require that parameters is chosen so that the absolute value 5(r,s) of the Somoyai function 5(r,s) is minimized within the envelope ( 1,02) of the given 3D property P(r) ... 

The molecular subrange of the 3D property F(r) is of special importance this range contains all thresholds a for which the level set F a) of property F(r) is arcwise connected. For the molecular subrange level sets F a) of the composite nuclear potential this condition implies that all nuclei are contained within each such F a). 

STEP 1. For each contour value a within a range of values for 3D property P(r), the IPCOs G(a) are partitioned into local curvature domains relative to each value b of a range of reference curvatures. 

By definition, the shape groups of the property P(r) are the algebraic homology groups of the family of topological equivalence classes of the truncated surfaces. The family of all of these equivalence classes involves all property thresholds a as well as all reference curvatures b. The shape groups provide a detailed shape description of the entire 3D property P(r). 

Molecules exist as flexible objects in 3D space. Therefore, although many properties can be calculated and understood from the structure diagrams of molecules, it is possible that using 3D properties directly would provide more insight into structure-activity relationships. A complication here is that to calculate 3D properties one must decide which conformation of the molecules to use. If there are structurally diverse molecules in the dataset, then one must usually also decide how to align the various molecules. 

QSARs include statistical methods to relate biological activities (most often expressed by logarithms of equipotent molar activities) with structural elements (Free Wilson analysis), physicochemical properties (Hansch analysis), or fields (3D QSAR). The parameters used in a QSAR model are also called (molecular) descriptors. Classical QSAR analyses (Hansch and Free Wilson analyses) consider only 2D structures. Their main field of application is in substituent variation of a common scaffold. 3D-QSAR analysis (CoMFA) has a much broader scope. It starts from 3D structures and correlates biological activities with 3D-property fields (McKinney et al. 2000). 

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