Molecular modeling coordinates

Molecules are usually represented as 2D formulas or 3D molecular models. WhOe the 3D coordinates of atoms in a molecule are sufficient to describe the spatial arrangement of atoms, they exhibit two major disadvantages as molecular descriptors they depend on the size of a molecule and they do not describe additional properties (e.g., atomic properties). The first feature is most important for computational analysis of data. Even a simple statistical function, e.g., a correlation, requires the information to be represented in equally sized vectors of a fixed dimension. The solution to this problem is a mathematical transformation of the Cartesian coordinates of a molecule into a vector of fixed length. The second point can... 

Protein Data Bank (Section 27 20) A central repository in which crystallographic coordinates for biological mole cules especially proteins are stored The data are accessi ble via the Worldwide Web and can be transformed into three dimensional images with appropriate molecular modeling software... 

Another group of macrocyclic ligands that have been extensively studied are the cycHc polyethers, such as dibenzo-[18]-crown-6 (5), in which the donor atoms are ether oxygen functions separated by two or three carbon atoms. The name crown ethers has been proposed (2) for this class of compounds because of the resemblance of their molecular models to a crown. Sandwich stmctures are also known in which the metal atom is coordinated with the oxygen atoms of two crown molecules. 

Internal coordinate molecular modeling is an efficient instrument with specific advantages that make it an indispensable complement to other existing approaches. It is best suited for simulation and analysis of large-scale structural transformations in biomacro-mole-cules, and at present ICMD is generally considered the most powerful tool in conforma-... 

So, back then to aspirin. Very often, X-ray data is available for the molecule of interest or related molecules. The lingua franca for molecular modelling purposes is a file of Cartesian coordinates such as the following. pdb (Protein Database) file. Figure 1.13, for aspirin. 

The formation of dimeric products is unique for the case of boron, because analogous complexes with other elements are all monomeric [95]. This can be attributed to the small covalent radius of the boron atom and its tetrahedral geometry in four-coordinate boron complexes. Molecular modeling shows that bipyramidal-trigonal and octahedral coordination geometries are more favorable for the formation of monomeric complexes with these ligands. 

Lipton, M Still, W. C. The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space. J. Comp. Chem. 1988, 9, 343-355. 

Application of coordination compounds in medicine, materials chemistry, and as catalysts are mentioned and are cross-referenced to a fuller discussion in Volume 9. Comment is made on application of complexes in nanotechnology, and on the molecular modeling of complexes. The material cannot be totally comprehensive because of space limitations, but is selected in such a way to give the most effective review of discoveries and new interpretations. 

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