Molecular structure internal representation

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

This is a very natural way to describe molecular structures because their most important feature for most applications, the connectivity of atoms, forms the basis of the internal representation. The big advantage of this model is that it transforms many problems of chemistry into problems of network topology. 

Recently, a universal string representation method was proposed and published. The International Chemical Identifier,17 or InChl , is a definition and set of methods maintained by the International Union of Pure and Applied Chemistry. It promises to provide a truly universal character string representation of molecular structure. Whether it will replace the widely used SMILES is yet to be seen. 

As with all data in an RDBMS, there is an external and internal representation of data. This was discussed in an earlier chapter for standard data types, such as text and numeric. For molecular structures, there is of course no SQL standard. When building a database containing molecular structures, a decision should first be made which internal representation will be used and which external representation. 

This chapter focused primarily on SMILES and canonical SMILES. It is feasible and common to use SMILES as the internal representation of molecular structure. Using the SQL functions described in this chapter,... 

Another choice for the internal representation of molecular structure is a molfile. It would be possible to construct SQL functions like those described in this chapter that would operate on this type of data. One disadvantage of molfiles is their greater size compared with SMILES. One advantage is that it is possible to store atomic coordinates, which is not possible with SMILES. There are other molecular file formats, but these are substantially the same as a molfile, except perhaps for specific atom types that may be of use in some database applications. 

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. 

The internal representation of molecules is accomplished using the technique developed by Wipke and Dyott (3), and later used by Molecular Design Limited (MDL) in several of their commercial programs. An MDL program, MACCS, is used to graphically input the molecular structure of the compound of interest, then save that structure into a file (molfile). The importation of this file provides CHESS with information such as the number and type of atoms and bonds, as well as stereochemical information. 

The generalized cylinder representation of a macromolecule is a much sparser description of the system than is the full set of Cartesian or internal coordinates which define the position of every atom. The generalized cylinder representation leaves the molecular structure seriously underdetermined. It is eventually necessary to recover an estimate of all the atomic coordinates for more detailed study. Here is where DOCENT takes on some of the features of an expert system, which must make plausible judgments without complete information. 

Distance geometry - is a general method for converting a set of distance ranges or bounds into a set of Cartesian coordinates consistent with these bounds. A molecular structure is described by the set of all pairwise interatomic distances in a distance matrix. Cartesian and internal coordinates have been used historically primarily for mathematical and computational convenience for many modeling applications a distance matrix representation is simpler because chemical struaure information is often described by distances. 

Figure 42 Molecular structure of internally double-locked state and schematic representation of the self-locking operation in response to the photoisomerization of l,2-di-(4-p3ridyl)ethylene. (Reproduced from Ref. 79. American Chemical Society, 2006.)...

Illustration of the local symmetry of the chiral and nonchiral SmC phases of rod-shape molecules. Both SmC and SmC have a two-fold symmetry axis normal to the c-director. In SmC (a) the yz plane is a mirror plane, because the molecules have no handedness in SmC (b) the mirror image would have opposite handedness, so it is not a symmetry operation of the material. For this reason the x component of the molecular dipoles do not average out, allowing the presence of a permanent electric polarization of the material. Note the double-twist representation of the molecules serves only to indicate the chirality, and we do not assume such internal molecular structure. 

As was said in the introduction (Section 2.1), chemical structures are the universal and the most natural language of chemists, but not for computers. Computers woi k with bits packed into words or bytes, and they perceive neither atoms noi bonds. On the other hand, human beings do not cope with bits very well. Instead of thinking in terms of 0 and 1, chemists try to build models of the world of molecules. The models ai e conceptually quite simple 2D plots of molecular sti uctures or projections of 3D structures onto a plane. The problem is how to transfer these models to computers and how to make computers understand them. This communication must somehow be handled by widely understood input and output processes. The chemists way of thinking about structures must be translated into computers internal, machine representation through one or more intermediate steps or representations (sec figure 2-23, The input/output processes defined... 

Fig. 10.16. Properties of the inner cavity. Half cut presentations of molecule A (left side view, center and right top views) with cut regions shown in dark gray. (Left) Surface representation of the internal tunnel illustrating its molecular-sieve character. Access is restricted to single secondary structure elements as shown by the modeled polyalanine helix, which is colored yellow. (Center) Top view on the...

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