The 3D-Structure

One more application area is composite materials where one wants to investigate the 3D structure and/or reaction to external influences. Fig.3a shows a shadow image of a block of composite material. It consists of an epoxy matrix with glass fibers. The reconstructed cross-sections, shown in Fig.3b, clearly show the fiber displacement inside the matrix. The sample can be loaded in situ to investigate the reaction of matrix and fibers to external strain. Also absorption and transmission by liquids can be visualized directly in three-dimensions. This method has been applied to the study of oil absorption in plastic granules and water collection inside artificial plant grounds. 

Clearly, the next step is the handling of a molecule as a real object with a spatial extension in 3D space. Quite often this is also a mandatory step, because in most cases the 3D structure of a molecule is closely related to a large variety of physical, chemical, and biological properties. In addition, the fundamental importance of an unambiguous definition of stereochemistry becomes obvious, if the 3D structure of a molecule needs to be derived from its chemical graph. The moleofles of stereoisomeric compounds differ in their spatial features and often exhibit quite different properties. Therefore, stereochemical information should always be taken into ac-count if chiral atom centers are present in a chemical structure. 

Tabic 2-6 gives an overview on the most common file formats for chemical structure information and their respective possibilities of representing or coding the constitution, the configuration, i.c., the stereochemistry, and the 3D structure or conformation (see also Sections 2..3 and 2.4). Except for the Z-matrix, all the other file formats in Table 2-6 which are able to code 3D structure information arc using Cartesian coordinates to represent a compound in 3D space. 

The 3D structure of a raolectile can be derived either from experiment or by computational methods. Regardless of the origin of the 3D model of the molecule under consideration, the user should alway.s be aware of how the data were obtain-... 

Figure 2-106. Ring teinplates foc a saturated siy-inernbei ed cing and a six-ineinbeced ring with one double bond as implemented in the ring conformation table of the 3D structure generator CORINA.

Having looked at the general structure of PDB files, let us now examine a sample PDB file. The file represents the structure of r conotoxin PNll polypeptide (PDB ID Ipcn) and was retrieved from the Protein Data Bank [53]. Figure 2-109 shows the 3D structure of the molecule. 

Figure 2-137. Screenshot of the 3D structure viewer and download options for the 3D structure generated on the CORINA web interface.

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

Physical, chemical, and biological properties are related to the 3D structure of a molecule. In essence, the experimental sources of 3D structure information are X-ray crystallography, electron diffraction, or NMR spectroscopy. For compounds without experimental data on their 3D structure, automatic methods for the conversion of the connectivity information into a 3D model are required (see Section 2.9 of this Textbook and Part 2, Chapter 7.1 of the Handbook) [16]. 

Two of the widely used programs for the generation of 3D structures are CONCORD and CORINA. CONCORD was developed by Pearlman and co-workers (17, 18] and is distributed by TRIPOS (19). The 3D-structure generator CORINA originates from Gasteiger s research group [20-23] and is available from Molecular Networks [24],... 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

In order to consider the 3D structure but make the chirality code independent of a specific conformer, r- is taken as the sum of the bond lengths between atoms i and j on the path with a minimum number of bond counts. 

Infrared spectra are strongly dependent on the 3D structure of a compound, as reflected by the success of attempts to simulate infrared spectra from 3D structure representations (see Section 10.2.5). Infrared spectra should therefore be taken as representations of a chemical compound for modeling properties that are suspected to be dependent on the 3D structure of a compound NMR spectra also depend on... 

D descriptors), the 3D structure, or the molecular surface (3D descriptors) of a structure. Which kind of descriptors should or can be used is primarily dependent on the si2e of the data set to be studied and the required accuracy for example, if a QSPR model is intended to be used for hundreds of thousands of compounds, a somehow reduced accuracy will probably be acceptable for the benefit of short processing times. Chapter 8 gives a detailed introduction to the calculation methods for molecular descriptors. 

The compounds were described by a set of 32 radial distribution function (RDF) code values [27] representing the 3D structure of a molecule and eight additional descriptors. The 3D coordinates were obtained using the 3D structure generator GORINA [33]. 

Since IR spectroscopy monitors the vibrations of atoms in a molecule in 3D space, information on the 3D arrangement of the atoms should somehow be contained in an IR spectrum. However, the relationships between the 3D structure and the IR spectrum are rather complex, so no general attempt has yet been successfiil in deriving the 3D structure of a molecule directly from the IR spectrum. 

Figure 10.M7. 3D structures of the reactants and products of Figure 10.3-16b as obtained by the 3D structure generator CORINA.

The structure database has been enriched with the 3D structures of all compounds as generated by the 3D structure generator CORINA (sec Section 2.9,... 

Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family.

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