2D structures

However, care has to be taken to keep this graphical 3D information in 2D structure diagrams unambiguous. Since the reference plane can be chosen arbitrarily, there exist different possible ways of displaying the stereochemistry (Figure 2-68). 

The commercial 2D structure editor. Chemistry 4D-Draw, from Chemlnnovativc Software Inc., includes two additional special modules besides conventional chemical drawing tools. NamExpert provides the interpretation ofa compound name according to the lUPAC nomenclature to create the corresponding chemical structure. The latter can be represented in three different styles the shorthand. Kckulc. or semi-structural formula. In contrast to NamExpert, the Nomenclature module assigns lUPAC names to drawn structures. 

The additional integrated module, the ACD/3D Viewer, can visualize 2D structures as 3D models, after geometry optimization (see Section 2.12.3.1 and Figure 2-132, below). 

ISlS/Draw has no genuine molecular visualization tool. The rotate tool changes only the 2D rotate tool into a 3D rotate tool which rotates 2D structures in three dimensions. In order to visualize chemical structures in different styles and perspectives, it is necessary to paste the drawing, e.g., to the ACD/3D Viewer. 

SymApps converts 2D structures From the ChemWindow drawing program into 3D representations with the help of a modified MM2 force field (see Section 7.2). Besides basic visualization tools such as display styles, perspective views, and light source adjustments, the module additionally provides calculations of bond lengths, angles, etc, Moreover, point groups and character tables can be determined. Animations of spinning movements and symmetry operations can also he created and saved as movie files (. avi). 

Stereochemistry can be represented graphically in 2D structures, but also by (permutations) descriptors. It is included in all line notations and exchange formats. 

Full structure search can be developed by using similar approaches to those employed in the case of 2D structure search. Thus, some topological indices can be modified in such a way that they include geometrical information. For example, the global index given by Eq. (4) can be modified to Eq. (11), where are real interatomic distances. 

When the structure is submitted its 3D coordinates arc calculated and the structure is shown at the left-hand side in the form of a 2D structure as well as a rotatable 3D structure (see Figure 10.2-11). The simulation can then be started the input structure is coded, the training data are selected, and the network training is launched. After approximately 30 seconds the simulation result is given as shown in Figure 10,2-11. 

Figure 10.4-7. Representative 2D structures of dopamine and benzodiazepine agonists.

Hashed fingerprints, structural keys 2D structure See Section 12.2... 

Counts of specific atoms, rings or other 2D structure Typically based on... 

Atom pairs, topological torsions 2D structure See Section 12.9.3... 

Partial atomic charge, polarisability 3D or 2D structure See Section 4.9... 

Many of the descriptors which can be calculated from the 2D structure rely upon the molecular graph representation because of the need for rapid calculations. Kier and Hall have developed a large number of topological indices, each of which characterises the molecular structure as a single number [Hall and Kier 1991]. Every non-hydrogen atom ir the molecule is characterised by two delta values, the simple delta Si and the valence delta SJ ... 

Fig. 2 Molecular structures of compounds 1 and 2. A 2D structures of 1 and 2, and B their energy-minimized 3D structures, which used the molecular modeling by Guyen et al. (2004) [11]...

Aimed 2D structures are completely artificially generated using appropriate tools. The favourite tool is, without doubt, the AFM tip. Mirkin et al. applied AFM tools to use it as a pen [53,54]. With the help of the water meniscus between tip and surface, which is always present at a room atmosphere, molecules from a reservoir on top of the tip are transported to a surface, which must have strong attraction to at least one end of the molecules. 

The anionic substructure of the salt Cs2[Ni(N3)4] H202183 consists of a 2D structure formed by Ni(N3)6 octahedra connected via four EE azido groups placed in a distorted plane, but no magnetic data have been reported. 

Ag2L2](C2F5C02)2 have been prepared and they show 2D structures. In (190) the ligands are positioned face to face by the two Ag atoms and form a box structure the 7r-7r stacking between pyridine rings gives the 2D framework.1159... 

In Figure 2 an example is given the 2D structure of DIMBOA is converted in a optimized 3D structure where the torsion angles have the biggest impact on the energy of the molecule and dictate the overall 3D molecular shape. 

The complex TBA2[Ni(dmit)2]7 2MeCN was the first reported conducting dmit2- salt.210 A 2D-structure was present in a-(Et2Me2N)[Ni(dmit)2]2,211 while the first superconductor containing a dithiolene system, (TTF)[Ni (dmit)2],212 was reported in 1986. To date, nine other compounds based on... 

As illustrated in the next section, the use of biological fingerprints, such as from a BioPrint profile, provides a way to characterize, differentiate and cluster compounds that is more relevant in terms ofthe biological activity of the compounds. The data also show that different in silico descriptors based on the chemical structure can produce quite different results. Thus, the selection of the in silico descriptor to be used, which can range from structural fragments (e.g. MACCS keys), through structural motifs (Daylight keys) to pharmacophore/shape keys (based on both the 2D structure via connectivity and from actual 3D conformations), is very important and some form of validation for the problem at hand should be performed. 

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