2D chemical structures

The drawing software comprises a comprehensive collection of standard tools to sketch 2D chemical structures. To specify all its facilities and tools would go far beyond the scope of this overview, but there are some nice features that are very useful for chemists so they are mentioned here briefly. One of these enables the prediction of H and NMR shifts from structures and the correlation of atoms with NMR peaks (Figure 2-127). lUPAC standard names can be generated... 

Raymond, J. W. and Willett, P. (2002) Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. 

The THECOMAC database contains the stability constant, enthalpy, and entropy values for the complexations of the alkaline and alkaline earth metal cations with cyclic polyethers in water and organic solvents, and includes more than 3,500 records. Each record contains 22 textual and digital fields and 2D chemical structures of ligands. The database includes thermodynamic values for 330 cyclic polyethers containing oxygen coordination centers only.41... 

An INTERNET compatible database for solvent extraction of metal ions (SEDATA), developed by H. Watarai et al., contains about 9,600 equilibrium constants, including distribution constants, extraction constants, and adduct formation constants, for more than 1,400 ligands and 82 metal ions.50 Raw data points of extraction curves are also incorporated to be reconstructed as a figure. However, SEDATA contains no fields for 2D chemical structures of extractants and allows one to perform a search using only eight fields (classification, metal, valence, reagent, solvent, title of the paper, author, and year). 

The ID nucleotide/amino acid sequences in character format (without index, e.g., fasta format) can be converted into the 2D chemical structures with ISIS Draw, which can be downloaded from MDL Information System at http //www.mdli.com/ download/isisdraw.html for academic use. Install the package by issuing Run command, C Isis Draw23.exe. Launch IsisDraw to open the Draw window. 

Structure building, manipulation, comparison. SYBYL energy minimization of organic and biomolecules. Stick, space-filling, or cylinder (thick bonds) display. Interface to Chemical Abstracts Service registry files. Molfile transfer to SYBYL and Lab Vision. ChemPrint (under Windows) for 2D chemical structure drawing. PowerSearch for systematic and Monte Carlo conformational searching under Windows environment. Macintosh and PCs (DOS and Windows). 

Tel. 44-0625-871126, fax 44-0625-871128 Structure building, manipulation. Force field minimization. Stick, ball-and-stick, and space-filling display. Sabre for managing a database of 2D chemical structures. Macintosh. PC-Chemmod for structure building, manipulation, energy minimization of molecules with up to 2000 atoms. Stick and space-filling display. PCs. 

Management of databases of 2D chemical structures. PsiGen for 2D chemical structure drawing. PCs under Windows. 

Drawing 2D chemical structures. IR Search to retrieve vibrational spectra. Carbon-13 Search to retrieve NMR spectra. PCs. 

Gesellschaft fiir Technisch-Wissenschaftliche Software mbH Rudolf Diesel Strasse 1 W-8032 Grafelfing, Germany Tel. 49-089-855056, fax 49-089-852170 Management of databases of 2D chemical structures. PC, IBM, and VAX. 

Tel. 415-884-3000, fax 415-884-2279, e-mail info megalon.com 2D chemical structure drawing. Compounds database with 27,000 organics. Unistat for statistical analysis. PCs under Windows. 

D chemical structure drawing for PCs (DOS and Windows). Chemintosh for 2D chemical structure drawing on Macintosh. C-13 NMR program for predicting chemical shifts. 

Tel. 800-232-2224, 203-335-0906, fax 203-336-2481 Display and manipulation of 3D models using keyboard input. Molecular Animator for creating and displaying 3D models. Molecular Graphics for display and manipulation of atomic coordinate data. ChemFile II for creating databases of 2D chemical structures with associated text. PCs and Macintosh. 

Drawing 2D chemical structures. ChemWhere for searching for MPG structures in word processing documents. Datalyst II for management of databases of chemical structure in dBASE-compatible files. ConSystant for reformatting data files between software applications. Chemeleon from Exographics for data file conversions. PCs. 

Figure 9.4. Basic types of 2D chemical structure data. The amount of information and the complexity of searching increases with the dimensionality of the data.

Palm et al. [3] took into account the flexibility of molecules by using molecular mechanics to calculate an averaged PSA according to a Boltzmann distribution. Later Clark [4,5] found that the use of a representative conformation was sufficient for the calculation of reliable PSA values. Ertl [6] developed a method to calculate PSA as the sum of fragment contributions and proposed a topological PSA (TPSA). The advantage of TPSA is that it can be directly calculated from the 2D chemical structure, which makes the calculation rapid and reproducible. 

Each fragment has different characteristic physicochemical properties. For example, representative properties of primary amines are hydrophilicity, the ability to form cations, and the ability to form hydrogen bonds. It is often difficult to know which property is the most important one. Nevertheless, representation by the 2D chemical structure is a good way to generate ideas for further chemical modification. 

Ease of calculation of descriptors is desirable so that the models derived can be conveniently used by medicinal chemists. Descriptors that can be calculated from 2D chemical structures without the use of software are recommended. 

The two-dimensional structure of a chemical compound defines the topology of a molecule — that is, the location of atoms and bonds. To represent 2D chemical structures in machine-readable form, the topology has to be defined in a unique manner. 

Another approach for representing 2D chemical structures is the linear notation. Linear notations are strings that represent the 2D structure as a more or less complex set of characters and symbols. Characters represent the atoms in a linear manner, whereas symbols are nsed to describe information about the connectivity [3]. The most commonly nsed notations are the Wiswesser line notation (WLN) and the simpUfled molecnlar inpnt line entry specihcation (SMILES) [2]. The WLN, invented by William J. Wiswesser in the 1949, was the hrst line notation capable of precisely describing complex molecnles [4]. It consists of a series of uppercase characters (A-Z), numerals (0-9), the ampersand ( ), the hyphen (-), the oblique stroke (/), and a blank space. 

One of the first approaches for substructure search was published by Feldmann et al. [7]. They used connection table representations of 2D chemical structures to search for particular substructures within these larger structures. The resulting system — the National Institutes of Health-Environmental Protection Agency (NIH-EPA) Chemical Information System — started in 1973 as a joint project in mass spectrometry and structure searching between the NIH and the EPA [8]. 

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