Structure-Based Tools

Structure-based tools such as applications databases and physicochemical prediction will not replace chromatographers, but rather allow them to use their knowledge of chromatography, relating it to the analyte functionality and making excellent choices of initial conditions that reap faster, better separations in less time. 

Several of the software tools used most frequently today include Beilstein Crossfire (information at www.mdli.com) and SciFinder from the Chemical Abstracts Service (www.cas.org/scifinder/) for structure-based reaction searches. Reagent availability information is often searched with MDL s ACD and CAS s SciFinder. Special compound collections and contract services offered by new companies such as ChemNavigator (www.chemnavigator.com)... 

Schulz-Gasch T, Stahl M. Binding site characteristics in structure-based virtual screening evaluation of current docking tools. J Mol Model 2003 9 47-57. 

Closely related to molecular structure are the energies associated with chemical bonds. It is frequently possible to make decisions regarding the stability of alternative structures based on the types of bonds present. However, because SF4 has four S-F single bonds, it is not possible to determine whether the trigonal pyramidal or irregular tetrahedron is the stable structure because each of them has four bonds. However, for many situations, bond energies provide a useful tool (see Table 4.1). 

Structural Imperfections. In many respects HREM has had a greater impact upon our knowledge of the nature of the atomic reorganization at crystalline imperfections than any other single technique. One of the very first contributions of HREM as a new analytical and structural tool was described in the paper by Iijimia (42) in 1971 on 2 10 29 v -ewe< down to its b - axis. Structural faults, arising from subtle fluctuations in composition, could be clearly seen in the block-structure (based on NbO octahedra) which is a feature of this ternary oxide system. More than a decade later similar materials are yielding to active scrutiny by HREM, and Horiuchi (43), for example, has shown how point defects may be directly viewed... 

Sotriffer C, Klebe G. 2002. Identification and mapping of smaU-molecule binding sites in proteins computational tools for structure-based drug design. Farmaco 57(3) 243-251. 

SemiChem products are available at http //www.semichem.com. AMPAC , available as a stand-alone product with Windows-based and workstation level interfaces, is a semiempirical quantum mechanical program featuring SAMI, AMI, MNDO, MNDO/d, PM3, MNDO/C, MINDO/3 semiempirical methods. AMPAC also includes a graphical user interface (GUI) that builds molecules and offers full visualization of results. The SYBYL/Base program offered by Tripos, Inc. (products described below) provides an interface with interactive graphing and structural display tools that can be used to access AMPAC s calculation tools. 

In our introduction we mentioned that there were three general areas where eventually it might be hoped to exploit the photochemical properties of metal complexes. These were (1) the use of the luminescence properties of the complexes as probes for DNA structure, base sequence or conformation (2) The employment of photochemical strand breaks as a tool in molecular biology and (3) The development of phototherapeutic procedures. 

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