Software programs are being employed in every aspect of biology and chemistry. A once painful and hand-drawn diagram that required the expertise of an artist can now be done on a routine basis by any researcher, without the need to worry about the precision of the structure. I believe that ChemOffice 8.0 Ultra is one such program available to chemists and biologists for drawing structures of small molecules and peptides. The software package contains ChemDraw, Chem3D, ChemFinder and an E-notebook.
ChemDraw is used for drawing any chemical structure. Default bond lengths are usually used, but this option can be disabled to obtain variable bond lengths. Several templates for amino acids (L- and D-) are already available in the library and can simply be imported. A large number of other templates, including RNA, aromatics, supramolecules, and functional groups, to name a few, have been provided. Different orientations of these templates are also available. Additionally, objects can be rotated in three dimensions. Figures for laboratory glassware are also pre-loaded and can simply be selected.
During the process of generating a chemical structure, the default atom is carbon. This can be changed to other atoms by selecting it and typing in the single letter code. A periodic table is provided for inserting other atoms. Valencies of different atoms are already available in the software and if additional bonds are added, it immediately warns the user of ‘exceeded atom valency’. Once a structure is complete, it can be selected and ‘cleaned up’ which sets all bond lengths and angles to ideal values. Derivation of the chemical name from the structure and calculation of its chemical properties (e.g. boiling point, melting point, molecular weight) are possible. Generated figures can be copied and pasted directly into Microsoft Word®.
Chem3D is required for generation of 3D structures of molecules. As with ChemDraw, several templates are already available in the library. The structures can be manipulated for rotation in three dimensions and zoomed to the desired size. The generation of stereo images and changing of atom colors are also straight-forward. Different energy minimization options using several functions are also available, such as MOPAC, Gaussian, Mechanics etc. Structure searches can be performed using a compound name; searches can also be performed using the structures generated using ChemFinder.
Setting the font, size and color is easily done. Special characters and symbols are available. Formatting and alignment of the structure(s) on a page can also be performed. The software can even predict the proton and carbon-13 NMR chemical shifts of compounds, as well as generate spectra. Object rendering can be adjusted as per requirements of certain chemistry journals. Online searches can be performed to retrieve structures of small molecules using their ACX number. Suppliers of the desired chemical can also be searched on ChemStore.
There are obviously other software packages available free-of-cost, but users of ChemOffice will immediately recognize the enormous benefits which its many features provide. The latest version of this software, 10.0, is said to have several new features integrated into it.
Molecular Biophysics Unit
Indian Institute of Science