Software
Drawing Molecular Structures way Pentium computer was straightfortool icons that can be selected to introward and similar to installation of other duce specific bond or ring types, enter laWindows applications. Because both probels and captions, or select or erase varigrams are 32-bit applications, one must ous segments of the drawing. A tutorial in also install the WIN32Sfilesthat accomChapter 2 of the user guide should bring pany the software. users quickly up to speed in using most of the major features of the program. Later To be truly useful, a structure-drawing chapters, which focus on specific tools program should include at least these attributes: ease of use with a gentle learning and menu items, are generally well written and clear. curve for the beginner, a wide variety of CS ChemOffice Pro drawing tools that minimize keystrokes The drawing tools and other features CambridgeSoft Corporation and mouse clicks, the ability to create of CS ChemDraw are comparable to re875 Massachusetts Ave. user-defined templatefilesof structures, lated programs such as ChemWindows. UsCambridge, MA 02139 the capability to define styles for drawings ers can draw different bond types (e.g., 617-491-2200; fax 617-491-8208; e-mail that match different journal or other pubwedge, hash, and multiple) and introduce info@camsci. com lication format standards, the ability to pro- 3- to 8-membered rings with a single Version 2.0; $1295; students, $249 duce attractive hard copy, easy export mouse click. Complex polycyclic aromatic and import to and from other applications, and aliphatic ring systems are available All chemists eventuallyfindit necessary to and good technical support. from dropdown menus, which appear draw publication-quality molecular strucwhen the template icon is selected. DrawOnce the program is loaded, the user tures. CS ChemDraw, part of Cambridgeis presented with a display typical of draw- ing various boxes around a group of Soft's suite of programs called CS ChemOfstructures or introducing special symbols ing software—a window for constructing fice, is one of several programs avaiiable molecules, which is framed on the left with for reaction mechanisms, such as charges for MS-DOS/windows machines that allow the user to produce structures, diagrams, and related text suitable for appearance in print form. Readers familiar with the Macintosh environment will recognize ChemDraw aa perhaps the first truly useful structureDrawing, Modeling and Information drawing program available. I suspect that many chemists, especially those of the orCS ChemDrawTM ganic persuasion, purchased Macintosh CS C h e m 3 D T M computers solely because of the existence of ChemDraw. .ow available ender Windows, CS ChemDraw is a powerful, userfriendly tool in a suite of programs called CS ChemOffice, which includes e structurevisualization and energy-minimization CS ChemFinderTM package called Chem 3D ind a molecular database named ChemFinder. The last program is available for the Macintosh but not as of this writing for Windows. Both CS ChemDraw and Chem3D require a machine equipped with an 80386 processor, 5 MB of RAM (8 MB or higher is much better), and 10 MB of avaiiable hard-disk space. Setup on a 60-MHz Gate- ChemOffice features drawing, structure visualization, and database programs.
CS C h e m O f f i c e T M
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Analytical Chemistry News & Features, March 1, 1996
or the transition state symbol, is straightthrough the clipboard or as an eps file forward. The Bezier curve tool is a particu- worked very well. A nice feature of CS larly attractive feature that enables the ChemDraw is the ebility to save structures user to draw, for example, a reaction in SMILES notation, a method of describprogress versus energy diagram with ing a chemical structure as a text string ease. Labels can be entered with the forused by several other software packages. mula style chosen under the Text menu; in CS Chem3D is the molecular visualizer this mode numbers are automatically enand energy minimization partner of the tered as subscripts. The latest version of ChemOffice suite. In the Pro version, the program reviewed (CS ChemDraw Allinger's MM2 molecular mechanics Pro 3.5) )ncludes s molecular formula cal- force field is used to perform mechanics or culator and structure syntax checker. dynamics computations on structures CS ChemDraw comes in two versions: that are either created using the screen editor or imported from other applications Standard and Pro. The major rifference between the two rests in the ability to cre- such as ChemDraw, Alchemy III, Hyperchem, PCMODEL, or MOBY. Strucate user-defined template files. The standard version comes with several files from tures can be pictured in ball-and-stick or space-filling formats. They can be scaled, CambridgeSoft but lacks the capability of creating user-defined templates. Creating translated, and rotated externally about the x y and z axes or internally about one my own template files with the Pro veror more bonds. A sequence of these rii3" sion was quite easy; the capability for do"movie" ing this is, in my opinion, an essential fea- nipulations can be saved file which can be played at a later ttme ture of any drawing program. Users of CS ChemDraw Pro may define This last feature is quite sensitive to availstyle formats for their drawings. For exam- able memory On several occasions I received out-of-memory messages that ple, if you wanted all labels in 14-point Arial typeface and all captions in red, these caused the program to crash Finally docking and overlay utilities allow the user settings could be saved as a "style sheet." to assess molecular similarity a property Then the next time you intended to make important in drug design drawings the same way, you would load this style sheet before starting a new drawUse of the screen editor to draw siming. CS ChemDraw also comes with sev- ple structures is straightforward (a tutoeral defined style sheets, such as the forrial in Chapter 2 of the documentation is mat required by the Journal of Organic helpful) and comparable to that for AlChemistry. The style sheet feature eener- chemy III and Molecules 3D. For comally works well, although the instructions plicated molecules, however, I recomfor changing style settings for new tem- mend that structuresfirstbe rendered in plate files were misleading and what ocChemDraw and imported into Chem3D. curred on the screen did not correspond to Although Chem3D doee have an exteninstructions in the documentation sive library of molecular fragments suitable for incorporation into the screen ediIt was easier to transfer files created tor, transferring these fragments is under the Windows metafile (wmf) or encapsulated PostScript (eps) format into cumbersome. Rather than selecting one and then clicking on the editor screen to Word than into WordPerfect. WordPerreproduce the fragment structure, fect users should import drawings saved Chem3D rreuires users so select the name under the wmf or eps format into the of the fragment it to a line editor Graphics-Draw utility as a file to prevent distortion. Importing structures into Excel and then click on the
Finding the so-called global minimum energy can be a difficult task, especially for complicated molecules. Chem3D offfes no systematic methods (except for molecular dynamics in the Pro version) for searching for the global minimum that are equivalent to those found in more sophisticated programs. Molecular dynamics calculations can suggest minimum energy conformations, but these must be further analyzed by tools such as sequential and exhaustive search. I tested output from both ChemDraw and Chem3D on four different trinters: aa HP Laser Jet IIP (with and without PostScript cartridge) and two Canon inkjets— the BJ 200 black and white and the Canon BJ600e color printer. All printers produced high-quality output when drawings were ported directly to the printer. When files were imported into Word for Windows (version 6.0) or WordPerfect through the clipboard, diefidelityof output was generally high and the appearance of the printing good, regardless of printer type. The quality of files that had been transferred to Word or WordPerfect from CS ChemDraw and then printed on a LJ IIP (without PostScript) on the other hand unacceptable CambridgeSoft offers technical support through the Internet or by phone or fax. The support service was helpful and responded to questions within a few hours via e-mail. CS ChemDraw is a powerful chemical structure-drawing program that is loaded with useful features. It ranks with the best of such programs available for the Windows environment. Chem3D Prr is an effective program for displaying and manipulating structures on screen. Although some of its analytical features are good for the price, the program suffers overall from the lack of systematic conformational searching routines. Reviewed by Gary O. Spessard, St. Olaf College, Northfield, MN
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