Text editing properties
In the case of chemical documents it is necessary to distinguish between two kinds of text: structural text (atomic symbols, functional groups, atom labels) and other text (captions, reaction conditions, annotations etc.). The structural text strings are connected to the atoms, the latter can be placed freely, usually into text boxes and can be edited independently. Of course, in these chemical applications only a minimal amount of text editing features can be found, like the basic manipulation of fonts, styles, sizes and colours. The technique is mostly that used in other Windows applications.
Templates and group abbreviations
Apart from Chemistry 4-D Draw, the programs contain several ready template pages of different ring systems, amino acids, carbohydrates etc. and these can be pasted quickly into the document. Other templates, for example laboratory glassware, are also available. The programs allow the user to create custom templates. Of course, the technique of the creation and use of the templates are differing in the five programs from each other, maybe the solution and organization used by ChemSketch is the most advanced one.
Another possibility is the use of so-called abbreviated groups (superatoms, nickname). This is the shorthand text string representation of functional groups (COOMe, NO2), meanwhile they keep their chemical significance with the underlying structure hidden. These are previously created small sketches in DrawIt or molecule files in ISIS/Draw and with the aid of a few keystrokes they appear at the cursor. In ISIS/Draw one can choose whether the abbreviated text form (as COOiPr) or the fully drawn structure should appear. In ISIS/Draw, ChemDraw and Chemistry 4-D the reverse operation is also possible: manual abbreviation of a side-chain to chemically meaningful structural text. This latter can be important in the case of databases. DrawIt is also capable to convert not too complicated side-chains into textual form, although this is a fully automated process and the result is not always according to the user‘s taste. In ChemDraw the previously defined abbreviations may have two connection points.
Chemical intelligence, nomenclature
As it was already mentioned, the programs ChemDraw, ChemSketch and DrawIt are capable of parsing the linearized forms of substituents and convert them to structures. ChemDraw Ultra, Chemistry 4-D Draw, DrawIt and ChemSketch are able to assign systematic names to structures according to IUPAC rules, and vice versa. ISIS/Draw‘s capacities can also be extended to naming by installing its AutoNom or the ACD/Name Freeware add-in. Therefore these are very convenient for generating chemical names.
Spectra and chromatograms
A novelty in these programs is the spectral data publishing feature, spectrum interpretation and database management tools. UV, IR, NMR, MS spectra and chromatograms can be embedded into the documents and join with structures etc. The most versatile are DrawIt and ChemSketch, a lot of filters are available, respectively (available only when purchasing the appropriate ACD/Labs modules), thus, a wide range of formats arising from different instruments can be imported. ChemDraw supports JCAMP and Galactic files. The curves can be resized, zoomed, scaled, corrected, annotated, and peak list and tables are easy to create. Finally they can be embedded into the final document. Of course only formation and editing of the curves are possible and not basic manipulations, such as Fourier transformation of the FID signals. Full processing capabilities are available using the ACD/SpecManager product suite which is integrated into ChemSketch. All of the three applications enables the user to assign structures to spectra. One can then display the structure associated with a specific peak by placing the pointer on that peak. Before making any decisions, it is highly recommended to check that what spectrum and database formats are supported by the current versions.
Different chemical and other adds
It is not easy for the reviewer to decide what and how to include, because these extras are changing quickly and depending on the owned version (freeware or standard vs. pro vs. ultra versions etc.), sometimes add-ins can be installed only into the purchased version, sometimes they are free, sometimes they are to be purchased separately or available as an Internet-based service (see table 1. too). It is highly recommended to look for information at the home pages of the manufacturers before making decisions.Molecular weight, and constitution %:
All of the programs.
NMR:13C: KnowItAll, ChemDraw, ChemSketch (to be purchased or via I-Lab), ISIS/Draw (with ACD/Labs Add-ins for ISIS )
1H: KnowItAll, ChemDraw, ChemSketch (to be purchased or via I-Lab), ISIS/Draw (with ACD/Labs Add-ins for ISIS )
19F, 31P and 15N NMR: ChemSketch (to be purchased or via I-Lab)
The chemical shifts are not ab initio calculated, but determined with the aid of the applied databases, therefore the precision of the results is a function of the included molecules. The 13C NMR module of the DrawIt/KnowItAll (if the full suite is installed) and ACD/CNMR can show molecules possessing analogue chemical environment to those of the carbons in question. ChemSketch has also developed this scheme into their NMR prediction modules through their "calculation protocol" environments.
MS Fragmentation tools:The MS fragmentation tool mimics the molecular fragmentation in a mass spectrometer, it allows the user to break existing structures across one or more bonds. ChemDraw, DrawIt, ChemSketch and Chemistry 4-D Draw have this tool; the first twoapplications have the most advanced one, it allows to fragment in zigzags and calculate the mass resulting from multiple fragment losses (if you need more, use ACD‘s MS Fragmenter or a similar package).
IR: KnowItAll, ChemSketch (with UV-IR Manager add-on):Manipulation and comparison of IR spectra.
Other chemical property prediction tools:ChemDraw: logP, CLogP, critical pressure, temperature and volume, Henry‘s constant, Gibbs energy, heat of formation, MP, BP, molrefraction. Some of these are available in the ultra version only
ChemSketch: free macroscopic properties (molar refractivity and volume, parachor, surface tension, index of refraction, density, polarizability), logP, pKa, Hammett σ etc. Some of the features are available through ACD/I-Lab. Consult ACD-Labs home page for current details.
DrawIt/KnowItAll: logP, logD, pKa, Rule of Five.
These calculated properties are to be handled with critic.ChemBasic Goodies of ChemSketch:
A bunch of handy utilities can be found in these extensions, among others handling of multipage documents, conversion to HTML, VRML or SDF formats, peptide, carbohydrate and nucleic acid builder.
ACD/ChemPalm, ACD/ChemPocket of ChemSketch:
These are applications for Pocket PC and Palm© OS-based PDAs (Personal Digital Assistants). They allow to view chemical structures and browse and search chemical databases containing structures.
Documentation
An ample amount of printed documentation is included with ChemDraw (it is available in pdf format on the program CD as well). DrawIt and Chemistry 4-D Draw, ISIS/Draw and ChemSketch have no printed documentation (but are available in pdf and/or doc formats of the latter). The available on-line documentation (Help) is good in the case of ISIS/Draw, ChemSketch and Chemistry 4-D Draw, it is practically the same as the printed one in the case of ChemDraw. The Chemistry 4-D Lite Help documentation is incomplete, several modules have no descriptions at all, no information could be found about the so-called Plasmid modul even from the web site of the program.
Worthy of note that for the sake of user‘s convenient, the Help of the purchased version of ChemSketch contains a huge number of internet links to the instructions-for-author pages of chemical journals, moreover, several dozens of these instructions are available off-line in pdf format too.
Drawing programs and the Web
Nowadays there are more and more applications (better to say browser plug-ins or Java applets), which can be used for the entering chemistry directly into the browser, for example to search an on-line database. A Java applet version of ChemSketch is available at no cost from the ACD website (via the ACD/Structure Drawing Applet). This is a full featured Java-based structure drawing editor including templates and periodic table. The afore-mentioned I-Lab add-on to ChemSketch is also an Internet-based service. The ChemDraw Plugin automatically turns the web browser into ChemDraw whenever a page containing an embedded ChemDraw document is encountered. However, we do not deal with this theme this time. Several Java applet versions are found among the programs mentioned in the next What else out there section, too.
Summary
Apart from small corrections, no new features can already be added to the drawing functions of pure chemistry. Little additions and corrections are continuously made of course, especially database functionality, such as support for Markush structures, polymers etc. is enhanced – this in mind the developers are recently concentrating on the intelligent to-and-fro chemical naming modules, and tools for viewing and representing spectra of different formats.
For the time being, ChemDraw and ChemSketch seem to be the most dynamically developed chemical drawing applications. ChemWindow has been replaced by the DrawIt/ReportIt modules of the KnowItAll Analytical Systems package – no special novelties but excellent team-work with spectroscopy and chromatography. The developers of ISIS/Draw are seemingly dealing with the database input features only, apart from small changes in the interface. It was the leading chemical drawing program 10-12 years ago, now overtaken by others. ISIS/Draw and ChemSketch are freely available via the Internet.
Progress never stops, hardware keeps growing stronger and stronger, and the developers have to add something new every year, therefore the originally really drawing-only applications have evolved into a complex of
What else out there?
Beyond these five drawing software applications there are several others to be considered or for experimentation. They are freewares or can be purchased for a shareware category price. Some are highly sophisticated, some are simple, some are only in beta-phase or are not bug-free. Here are a few of them (no extensive tests were done):
WinPLT 7.1
ChemPen
A very useful application, different versions are available (NMR prediction, fast force field based geometry optimisation and 2D → 3D conversion). Worth trying.XDrawChem 1.9.5
WinDrawChem 1.7
JChemPaint 2.0
Java based multiplatform, simple 2D drawing program, worth trying. Java applet version is available as well. Among others supports CML, SVG, Smiles and MDL MOL/SDF formats, and 13C NMR prediction.MarvinSketch 3.5
MarvinSketch is an interesting Java based multiplatform application. Although it is only a basic 2D drawing software, it includes some features characteristic only on modelling softwares, for example coloring of the atoms by type or display in ball-and stick and CPK models. It is possible to import 3D molfiles (ISIS, Sybyl, PDB, xyz) or to use the 3D clean-up module. Only pure molecules can be drawn and saved/exported as molfiles. MarvinSketch is available as Java applet or application (bean) for developers and may serve as the graphical input module for example on-line databases (therefore query bond and atom types á la ISIS are also supported). It contains several calculation options (pKa, logP, logD, partial charge, H-bond donor-acceptor, topology analysis, polarizability etc). Sister program: MarvinView.![]() Not horizontal or vertical lines look jagged on the screen | ![]() Contures are antialiased and therefore are |
JME Editor 2004.10
The simple and user friendly JME Molecular Editor is a free Java applet which allows to draw, edit and display molecules and reactions directly within an HTML page. The editor can generate or input SMILES, MDL mol/rxn or proprietary own formats of the created molecules. Its JME Professional version is not an applet, but a stand-alone Swing application. Only pure molecules, query structures, and reactions can be drawn and saved/exported as molfiles. Creation of substructure queries is also supported. JME is an excellent tool for developers and may serve as the graphical input module for example on-line databases or property calculation services.
The applet may be used also in a depiction mode to visualise molecules:
URL: http://www.molinspiration.com/jme (Peter Ertl, Novartis Pharma AG)
BKChem 0.9
BKChem is a free chemical 2D drawing program in developing phase, written in Python, therefore it is a multiplatform application (GNU/Linux, Windows). It has the basic drawing features. Supports CML and Adobe SVG graphics. The latter allows to embed good quality antialiased graphics into web pages (needs the Adobe SVG plugin).
References
1) ISIS/Draw 2.5, MDL Informations System, 14600 Catalina Street, San-Leandro, California 94677, USA. URL: http://www.mdli.com
2) ChemDraw 9.1 Ultra, CambridgeSoft Corporation, 875 Massachusetts Ave, Cambridge, MA 02139, USA; URL: http://www.camsoft.com
3) DrawIt 4.1 (KnowItAll Academic Edition), Bio-Rad Laboratories Informatics Division, Philadelphia PA 19104; URL: http://www.chemwindow.com or http://www.bio-rad.com
4) Testing and comparison was made on a PC Pentium IV 2.54 GHz, 1024 Mb memory, Windows XP SP1 (International English release). Text editor: MS Word 2002 (English). Printers: HP Laserjet 5, HP Deskjet 600 and 840.
5) ACD/ChemSketch 8.0 commercial, Advanced Chemistry Development Inc, Toronto, Canada, URL.: http://www.acdlabs.com
6) Chemistry 4-D Draw 6.0 and 7.6 Lite, ChemInnovation Software Inc., San Diego, USA, http://www.cheminnovation.com.
7) A previous version of this document can be found in a reshaped article form at: Internet J. Chem. 3, L 25 (2000) (ISSN 1099-8292) http://www.ijc.com/articles/library/25.
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