ChemSketch

ChemSketch draws chemical structures and knows what it is drawing. Click a carbon, drag a bond, add a benzene ring from a template, and the program tracks valences, fills in the hydrogens and shows the molecular formula and weight in the status bar as you go. Draw a reaction with arrows and conditions and it adds up both sides. Ask for a name and it writes the systematic IUPAC name under the structure. Ask for a 3D model and it optimises the geometry and lets you spin the molecule in a viewer. That combination, a drawing tool that understands chemistry, is why it turns up in so many school and university labs.

It works in two modes, one for chemistry and one for page layout, and the line between them explains most of what newcomers find confusing. ChemSketch also carries a structure dictionary, tautomer checking, property estimates such as logP and a tool that shows how a molecule might break apart in a mass spectrometer. Some of its features have firm limits, the naming above all, and the 3D side has one trap to learn early. The sections below go through drawing, naming, properties and 3D, and then say where the program shows its age.

Structure mode and Draw mode

Structure mode is where ChemSketch molecules are drawn. Every atom and bond here is chemistry, so the program checks it, calculates from it and can name it. Draw mode is for the page around the molecules. Text boxes and shapes live there, along with arrows that are just arrows and pictures of lab equipment, for building a slide, a worksheet or a report figure.

The split is sensible once understood. A label typed in Draw mode is only text, and the program will not treat it as an atom. A structure drawn in Structure mode can be moved into a layout without losing its chemistry. Switch between the two with the buttons at the top left, and keep chemistry in the first and decoration in the second.

Drawing structures and reactions

Drawing in ChemSketch is quick. Pick an element from the left toolbar, or open the periodic table for anything unusual, then click to place atoms and drag to draw bonds. Rings and common groups come from templates. The Template Window holds pre-drawn amino acids and sugars, steroids and aromatics, orbitals and even lab glassware, and a Table of Radicals inserts common substituents in one click. A Clean Structure command tidies the bond lengths and angles of a rough sketch.

Reactions go in with the plus sign and reaction arrows, with labels for conditions. A reaction calculator adds summarised properties of each side to the drawing, which is a quick check that atoms balance. Organometallics, polymers and Markush structures for generic families are all drawable. For checking an element’s properties while drawing, PTable keeps an interactive periodic table open beside the window.

Names, SMILES, InChI and the dictionary

Select a structure and the ChemSketch Generate Name command writes its IUPAC name as a text field in the drawing. The limit is firm, though. Naming works only for structures of up to fifty atoms, built from a short list of common elements, with no more than three rings and a name under a hundred characters. Beyond that, a larger molecule simply gets no name.

The same Generate menu produces SMILES and InChI strings, and the reverse works too, so a string pasted from a paper or a database becomes a drawn structure. Stereochemistry now travels with the exported strings. A built-in dictionary of systematic and trade names looks up the structure for a common drug or compound. Structures can also be pasted in from other drawing programs. For processing whole lists of SMILES strings, a visual data analytics platform with chemistry extensions picks up where single drawings stop.

Properties and the mass spectrometer scissors

The ChemSketch status bar shows the formula and weight of what you have drawn at all times. A property calculator goes further, adding molecular weight, density, molar refractivity, refractive index, surface tension and an estimate of logP, the measure of how a compound splits between oil and water. These are predictions, good for teaching and first estimates, not a substitute for measured data.

Tautomer checking lists the reasonable tautomeric forms of an organic structure, which helps when a molecule can shift a hydrogen and a double bond between positions. The MassSpec Scissors tool is a clever touch for students. Select a bond and it shows the formula and weight of the two fragments, the pieces you would look for in a mass spectrum.

The 3D viewer, and its trap

A structure copies into the ChemSketch 3D viewer, where it can be shown in several styles, from sticks to spheres, rotated freely and even saved as an animated GIF of the spin. Here is the trap. Copying to 3D does not make the structure three-dimensional. It sends the flat drawing, and the viewer will happily show it flat.

Run the 3D Structure Optimization command after copying. That calculates a sensible geometry, and only then are the bond angles and shapes in the viewer meaningful. Without it, the naming tool may also leave out stereochemical descriptors on a structure that was never properly built in three dimensions. Make optimisation a habit, and the viewer becomes a good teaching tool for shape and chirality.

Where it asks patience

The ChemSketch interface looks like software from an earlier generation, with dense toolbars and small icons, and the two-mode design takes a lesson to grasp. The naming limit stops at modest molecules, which rules out most natural products and large drug molecules. Property figures are estimates. And the help, while thorough, is a manual rather than a guided tour.

For writing up the results in a formal paper, a LaTeX distribution handles chemical formulas and equations in the text, with the structures exported from here as images. For the everyday work of a chemistry student, the program is complete enough that many never look further.

Conclusion

ChemSketch suits students and teachers, and researchers, who need to draw structures and reactions that the program understands, from a first-year worksheet to a figure for a report. The templates make drawing fast, the naming and the SMILES and InChI tools connect a drawing to the literature, and the property and fragment tools turn it into a small teaching lab.

Its naming stops at small molecules, its 3D needs an extra step and its interface shows its age. Keep chemistry in Structure mode, run the optimisation before trusting any 3D shape, and it covers most of what a chemistry course asks.