Draw your own conclusion

New free software makes drawing chemical structures faster, easier, and more precise say its designers – but is it just a sketchy idea or a picture perfect solution?

Symyx Draw 3.1 enables the rapid determination of 3D structural conformations so that chemists can visualise a structure’s overall shape and charge distribution.

Most chemistry begins with a picture. This makes chemical sketching one of the most important capabilities in a chemist’s toolkit, particularly given that chemical structures and reactions are among the most valuable intellectual property of research organisations. To ensure that chemists are able to represent these critical building blocks accurately, Symyx Draw 3.1 - available as a free download (www.symyx.com/getdraw) for academic and home use - makes drawing simple or complex chemical structures for presentations or querying faster and easier.

Symyx Draw 3.1 is the successor for widely used ISIS/Draw package and a key component of the Symyx Isentris system that replaces ISIS. It was designed to improve scientists’ ability to capture and share complex chemical structures and reactions. The new software handles drawing of polymers and mixtures with full Sgroup support, as well as Rgroup and 3D queries. Other enhancements include name-to-structure and structure-to-name conversions and an ever-increasing number no-charge add-ins.

For scientists engaged in biologics research, new enhancements supporting

"chemical sketching is one of the most important capabilities in a chemist's toolkit, particularly given that chemical structures are among the most valuable intellectual property"

biomolecules make Symyx Draw 3.1 more efficient than its predecessor ISIS/Draw when it comes to creating, registering, and searching chemically modified peptide or nucleotide sequences. Convenient sequence tools enable scientists to quickly create one- or three-letter amino acids or RNA and DNA sequences. Scientists can easily draw crossing bonds and disulfide bridges and attach side-chain protecting groups using a single tool set. A simple right-mouse click is all it takes to expand an abbreviation to the full structure, change from one-letter to three-letter display, or hide end termini.

Symyx Draw 3.1 supports enhanced stereochemical perception so that chemists can differentiate between absolute and relative stereogenic centers in a single structure. “This advanced representation also supports the recording, storage, and searching of optical purity information using Symyx's established Data Sgroup representation,” said Dr Keith T. Taylor, senior product manager for Symyx Draw. “This makes it possible for chemists to represent and register exact proportions of the compounds they make.”

Enumeration of a diazepam library enables the rapid exploration of chemical space. The results can be pasted into a laboratory notebook or exported into an SDFile with additional properties calculated automatically and saved to a database (or imported into Isentris for Excel for further processing and refinement).

The new software package enables chemists to convert from name-to-structure and structure-to-name, supporting several different methods of generating the name or the structure. When converting from name-to-structure, use the Generate Structure from Text option and choose IUPAC name, SMILES string, or InChI string as your source of information. When converting from structure-to-name, use the Generate Text from Structure option and select IUPAC name, SMILES string, InChI string, or NEMA key as the output text.

The developers of the program say that Symyx Draw is a cut above ISIS/Draw in offering a growing number of no-fee software add-ins that improve workflow efficiency (including 3D minimisation, reaction stoichiometry calculation, molecular property calculation/prediction, enumeration, bioavailability, calculate-as-you-draw, and isotopomer distribution tools). “For example, you can easily add scientific calculators, predictors, enumerators, business rule checks, and vocabulary for your stereochemistry rules to your personalised toolkit within Symyx Draw,” said Taylor.

It has the same look-and-feel as its predecessor ISIS/Draw but offers several usability improvements. The all-purpose drawing tool can be used to rapidly sketch structures freehand, including bonds, rings, chains, and atoms, without switching back and forth between tools. Create complex structures and reactions with a single click using a large library of dynamic protecting group templates. Easily rotate part or all of a structure or use the chemical flip tool to flip a structure around its center or around an atom or bond. Rapidly clean up structures or portions of structures by giving them uniform bond lengths and angles and by removing invalid bond marks.

By supporting fast, efficient, and accurate structure and query drawing, its makers say Symyx Draw meets the needs of scientists for a flexible, extensible, industry-standard chemical structure editor and viewer. Symyx Draw is an ideal tool for transforming the sketchiest of chemical ideas into valuable intellectual property.