SMARTS hints for ChemDraw

This document provides a few hints for using the ChemDraw plugin to draw structures that can be used for SMARTS seaches in ChemMart. Normally, ChemDraw is used in ChemMart to draw simple molecules with no wildcard atoms or bonds. Structures drawn in this way can be used with all the ChemMart functions, such as Substructure, Neighbors and clogP. The SMARTS function in ChemMart allows for much more flexibility in the way the search is carried out, but the user must know the SMARTS language in order to take full advantage of the complete flexibility of SMARTS. Here are several hints that will allow you to draw structures using ChemDraw to take advantage of important and useful aspects of SMARTS. If you use these drawing "tricks", the resulting structures will be useable ONLY with the SMARTS function of ChemDraw.

The following examples of ChemDraw sketches should help you understand how to specify a wide-variety of SMARTS searches. Before pressing the SMARTS button in ChemMart, be sure to

Make any aromatic bonds truly aromatic (not Kekele structures) using the Structure/Bond Properties tool in ChemDraw, or by drawing in the aromatic ring symbol using the orbital tool.

In other words, your drawings should look like the ones here. You must use lower-case atomic symbols when specifying atomic symbols in aromatic rings. You can cut these structures drawn below and paste them into ChemDraw as a starting point for your SMARTS searches. Use right-mouse, copy.

Draw this	or this	NOT	to search for
			Para-halo-substituted toluenes, allowing ortho- and meta- substitution of any type. Also allows substitution of the methyl, and will return many non-toluene like structures.
			Para-halo-substituted toluenes, forcing no substitution of any other type. Note the use of lower case c;H1 in phenyl ring and upper case C;H3 for methyl.
			Structures containing cyclohexane or piperazine rings.

Some basic SMARTS rules for atom symbols. Use the A (alpha) tool in ChemDraw to modify the atom symbols when doing a SMARTS search.

Any normal atom symbol can always be used.
A list of atom types can be used. Separate the atoms with a comma. The comma means OR.
A charged atom is specified using the symbol followed by a colon and the charge, e.g. N;+ or O;-. The colon means AND.
An exact hydrogen count is specified using the symbol followed by colon, then H then the H count. For example, C;H2 or N;H2 or even N;+;H2 or N;H2;+.
The exclamation mark means NOT. For example, !C disallows carbons at the position where you use that symbol.
If you combine these OR and AND symbols, you might need to use the & symbol instead of the colon. e.g. C&H2,N&+&H3. The & is an AND just like the colon, but it has a higher priority relative to the comma (OR). For example C;H2,N;+;H3 is not equivalent to the above example.
A more complete description of the SMARTS language is available.