Usage Tutorial

Input to DREAM

DREAM accepts balanced chemical reactions in a variety of formats:

If the input is provided by the Interactive Editor or in SMILES Format, DREAM will convert the input to two-dimensional MDL RXN format, automatically including implicit hydrogen atoms and recognizing stereochemistry annotations. Input provided in MDL RXN format can be two-dimensional, in which case stereochemistry annotations will be read, or three-dimensional, in which case stereochemistry will be detected. Implicit hydrogen atoms may also be automatically added to MDL RXN format input by selecting the appropriate option.

DREAM Options

DREAM can be configured to provide either a single optimal mapping or to locate multiple optimal mappings, each corresponding to a distinct reaction mechanism. The objective function is either to minimize the number of bonds that break or form in the corresponding reaction mechanism or to minimize the number of bond order changes that occur.

Output from DREAM

DREAM will annotate the MDL RXN input file to include the reaction mapping in column 14 of the atom description section. The output of an example reaction is provided in output.rxn. In the example, notice that the reactant atoms are numbered sequentially, and the product atoms are numbered based on the reactant atom to which they are mapped. For instance, the first reactant atom, numbered as 1, maps to the second product atom, also numbered as 1. The second reactant atom, numbered as 2, maps to the fourth product atom, also numbered as 2.

DREAM provides the option to search for multiple mechanisms. If multiple mechanisms are located, a separate output file will be generated for each corresponding mapping.

Upon completion of the calculations, DREAM will send the results by email. The output files will be attached to the message, and the objective function value will be indicated in the body of the message. A reaction viewer is also provided to visualize the reaction mapping results.

Citing DREAM

Please acknowledge use of reaction mapping results from DREAM using the following citation:

First, E. L., Gounaris, C. E., and Floudas, C. A. Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization. Journal of Chemical Information and Modeling, 52(1):84–92, 2012.