A Novel Automated Computational Method for Calculating Atomic Mappings for Chemical Reactions

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A novel automated computational method for calculating atomic mappings for chemical reactions

Princeton Docket # 13-2860-1


Researchers at Chemical and Biological Engineering in Princeton University have developed a novel method for computing atomic mappings for chemical reactions.


Reaction mapping can be used to infer which bonds break and form and thus implies a possible chemical reaction mechanism. It is also important for the calculation of chemical kinetics and the generation of transition state structures. Reaction mapping methods have great importance for scientists interested in studying the kinetics of chemical reactions. To address this need, Princeton researchers have for the first time developed an automated computational method to generate stereochemically consistent reaction mappings.


This novel method is capable of identifying all distinct and chemically relevant reaction mechanisms for a chemical reaction, enabling researchers to consider multiple pathways. In addition to being applied to single reactions, this method can be used to process chemical reaction databases in an automated fashion. It is anticipated that this functionality is particularly important for biochemical pathways, which can involve networks of complex reactions. The resulting mappings can be used to cluster reactions, classify reactions, or to enhance the dissemination of data through the generation of atom rearrangement diagrams. Furthermore, this method enables the filtering of multiple reaction mappings to remove equivalent ones, and more generally to compare whether two reaction mappings correspond to the same reaction mechanism. The identification of molecular symmetries also has applications outside of reaction mapping, as it can be used to determine chirality and polarity and predict the results of diffraction patterns and various spectroscopic techniques. This method is completely novel and is invaluable to researchers investigating possible chemical pathways.




Method can be used:

·         To identify distinct chemical reaction mechanisms;

·         In networks of complex reactions such as biochemical pathways;

·         Filter multiple reaction mappings;

·         Determine chirality and polarity;

·         Predict results of diffraction patterns and other spectroscopic techniques.



·         Novel automatic computational method.

·         Can solve multiple problems in one software package.

·         Easy to apply.


The Faculty Inventor


Christodoulos A. Floudas is Stephen C. Macaleer '63 Professor in Engineering and Applied Science and Professor of Chemical and Biological Engineering at Princeton University.  Professor Floudas is a world-renowned authority in mathematical modeling and optimization of complex systems at the macroscopic and microscopic level.  His research interests lie at the interface of chemical engineering, applied mathematics, and operations research, with principal areas of focus including chemical process synthesis and design, process control and operations, discrete-continuous nonlinear optimization, local and global optimization, and computational chemistry and molecular biology.  Among Prof. Floudas¿ numerous honors and awards are Member of National Academy of Engineering (2011), Princeton University Graduate Mentoring Award (2007), AIChE Computing in Chemical Engineering Award (2006) and AIChE Professional Progress Award for Outstanding Progress in Chemical Engineering (2001), to name a few.





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.



Intellectual Property & Development Status


Patent protection is pending.

Princeton is currently seeking commercial partners for the further development and commercialization of this opportunity.



Laurie Tzodikov
Princeton University Office of Technology Licensing

(609) 258-7256  tzodikov@princeton.edu

Wenting Luo

Princeton University Office of Technology Licensing 

(609) 258-5579  wluo@princeton.edu

Patent Information:
For Information, Contact:
Laurie Tzodikov
Licensing Associates
Princeton University
Christodoulos Floudas (DECEASED) See Fotini P. Baba
Eric First
Chrysanthos Gounaris
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