SBIR-STTR Award

An accurate and rapid computational method for predicting reaction rates for biochemical processes would be developed as a tool for biochemistry research. Existing semiempirical methods, while rapid, are not sufficiently accurate. The recently completed PM6 methods, while rapid, are not sufficiently accurate. The recently completed PM6 method has increased the accuracy of prediction of heats of formation of stable ground-state systems, but is still not accurate for predicting transition state energies. The purposed work would involve developing a method specifically designed for predicting activation barriers. This would involve the construction of a database of activation barriers, and using that database to optimize parameters to reproduce the activation barriers. Existing semiempirical methods use a consistent set of parameters in predicting geometries and energies. In the new approach, geometries would be predicted using PM6, and energies would be predicted using the proposed method. Although this two-step procedure would be less elegant than conventional methods if would allow activation barriers to be predicted with much better accuracy. Construction of the database of activation barriers would involve using results over very high-level ab-initio calculations. Other groups have already done calculations of this type, so this step would involve only literature research. Development of the new method involves parameter optimization only. The issues involved are now well understood, and available optimization programs should be sufficient. Finally, the new method would be integrated into the existing commercial program MOPAC2007.

Public Health Relevance:
This Public Health Relevance is not available.

Thesaurus Terms:
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An accurate and rapid computational method for predicting reaction rates for biochemical processes would be developed as a tool for biochemistry research. Existing semiempirical methods, while rapid, are not sufficiently accurate. The recently completed PM6 method has increased the accuracy of prediction of heats of formation of stable ground-state systems, but is still not accurate for predicting transition state energies. The proposed work would involve developing a method specifically designed for predicting activation barriers. This would involve the construction of a database of activation barriers. Existing semiempirical methods use a consistent set of parameters in predicting geometries and energies. In the new approach, Geometries would be predicted using PM6, and energies would be less elegant than conventional methods it would allow activation barriers to be predicted with much better accuracy. Construction of the database of activation barriers would involve using results of very high-level ab-initio calculations. Other groups have done calculations of this type, so this step would involve only literature research. Development of the new method involves parameter optimization only. The issues involved are now well understood, and available optimization programs should be sufficient. Finally, the new method would be integrated into existing commercial program MOPAC2009, which would be re-named MOPAC2011.

Public Health Relevance:
The work to be done involves developing a method to predict accurately the size of reaction barriers, giving an indication of which biochemical processes are feasible.

Thesaurus Terms:
Biochemical; Biochemical Process; Biochemical Reaction; Biochemistry; Chemistry; Chemistry, Biological; Computer Programs And Programming; Computer Simulation; Computerized Models; Computing Methodologies; Data; Data Banks; Data Bases; Databank, Electronic; Databanks; Database, Electronic; Databases; Development; Documentation; Educational Process Of Instructing; Enzymatic Reaction; Enzymes; Equation; Graphical Interface; Heating; Height; Journals; Literature; Magazine; Manuals; Marketing; Mathematical Model Simulation; Mathematical Models And Simulations; Methods; Modeling; Models, Computer; Names; Pharmaceutical Agent; Pharmaceuticals; Pharmacologic Substance; Pharmacological Substance; Phase; Procedures; Programs (Pt); Programs [publication Type]; Property; Property, Loinc Axis 2; Publications; Reaction; Relative; Relative (Related Person); Research; Science Of Chemistry; Scientific Publication; Simulation, Computer Based; System; System, Loinc Axis 4; Teaching; Time; Training; Validation; Work; Writing; Aqueous; Clinical Data Repository; Clinical Data Warehouse; Computational Chemistry; Computational Methodology; Computational Methods; Computational Modeling; Computational Models; Computational Simulation; Computer Based Models; Computer Methods; Computer Program; Computer Programming; Computerized Modeling; Computerized Simulation; Data Repository; Design; Designing; Graphic User Interface; Graphical User Interface; In Silico; New Approaches; Novel Approaches; Novel Strategies; Novel Strategy; Programs; Public Health Relevance; Reaction Rate; Relational Database; Tool; Virtual Simulation