Award Abstract #0321397
MRI/RUI: 32-processor Beowulf cluster for the application of ab initio and density functional methods to Quantitative Structure Thermodynamic Relationships

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	August 16, 2003
Latest Amendment Date:	September 19, 2005
Award Number:	0321397
Award Instrument:	Standard Grant
Program Manager:	Helen G. Hansma DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	August 15, 2003
Expires:	July 31, 2006 (Estimated)
Awarded Amount to Date:	$79275
Investigator(s):	David Magers magers@mc.edu (Principal Investigator) Reid Bishop (Co-Principal Investigator)
Sponsor:	Mississippi College Clinton, MS 39058 601/924-5131
NSF Program(s):	MAJOR RESEARCH INSTRUMENTATION
Field Application(s):
Program Reference Code(s):	BIOT, 9184, 9150, 7582
Program Element Code(s):	1189

ABSTRACT

A grant has been awarded to Mississippi College (MC) under the direction of Dr. David Magers for the acquisition of a 32-processor Beowulf cluster and integrated parallel computational chemistry software for the calculation of conformational energetics and molecular parameters of a series of biologically significant molecules. All biochemical reactions require the formation of stable complexes between the molecular participants. Thoroughly understanding the physical basis for the recognition of small molecules by protein and nucleic acid targets requires a detailed knowledge of both molecular structure as well as the thermodynamics which describe the strength of the binding interactions. It is well recognized that the structures of the reactants and the solvent dictate these binding energetics. However, it is still not possible to predict precisely the binding affinity of small molecules to their cognate protein or nucleic acid targets.

With the advance of multi-processor computers running in parallel, it is now possible to treat small molecules rigorously by density functional theory and ab initio methods. Specifically, the Beowulf cluster and integrated software acquired through the grant will be used to examine the quantitative relationships that exist between the structure and the binding thermodynamics of a small library of novel naphthylquinolines that specifically recognize triple helical DNA structures. These structures such as H-DNA are currently thought to help regulate gene expression since they have been found to occur in the promoter regions of some mammalian genes. High level quantum mechanical calculations will be used to predict the molecular properties of these naphthylquinolines and then to correlate them to experimentally determined binding energetics.

The Committee on Professional Training of the American Chemical Society, which sets the guidelines for accredited undergraduate chemistry programs recently announced updated guidelines recognizing the increasing importance of computers in chemistry. Computational laboratory assignments have already been added to several courses at MC, and the third semester course in Physical Chemistry is designed exclusively around theoretical and computational chemistry. The new computer will have a direct impact on the computer assignments in these courses allowing larger and biologically relevant systems to be investigated. Finally, the Beowulf cluster will increase MC's overall research infrastructure and broaden the possibilities for collaboration with nearby colleges and universities.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Ashley L. Ringer and David H. Magers.  "Conventional Strain Energy in Dimethyl-substituted Cyclobutane and the Gem-Dimethyl Effect,"  Journal of Organic Chemistry,  v.72,  2007,  p. 2533.

Nathan J. DeYonker, Thomas R. Cundari, Angela K. Wilson, Chanchaldeep Amika Sood, and David H. Magers.  "Computation of Gas-phase Enthalpies of Formation with Chemical Accuracy: The Curious Case of 3-nitroaniline,"  Journal of Molecular Structure (Theochem),  v.775,  2006,  p. 77.

Todd M. Roper, Charles E. Hoyle, and David H. Magers.  "Reaction Enthalpies of Monomers Involved in Photopolymerization,"  Photochemistry and UV Curing: New Trends,  2006,  p. 253.


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