个人简介

Ph.D., Organic Chemistry, with High Honors, the University of California, Santa Barbara, 1987 B.S., Chemistry, University of California, Los Angeles, 1980

研究领域

Physical/Organic/Computational/Materials

Breneman’s research focuses on understanding and modeling the relationships that exist between molecular structure and function. The highlight of his research is his invention of an entirely new kind of molecular modeling called the Transferable Atom Equivalent (TAE) method. The TAE method allows accurate reconstruction of electron density distributions for very large numbers of drug-sized molecules, or for a few very large protein-sized molecules in a short time frame. Small molecule electron densities can be reconstructed with great speed, enabling large databases to be scanned for desirable combinations of electronic properties in a short period of time. The results of the reconstruction efforts yield sets of electron density-derived molecular property descriptors, as well as atom-centered multipolar representations of molecular electrostatic potential fields. His team’s work in TAE modeling has received international attention from research groups and pharmaceutical companies, and is being developed through contributions from the NSF, GE, Millennium Pharmaceuticals, ICAGEN Pharmaceuticals, Pfizer Global Research and the Eastman Kodak Company. Breneman’s group is now applying TAE to problems in large and small molecule binding, protein binding site selectivity, and drug design QSAR modeling. Since the TAE method has allowed the development of an entirely new kind of QSAR/QSPR electronic property descriptors, researchers are exploring the application of these indicators for producing accurate statistical models for many classes of intermolecular interactions. Preliminary results on High Performance Liquid Chromatography (HPLC) capacity factors suggest that the new electronic property indicators are highly correlated with specific modes of molecular binding, and should prove to be of general use in QSAR/QSPR work. Breneman’s researchers also were the first to reconcile the controversial issue of how the atomic charges derived from density partitioning are related to the more familiar electrostatic potential-derived charges. In addition, through the use of electron density partitioning methods, they were the first to show that the conformational preferences of sulfonamides were controlled by the same redistribution of charge and electronic kinetic energy that governs amide stability.

近期论文

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Zaretzki, J.; Bergeron, C.; Rydberg, P.; Huang, T.-w.; Bennett, K. P.; Breneman, C. M. "Rs-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to Cyp 3a4" J. Chem. Inf. Model. 2011, 51, 1667-1689. Das, S.; Krein, M. P.; Breneman, C. M. "Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures" J. Chem. Inf. Model. 2010, 50, 298-308. Das, S.; Krein, M. P.; Breneman, C. M. "Pesdserv: A Server for High-Throughput Comparison of Protein Binding Site Surfaces" Bioinformatics 2010, 26, 1913-1914. Morrison, C. J.; Breneman, C. M.; Moore, J. A.; Cramer, S. M. "Evaluation of Chemically Selective Displacer Analogues for Protein Purification" Anal. Chem. 2009, 81, 6186-6194. Das, S.; Kokardekar, A.; Breneman, C. M. "Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions" J. Chem. Inf. Model. 2009, 49, 2863-2872. Sukumar, N.; Krein, M.; Breneman, C. M. "Bioinformatics and Cheminformatics: Where Do the Twain Meet?" Curr. Opin. Drug Discovery Dev. 2008, 11, 311-319. Yang, T.; Sundling, M. C.; Freed, A. S.; Breneman, C. M.; Cramer, S. M. "Prediction of Ph-Dependent Chromatographic Behavior in Ion-Exchange Systems" Anal. Chem. 2007, 79, 8927-8939. Yang, T.; Breneman, C. M.; Cramer, S. M. "Investigation of Multi-Modal High-Salt Binding Ion-Exchange Chromatography Using Quantitative Structure-Property Relationship Modeling" J. Chromatogr. A 2007, 1175, 96-105. Chen, J.; Yang, T.; Luo, Q.; Breneman, C. M.; Cramer, S. M. "Investigation of Protein Retention in Hydrophobic Interaction Chromatographic (Hic) Systems Using the Preferential Interaction Theory and Quantitative Structure Property Relationship Models" React. Funct. Polym. 2007, 67, 1561-1569. Chen, J.; Luo, Q.; Breneman, C. M.; Cramer, S. M. "Classification of Protein Adsorption and Recovery at Low Salt Conditions in Hydrophobic Interaction Chromatographic Systems" J. Chromatogr. A 2007, 1139, 236-246. Liu, J.; Yang, T.; Ladiwala, A.; Cramer, S. M.; Breneman, C. M. "High Throughput Determination and Qser Modeling of Displacer Dc-50 Values for Ion Exchange Systems" Sep. Sci. Technol. 2006, 41, 3079-3107. Ladiwala, A.; Xia, F.; Luo, Q. O.; Breneman, C. M.; Cramer, S. M. "Investigation of Protein Retention and Selectivity in Hic Systems Using Quantitative Structure Retention Relationship Models" Biotechnol. Bioeng. 2006, 93, 836-850. Rege, K.; Ladiwala, A.; Hu, S. H.; Breneman, C. M.; Dordick, J. S.; Cramer, S. M. "Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (Qsar) Models" J. Chem. Inf. Model. 2005, 45, 1854-1863. Ladiwala, A.; Rege, K.; Breneman, C. M.; Cramer, S. M. "A Priori Prediction of Adsorption Isotherm Parameters and Chromatographic Behavior in Ion-Exchange Systems" PNAS 2005, 102, 11710-11715.