Dr. Benjamin Gherman
Carnegie Mellon University (1998), B.S. Chemistry (with Computational Chemistry option)
Carnegie Mellon University (1998), B.S. Mathematics
Columbia University (1999), M.A. Chemistry
Columbia University (2002), M. Phil. Chemistry
Columbia University (2003), Ph.D. Chemistry
Office: SQU 416C
Phone: (916) 278-6600
Chem. 1A - General Chemistry I
Chem. 140A - Physical Chemistry Lecture I
Chem. 140B - Physical Chemistry Lecture II
Chem. 142 - Introduction to Physical Chemistry
Chem. 245 - Computational Chemistry
Computational Modeling of Bioinorganic, Organometallic, and Organic Chemistry
(1) Peptide deformylase (PDF) catalyzes the hydrolytic cleavage of the formyl group at the N-terminus of nascent eubacterial proteins during protein synthesis. As PDF is essential for bacterial survival but absent in higher animals, PDF constitutes a promising target for a new class of antibacterial agents, making investigation of the structure and function of this enzyme an important endeavor. PDF is also of great interest from the bioinorganic viewpoint, as it is the only example of an iron metalloamidase. The choice of iron by nature is intriguing considering the inherent instability of FeII towards oxidation and that PDF catalyzes a non-redox-active reaction. Research here will focus on (a) how enzyme activity and catalytic mechanism vary when different metals (e.g., FeII, ZnII, NiII) are present at the PDF active site, (b) how electronic changes at the active site affect the deformylation reaction, and (c) how the hydrogen bonding environment of the protein active site affects the deformylation reaction.
(2) Collaborative research is being carried out with Prof. James Miranda in the area of metal-salen electrochemistry. We are focusing on using computational chemistry methods (a) to predict reduction potentials for metal-salen compounds and (b) to study the mechanism of substrate cyclization in electroreductive cyclization (ERC) reactions catalyzed by reduced metal-salens.
(3) Collaborative research is being carried out with Prof. John Spence, examining the cyclization reactivity of enediynes. Computational chemistry methods are being used to study the thermal reactivity and photoreactivity of a variety of enediynes with different supporting groups and substituents. Research here is also being extended towards investigating the cyclization reactivity of enediynones and dieneynones.
- California State University, Sacramento Provost’s Research Incentive Fund grant (2014).
- California State University, Sacramento University Enterprises, Inc. Faculty Grant (2014).
- California State University CSUPERB faculty-student collaborative research seed grant (2010).
- California State University, Sacramento research and creativity award (2008, 2009, 2011).
- California State University, Sacramento pedagogy enhancement award (2009).
- Wiley-International Journal of Quantum Chemistry Young Investigator Award (2008).
- Developmental project allocation (title: “Using Mixed Quantum Mechanics/Molecular Mechanics Calculations to Assess the Effects of Mutations on the Catalytic Activity of Peptide Deformylase”) of 24,000 service units from the National Center for Supercomputing Applications (NCSA), 2007-2008.
Recent Publications and Presentations:
(undergraduate students denoted with asterisk; graduate students denoted with two asterisks)
- J. M. Yates**, J. S. Fell**, J. A. Miranda, B. F. Gherman. “Metal-Salens as Catalysts in Electroreductive Cyclization and Electrohydrocyclization: Computational and Experimental Studies.” J. Electrochem. Soc., 160, G3080-G3090 (2013).
- J. D. Spence, A. C. Rios*, M. A. Frost*, C. M. McCutcheon*, C. D. Cox*, S. Chavez*, R. Fernandez*, B. F. Gherman. “Syntheses, Thermal Reactivities, and Computational Studies of Aryl-Fused Quinoxalenediynes: Effect of Extended Benzannelation on Bergman Cyclization Energetics.” J. Org. Chem., 77, 10329-10339 (2012).
- N. G. Spiropulos, E. A. Standley, I. R. Shaw, B. L. Ingalls, B. Diebels, S. V. Krawczyk*, B. F. Gherman, A. M. Arif, E. C. Brown. “Synthesis of Zinc and Cadmium O-Alkyl Thiocarbonate and Dithiocarbonate Complexes and a Cationic Zinc Hydrosulfide Complex.” Inorg. Chim. Acta, 386, 83-92 (2012).
- N. V. Korovina*, M. L. Chang*, T. T. Nguyen*, H. J. Walker, R. P. Fernandez*, M. M. Olmstead, B. F. Gherman, J. D. Spence. “Syntheses and Reactivity of Naphthalenyl-Substituted Arenediynes.” Org. Lett., 13, 3660-3663 (2011).
- M. F. Brown*, B. F. Gherman. “Importance of Iron as the Metal Ion in Peptide Deformylase: A Biomimetic Computational Study.” Theor. Chem. Acc., 128, 137-146 (2011).
- S. B. Bateni*, K. R. England*, A. T. Galatti*, H. Kaur*, V. A. Mendiola*, A. R. Mitchell*, M. H. Vu*, B. F. Gherman, J. A. Miranda. “Prediction of Reduction Potentials from Calculated Electron Affinities for Metal-Salen Compounds.” Beilstein J. Org. Chem., 5 (2009), doi:10.3762/bjoc.5.82.
- B. F. Gherman and C. J. Cramer. “Quantum Chemical Studies of Molecules Incorporating a Cu2O22+ Core.” Coord. Chem. Rev., 253, 723-753 (2009).
- B. E. Silva*, B. F. Gherman, J. A. Miranda. “Computational Study of the Mechanism of Metal-Salen Mediated Electroreductive Cyclization Reactions.” (poster) 248th American Chemical Society National Meeting; San Francisco, California; August 2014.
- P. J. Marzouk**, B. F. Gherman, J. D. Spence. “Time-Dependent Density Functional Theory Study of the Bergman Photocyclization Reactivity of Enediynes.” (poster) 248th American Chemical Society National Meeting; San Francisco, California; August 2014.
- A. B. Ung*, B. F. Gherman, J. D. Spence. “Computational Study of the Cyclization Reactions of Phenyl-Substituted Enediynes with Benzannelated and Quinoxaline-based Supporting Groups.” (poster) 26th Annual Undergraduate American Chemical Society Research Conference for Northern California; San Francisco, California; May 2014.
- C. Q. Li**, B. F. Gherman, J. D. Spence. “Computational and Experimental Study of the Thermal Cyclization of Enediynones and Dieneynones.” (poster) 26th California State University Biotechnology Symposium; Santa Clara, California; January 2014.
- P. J. Marzouk**, B. F. Gherman, J. D. Spence. “Photoexcitation of Enediyne Compounds and Implications for Their Bergman Cyclization Reactivity.” (poster) 44th Western Regional Meeting of the American Chemical Society; Santa Clara, California; October 2013.
- K. Minnick*, B. F. Gherman. “Using Computational Chemistry to Design an Optimal Biomimetic Ligand for the Active Site of the Peptide Deformylase Enzyme.” (poster) 44th Western Regional Meeting of the American Chemical Society; Santa Clara, California; October 2013.
- K. Minnick*, R. P. Fernandez*, B. F. Gherman, J. D. Spence. “Computational Analysis of Cyclization Reactions of Monosubstituted Enediynes and Comparison to Disubstituted Enediynes.” (poster) 25th California State University Biotechnology Symposium; Anaheim, California; January 2013.
- J. S. Fell**, B. F. Gherman, J. A. Miranda. “Mechanism of Electron Transfer in Metal-Salen Mediated Electroreductive Cyclizations.” (poster) 25th California State University Biotechnology Symposium; Anaheim, California; January 2013.
- S. Krawczyk*, B. F. Gherman, E. C. Brown. “Computational Investigation of the Effects of Hydrogen Bonding on Reaction Thermodynamics in a Carbonic Anhydrase Biomimetic System.” (poster) 24th Annual Undergraduate American Chemical Society Research Conference for Northern California; Oakland, California; May 2012.
- M. Safi*, R. Fernandez*, B. F. Gherman, J. D. Spence. “Electronic Effects on the Cyclization Reactions of Enediynes Explored Through Modifications to the Enediyne Supporting Group.” (poster) 24th Annual Undergraduate American Chemical Society Research Conference for Northern California; Oakland, California; May 2012.
- S. J. Bertolani*, A. E. Zamora*, B. F. Gherman. “Computational Study of Hydrogen Bonding Residues and Thiolate Coordination in the Active Site of Eubacterial Peptide Deformylase.” (poster) 24th California State University Biotechnology Symposium; Santa Clara, California; January 2012.