I am a Theoretical/Computational Physical Chemist who is interested in weak, van der Waals forces and their role in the binding of biologically active molecules to enzymes, neurotransmitter receptor proteins, and DNA. I teach Foundations of Chemistry and Physical Chemistry classes.
My research has two main emphases: (1) we are interested in the interactions between small molecule ligands and biological macromolecules, including proteins and nucleic acids, and (2) we are interested in developing novel quantum chemical methods for describing these interactions. One of our most interesting projects has explored the interactions of boronated, anti-aromatic molecules and DNA. A boronated molecule in our study is an aromatic ring molecule where the carbon atoms have been replaced with alternating boron and nitrogen atoms. The boronated molecules are isoelectronic with the analogous organic molecules, but they have alternating pockets of positive charge (B) and negative charge (N), which give the boronated rings access to a wider range of intermolecular forces. We have used CCSD, MP2 and DFT methods to study the interaction of boronated molecules with DNA and compared it with similar interactions of organic molecules. Boronated molecules bound to DNA are used in an experimental type of cancer treatment, and we hope our work can help in refining this technique. We are also studying the metabolism of acetaminophen by two pathways: sulfation, and glucoronidation. Acetaminophen is toxic in relatively small amounts, and some common chemicals can act as inhibitors for acetaminophen metabolism, effectively increasing acetaminophen’s toxicity. We have used MP2 and DFT methods to study the ability of cresols and other small molecule to inhibit the metabolism of acetaminophen. All of our work is correlated with experimental results in order to ensure the viability of the theoretical models.
The two methods we employ in our DFT designs are simple modifications of current methods, and the ground-up design of a two-electron density dependant DFT. In the first approach, we have taken apart the DFT exchange-correlation potential and used scale factors to calibrate these methods to correctly calculate aromatic-aromatic interactions. In our second approach we use Boys’ transcorrelated method to derive a form of an exchange-correlation potential that depends on the second order electron density. We have coded this DFT method and run proof of concept calculations for simple systems. This approach, which should rigorously be able to account for dispersion forces, is quite promising. This work has been funded by the Research Corporation or Science Advancement and the National Science Foundation.
*Rhodes Undergraduates are underlined
M. Cafiero ′′Scaled Gradient Corrected Correlation Functionals for use with Exact Exchange,′′ Chem. Phys. Lett .418, 126 (2006).
A. Godfrey_Kittle, M. Cafiero "Interaction energies for mono-substituted benzene ring dimers using DFT", Int. J. Quantum Chem., 106, 2035 (2006).
K. Van Sickle, L.M. Culberson, J.L. Holzmacher and M. Cafiero, “Evaluation of Density Functional Theory methods for the electronic interactions between indole and substituted benzene: Applications to Horseradish Peroxidase”. Int. J. Quantum Chem. 107, 1523-1531 (2007).
M. E. Hofto , A. Godfrey_Kittle, and M. Cafiero " Substrate-Protein interaction energy in the enzyme Phenylalanine Hydroxylase: DFT and ab initio Results ", THEOCHEM, 809, 125 (2007).
M Cafiero and L. Adamowicz, “Non-Born-Oppenheimer calculations of the ground state of H3” Int. J. Quantum Chem., 107, 2679 (2007).
L. R. Hofto, K. Van Sickle, and M. Cafiero, “Evaluation of sandwich-type electronic interactions in fourteen polyaromatic molecules.” Int. J. Quantum Chem., 108, 112 (2008).
M. E. Hofto, J.N. Cross, and M. Cafiero "Interaction energies between tetrahydrobiopterin analogues and phenylalanine residues in tyrosine hydroxylase and phenylalanine hydroxylase.", J. Phys. Chem. B,32, 111 (2007).
L.R. Hofto, M.E. Hofto, J.N. Cross, and M. Cafiero, “Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson’s diseas, and obsessive compulsive disorder.” AIP Conf. Proc., 940, 127-136 (2007).
M. Pavanello, M. Cafiero, S. Bubin, and L. Adamowicz, “Born--Oppenheimer calculations of the low-lying 3S+g and 3S+u excited states of the Helium Dimer.” Int. J. Quantum Chem. 108, 2291 (2008)
L.R. Hofto, C.E. Lee, and Mauricio Cafiero “Scaling gradient dependant corrections to LSDA DFT methods for aromatic interactions: applications to Tryptophan hydroxylase” J. Comp. Chem. 30, 1111 (2009).
E. A. Kee, M. C. Livengood, E. E. Carter, M. L. McKenna, and M. Cafiero, “Aromatic Interactions in the Binding of Ligands to HMGCoA Reductase.” J. Phys. Chem. B. 113, 14810 (2009)
K. Van Sickle, M. C. Shroyer, and M. Cafiero, “Relative stability of complexes of six-carbon-rings with variable numbers of double bonds: DFT and ab initio results” Journal of Molecular Structure: THEOCHEM, 941, 78 (2010).
H.E. Utkov, M. C. Livengood, and M. Cafiero, “Using Density Functional Theory methods for modeling induction and dispersion interactions in ligand-protein complexes.” Annual Reports in Computational Chemistry, 6 (2010).
H.E. Utkov, A.M. Price, and M. Cafiero, “MP2, Density Functional Theory, and Semi-empirical calculations of the interaction energies between a series of statin-drug-like molecules and the HMG-CoA reductase active site.” Computational and Theoretical Chemistry, 967, 171 (2011).
K.M. DiGiovanni, A. Katherine Hatstat, Jennifer Rote and M. Cafiero, “MP2//DFT Calculations of Interaction Energies Between Acetaminophen and Acetaminophen Analogues and the Aryl Sulfotransferase Active Site.” Computational and Theoretical Chemistry, DOI: 10.1016/j.comptc.2012.12.004. (2012).
K. Copeland, Kari; S. Pellock; J. Cox; M. Cafiero; G. Tschumper. “Examination of Tyrosine/Adenine Stacking Interactions in Protein Complexes.” J. Phys. Chem. B, DOI:10.1021/jp408027j (2013).
D. J. Bigler, L. W. Peterson, M. Cafiero. “Effects of Implicit Solvent and Relaxed Amino Acid Side Chains on the MP2 and DFT Calculations of Ligand-protein Structure and Electronic Interaction Energies of Dopaminergic Ligands in the SULT1A3 Enzyme Active Site.” Computational and Theoretical Chemistry, 1051, 79 (2015).
Ph.D. University of Arizona (Physical Chemistry)
M.A. University of Arizona (Chemistry)
B.S. University of North Florida (Chemistry)