Contact Information:

office 1321bN (tel 212-772-5343), lab 1322N (tel 212-772-5751), dept fax 212-772-5332, email jdannenberg@gc.cuny.edu, group webpage Dennenberg Group Homepage

Education:

A.B. Columbia College, Ph.D. California Institute of Technology

Research Summary: 

We do molecular orbital and density functional theory calculations on problems of chemical and biochemical interest.

Our recent work has focused on the importance of H-hydrogen bonding and cooperativity in determining the structures of natural (biological) materials such as peptides and unnatural materials such as self assembling nanomaterials. We have also used studies of molecular crystals for comparison. We have shown that H-bond cooperativity can play a determinant role in the energetic preferences for one peptide secondary structure (such as alpha-helix) over another (such as beta-sheet or collagen-like triple helix).

We have also calculated the vibrational frequencies and trans-Hydrogen-bond 13C-15N J-couplings for peptides.

Selected Publications

Tsai, M.I.-H., Y. Xu, and J.J. Dannenberg, Ramachandran Revisited. DFT Energy  Surfaces of Diastereomeric Trialanine Peptides in the Gas Phase and Aqueous Solution. J. Phys. Chem. B, 2009: p. in press

Viswanathan, R. and J.J. Dannenberg, A Density Functional Theory Study of Vibrational Coupling in the Amide I Band of b-Sheet Models. J. Phys. Chem. B, 2008. 112(16):  5199-5208

Wieczorek, R. and J.J. Dannenberg, Amide I Vibrational Frequencies of alpha-Helical Peptides Based upon ONIOM and Density Functional Theory (DFT) Studies. J. Phys. Chem. B, 2008. 112(4): 1320-8

Oliva, A., J. Bertran, and J.J. Dannenberg, Attractive Strain - The Disadvantages of Rigid Multiple H-bond Donors and Acceptors. A Theoretical Analysis of the Hydrogen-Bonding Interactions in Heterodimers of Tetraazaanthracenedione with Pyridylureas. J. Phys. Chem. A, 2008, 112(12): 1765-9

Poater, J., et al., Biphenyls, Bond Paths and Repulsions: Do the Ortho and Ortho' Substituents in Biphenyls Repel or Attract (Bind to) Each Other? Int. J. Chem. Mod., 2008. 1(1):  63-78.

Juranic, N., et al., Structural Dependencies of Protein Backbone 2JNC' Couplings. Protein Sci., 2008  17(4): p. 768-76

Salvador, P., A. Asensio, and J.J. Dannenberg, The Effect of Aqueous Solvation upon a-Helix Formation for Polyalanines. J. Phys. Chem. B, 2007. 111: 7462-7466.

Direct Calculation of trans-Hydrogen-Bond 13C-15N 3-Bond J-Couplings in Entire Polyalanine alpha-Helices. A Density Functional Theory Study Salvador, P.; Wieczorek, R.; Dannenberg, J. J. J. Phys. Chem. B., 2007, 111, 2398-2403.

Dannenberg, J.J., Enthalpies of Hydration of N-Methylacetamide by One, Two and Three waters. An Ab Initio DFT Study. J. Phys. Chem. A, 2006. 110(17), 5798-5802.

Dannenberg, J.J., The Importance of Cooperative Interactions and a Solid State Paradigm to Proteins - What Peptide Chemists Can Learn from Molecular Crystals. Advances in Protein Chemistry, 2006. 72, 227-73.

Chen, Y.-f. and J.J. Dannenberg, Cooperative 4-Pyridone H-bonds with Extraordinary Stability. A DFT Molecular Orbital Study. J. Am. Chem. Soc., 2006. 128, 8100-1.