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Joseph J. Dannenberg, Ph.D.

Professor - Theoretical Chemistry with Emphasis on Hydrogen Bonds and Peptides


Contact Information:

office 1321bN (tel 212-772-5343), lab 1322N (tel 212-772-5751), dept fax 212-772-5332, email,


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

Marianski, M., A. Asensio and J. J. Dannenberg. "Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives." J. Chem. Phys. 137(4), 2012: 044109.

Marianski, M., A. Oliva and J. J. Dannenberg. "A Reinvestigation of the Dimer of para-Benzoquinone and Pyrimidine with MP2, CCSD(T), and DFT Using Functionals Including Those Designed to Describe Dispersion." J. Phys. Chem. A 2012.doi: 10.1021/jp3050274

Roy, D., G. Pohl,  J., Ali-Torres, M. Marianski and J. J. Dannenberg. (2012). "Density Functional Theory Study of beta-Hairpins in Antiparallel beta-Sheets, a New Classification Based upon H-Bond Topology." Biochemistry 51(27): 5387-5393.

Mateusz Marianski and J. J. Dannenberg, Aqueous Solvation of Polyalanine alpha-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models Using Density Functional Theory, J. Phys. Chem. B, 2012, 116 (4), pp 1437–1445, DOI: 10.1021/jp209177u

Pedro Salvador, I-Hsien (Midas) Tsai and J. J. Dannenberg, J-coupling constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the full Ramachandran space, Phys. Chem. Chem. Phys., 2011, 13, 17484–17493.

Joshua A. Plumley and J. J. Dannenberg, Comparison of β-Sheets of Capped Polyalanine with Those of the Tau-Amyloid Structures VQIVYK and VQIINK. A Density Functional Theory Study, J. Phys. Chem. B 2011, 115, 10560–10566.

E. Arunan, G. R. Desiraju, R. A. Klein, J. Sadlej, S. Scheiner, I. Alkorta, D. C. Clary, R. H.
Crabtree, J. J. Dannenberg, P. Hobza, H. G. Kjaergaard, A. C. Legon, B. Mennucci, D. J. Nesbitt,
Definition of the Hydrogen Bond Pure Appl. Chem. 83, 1637 (2011) DOI: 10.1351/PAC-REP-10-01-01

E. Arunan, G. R. Desiraju, R. A. Klein, J. Sadlej, S. Scheiner, I. Alkorta, D. C. Clary, R. H.
Crabtree, J. J. Dannenberg, P. Hobza, H. G. Kjaergaard, A. C. Legon, B. Mennucci, D. J. Nesbitt, Defining the Hydrogen Bond: An Account, Pure Appl. Chem. 83, 1619 (2011) DOI:10.1351/PAC-REP-10-01-01

Dipankar Roy, J. J. Dannenberg, The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study, Chem. Phys. Lett., 2011, 255.

Chen, Yung-Fou; Dannenberg, J. J., The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials, J. Comput. Chem., 2011, 2890.

Joshua A. Plumley,J. J. Dannenberg, A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error, J. Comput. Chem., 2011, 32(8) 1519–1527

Plumley, Joshua A.; Tsai, Midas; Dannenberg, J. J., Aggregation of Capped Hexaglycine Strands into Hydrogen-Bonding Motifs Representative of Pleated and Rippled β-Sheets, Collagen, and Polyglycine I and II Crystal Structures. A Density Functional Theory Study, J. Phys. Chem. B 2011, 115, 1562–1570

Joshua A. Plumley and J. J. Dannenberg, The Importance of Hydrogen Bonding between the Glutamine Side Chains to the Formation of Amyloid VQIVYK Parallel beta-Sheets: An ONIOM DFT/AM1 Study, J. Am Chem. Soc., 2010, 132, 1758–1759

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, 113; 309-18

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.