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2008
Zuber, G., Wipf, P. and Beratan, D. N. "Exploring the Optical Activity Tensor by Anisotropic Rayleigh Optical Activity Scattering." ChemPhysChem, 9 (2):265-271, 2008
Skourtis S.S., Beratan, D.N., "Biochemistry. Photosynthesis from the protein's perspective." Science, 316(5825):703-4. No abstract available. 2007.
Zollner, A, Pasquinelli M.A., Bernhardt, R., Beratan, D.N., "Protein phosphorylation and intermolecular electron transfer: a joint experimental and computational study of a hormone biosynthesis pathway." J Am Chem Soc . 129(14):4206-16. 2007.
Prytkova T.R., Kurnikov I. V. and Beratan, D.N., "Coupling coherence distinguishes structure sensitivity in protein electron transfer." Science . 315(5812):622-5. 2007.
Prytkova T.R., Beratan, D.N. and Skourtis, S.S., "Photoselected electron transfer pathways in DNA photolyase." Proc Natl Acad Sci U S A . 104(3):802-7. 2007.
Keinan, S., Hu, X., Beratan, D.N., and Yang, W., "Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework." J Phys Chem A . 111(1):176-81. 2007.
Mukhopadhyay, P., Zuber, G., Wipf, P. and Beratan, D.N., "Contribution of a Solute's Chiral Solvent Imprint to Optical Rotation." Angew Chem Int Ed Engl . 46(34):6450-6452. No abstract available. 2007.
Parag Mukhopadhyay, Gerard Zuber, Michael-Rock Goldsmith, Peter Wipf and David N. Beratan, "Solvent Effect on Optical Rotation: a Case Study of Methyloxirane in Water," ChemPhysChem, 7(12):2483-6, 2006.
T. Kawatsu, D.N. Beratan, and T. Kakitani, "Conformationally Averaged Score Functions for Electronic Propagation in Proteins", J. Phys. Chem. B, 110, 5747-5757, 2006 .
M. R. Goldsmith, C.B. George, G. Zuber, R. Naaman, D.H. Waldeck, P. Wipf and D.N. Beratan. "The Chiroptical Signature of Archiral Metal Clusters Induced by Dissymmetric Adsorbates," Physical Chemistry Chemical Physics, 8, 63-67, 2006.
M. Wang, X. Hu, D.N. Beratan and W. Yang. "Designing Molecules by Optimizing Potentials," J. Am. Chem. Soc., 128, 3228-3232, 2006.
S.S. Skourtis, J. Lin, and D.N. Beratan, "The effects of bridge motion on electron transfer reactions mediated by tunneling" Chapter 18 in Modern methods for theoretical physical chemistry of biopolymers, edited by E. B. Starikov, J. P. Lewis, and S. Tanaka, Elsevier, June, 2006.
T. Kawatsu and D. N. Beratan, "Electron transfer between cofactors in protein domains linked by a flexible tether" Chem. Phys. 326, 259-269, 2006 .
D. Kazmin, T. Prytkova, C.E. Cook, R. Wolfinger, T. Chu, D. Beratan, C. Chang, and D.P. McDonnell, "Linking ligand induced alterations in androgen receptor structure to differential gene expression: a first step in the rational design of selective androgen receptor modulators (SARMs), Mol. Endocrinol., 20, 1201-1217, 2006 .
T. Kawatsu and D. N. Beratan, "Score Functions for Protein ET: Single vs. Multi-Pathway Models" J. Phys. Chem. B, in press, 2006.
J. Lin, Balabin, I. A. and D.N. Beratan, "The Nature of Aqueous Tunneling Pathways Between Electron-Transfer Proteins,", Science (310), 1311-1313, 2005.
G. Zuber, M.R. Goldsmith, and T. D. Hopkins. "Systematic assignment of the configuration of flexible natural products by spectroscopic and computational methods: The Bistramide C Analysis", Org. Lett. 7, 5269-5272, 2005 .
G. Zuber, M.R. Goldsmith, and D.N. Beratan, "Towards Raman Optical Activity Calculations of Large Molecules," Chem. Phys. Chem 6, 595-597, 2005.
J.P. Lin and D.N. Beratan, "Simulation of Electron Transfer Between Cytochrome c(2) and the Bacterial Photosynthetic Reaction Center: Brownian Dynamics Analysis of the Native Proteins and Double Mutants," J. Phys. Chem. B, 109, 7529-7534, 2005.
J. Lee, I.A. Balabin, D.N. Beratan, and J.T. Yates, Jr. "Charge transfer through chemisorbed organic molecules--neutralization of ionization processes at local sites in the molecule", Chem, Phys. Lett., 412, 171-175, 2005.
J. Zheng, Y.K. Kang, M.J. Therien, M.J. and D,N, Beratan, "Generalized Mulliken-Hush analysis of electronic coupling interactions in compressed-stacked porphyrin-bridge-quinon systems", J. Am. Chem. Soc., 127, 11303-11310, 2005.
G. Zuber, M.R. Goldsmith, D.N. Beratan, and P. Wipf, "Assignment of the absolute configuration of [n]-Ladderanes by TD-DFT optical rotation calculations", Chirality, 17, 507-510, 2005.
S.S. Skourtis, I.A. Balabin, T. Kawatsu, T. and D. N. Beratan "Protein Dynamics and Electron Transfer: Electronic Decoherence and Non-Condon Effects," Proceedings of the National Academy of Sciences of the USA, 102, 3552-3557, 2005.
M. Galperin and D.N. Beratan, "Simulation of Scanning Tunneling Microscope Images of 1,3-cyclohexadiene Bound to a Silicon Surface," J. Phys. Chem. B, 109, 1473-1480, 2005.
T.R. Prytkova, I.V. Kurnikov, and D.N. Beratan "Ab Initio Based Calculations of Electron-Transfer Rates in Metalloproteins," J. Phys Chem. B, 109, 1618-1625, 2005.J.
J. R. Winkler, H. B. Gray, T. R. Prytkova, I.V. Kurnikov and D.N. Beratan, "Electron transfer through proteins", in Bioelectronics, edited by I. Willner and E. Katz, Wiley-VCH, 15-33, 2005.
S.S. Skourtis, J. Lin and D.N. Beratan, "The effects of bridge motion on electron transfer reactions mediated by tunneling", in Modern Methods for Theoretical Physical Chemistry of Biopolymers, edited by E. B. Starikov, S. Tanaka and J. P. Lewis, 2005.
J. L. Perry, M. R. Goldsmith, M. A. Peterson, D,N. Beratan, G. Wozniak, F. Ruker, and J. D. Simon; "Structure of the Ochratoxin A Binding Site within Human Serum Albumin," J. Phys. Chem. B., 108, 16960-16964, 2004.
S.S. Skourtis, D.H. Waldeck, and D.N. Beratan "Inelastic Electron Tunneling Erases Coupling-Pathway Interferences," Journal of Phys. Chem. B, 108, 15511-15518, 2004.
J. Liao and D.N. Beratan "How Does Protein Architecture Facilitate the Transduction of ATP Chemical-Bond Energy into Mechanical Work?" Biophysical Journal, 87, 1369-1377, 2004.
J. Lin and D.N. Beratan "Tunneling While Pulling: The Dependence of Tunneling Current on End-to-End Distance in a Flexible Molecule," Journ. of Phys. Chem. A, 108, 5655-5661, 2004.
I.V. Rubtsov, Y.K. Kang, N.P. Redmore, R.M. Allen, J. Zheng, D.N. Beratan and M.J. Therien "The Degree of Charge Transfer in Ground and Charge Separated States Revealed by Ultrafast Visible Pump/Mid-IR Prob Spectroscopy," Journ. of the Amer. Chem. Soc. 126, 5022-5023, 2004.
Z. Liang, I.V. Kurnikov, J. M. Nocek, A. Mauk, D.N. Beratan, and B.M. Hoffman "Dynamic Docking and Electron-Transfer Between Cytochrome b5 and a Suite of Myoglobin Surface-Charge Mutants--Introduction of a Functional-Docking Algorithm for Protein-Protein Complexes," Journ. of the Amer. Chem. Soc., 126, 2785-2798, 2004.
Y.A. Berlin, I.V. Kurnikov, D.N. Beratan, M. A. Ratner, and A.L. Burin. "DNA Electron Transfer Processes: Some Theoretical Notions," Topics in Current Chem., 237, 1-36, 2004 .
M. R. Goldsmith, N. Jayasuriya, D.N. Beratan, and P. Wipf, "Optical Rotation of Noncovalent Aggregates," J. Am. Chem. Soc., 125, 15696-15697, 2003.
D.N. Beratan, "Molecular Control of
Electon Transfer Events Within and Between Biomolecules," Molecular
Electronics: Bio-sensors and Bio-computers, L. Barsanti et al
(eds.), Kluwer Academic Publishers, The Netherlands, 227-236, 2003.
J.L.
Perry, T. Christensen, M.R. Goldsmith, E.J. Toone, D.N. Beratan, and
J.D. Simon, "Binding of Ochratoxin A to Human Serum Albumin Stabilized
by a Protein-Ligand Ion Pair," J. Phys. Chem. B, Web Release
Date: 03-Jul-2003, (Article) DOI: 10.1021/jp034783x.
M.A. Pasquinelli and D.N. Beratan, "Theoretical
studies of the effects of phosphorylation on protein electron transfer
chains," Biophys. J., 84:149A-150A Part 2 Suppl. S, Feb., 2003.
D.N. Beratan, "Molecular control of electron transfer events within and between biomolecules", in Molecular electronics: biosensors and biocomputers, edited by L. Barsanti, V. Evangelista, P. Gualtieri, V. Passarelli, and S. Vestri, Kluwer Academic Publishers, 227-236, 2003.
F.
Lewis, J. Liu, W. Weigel, W. Rettig, I.V. Kurnikov, and D.N. Beratan,
"Donor-bridge-acceptor energetics determine the distance dependence
of electron tunneling in DNA," Proc. Natl. Acad. Sci. (USA),
99, 12536-12541, 2002.
Z.X.
Liang, J.M. Nocek, K.H. Huang, R.T. Hayes, I.V. Kurnikov, D.N. Beratan,
and B.M. Hoffman, "Dynamic docking and electron transfer between
Zn-myoglobin and cytochrome b5, "
J. Am. Chem. Soc., 124, 6849-6859, 2002.
G.S.M.
Tong, I.V. Kurnikov, and D.N. Beratan, "Tunneling energy effects
on GC oxidation in DNA," J. Phys. Chem. B, 106, 2381-2392, 2002.
M.
Jones, I.V. Kurnikov, and D.N. Beratan, "The nature of tunneling
pathway and average packing density models for protein-mediated electron
transfer," J. Phys. Chem. A, 106, 2002-2006, 2002.
F.D. Lewis, J. Liu, W. Weigel, W. Retting, I.V. Kurnikov, and D. N. Beratan, "Tunneling energy controls DNA electron transfer distance dependence," Proc. Natl. Acad. Sci., 99, 99, 12536-12541, 2002.
D.N. Beratan, R.K. Kondru, and P. Wipf, "Optical activity: from structure-function to structure predictions," in ACS Symposium Series, Chiralty: Physical Chemistry, J. Hicks, editor, Oxford University Press, 104-118, 2002.
2001
K. M. Specht, J. Nam, D.M. Ho, N. Berova, R. K. Kondru, D. N. Beratan, P. Wipf, R. A Pascal Jr., D. Kahne, "Determining absolute configuration in flexible molecules: a case study", J. Am Chem. Soc., 123, 8961-8966, 2001.
T.L.
Perry, A. Dickerson, A.A. Khan, M. Kelley, R.K. Kondru, D.N. Beratan,
R.K. Kondru, P. Wipf, M.T. Hamann, "New peroxylactones from a Jamaican
marine sponge of the genus Plakortis onkodes, with inhibitory activity
against the AIDS opportunistic infection Toxoplasma gondii," Tetrahedron,
57, 1483-1487, 2001.
S.S. Skourtis and D.N. Beratan,
"Multi-center and multi-electron transfer in biology," in
Electron Transfer Reactions, Vol. 1: Theory & Principles, Wiley-VCH
(Weinheim), V. Balzani editor, 109-125, 2001.
G.C. Walker and D.N. Beratan,
"Electron Transfer Reactions," in Encyclopedia of Chemical
Physics and Physical Chemistry, Institute of Physics Publishing, editors:
J. Moore and N. Spencer, Institute of Physics Press, 3, 2001.
S.
Ribe, R.K. Kondru, D.N. Beratan, and P. Wipf, "Optical rotation
computation, total synthesis, and stereochemistry assignment of the
marine natural product Pitiamide A," J. Am. Chem. Soc., 122, 4608-4617, 2000. M.
Lee, M.J. Shephard, S.M. Risser, S. Priyadarshy, M.N. Paddon-Row, and
D.N. Beratan, "The nature of tunnel splitting mediated by stacked
aromatics," J. Phys. Chem. A, 104, 7593-7599, 2000.
E.
Babini, I. Bertini, M. Borsari, F. Capozzi, C. Luchinat, X.-Y. Zhang,
G.L.C. Moura, I.V. Kurnikov, D.N. Beratan, A. Ponce, A.J. DiBilio,
J.R. Winkler, and H.B. Gray, "Bond-mediated electron tunneling
in ruthenium-modified high-potential iron-sulfur protein," J.
Am. Chem. Soc., 122, 4532-4533, 2000.
R.K.
Kondru, C.H.-T. Chen, D.P. Curran, P. Wipf and D.N. Beratan, "Determination
of the absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one
by optical rotation computation," Tetrahedron: Asymmetry, 10,
4143-4150, 1999.
S.S. Skourtis and D.N.
Beratan, "Theories of structure-function relationships for bridge-mediated
electron transfer," Adv. Chem. Phys., vol. 106, Chapter 8, 1999,
377-452.
D.N. Beratan and S.S.
Skourtis, "Protein-mediated electron transfer: pathways, orbital
interactions and contact maps." In Biological electron-transfer
chains: genetics, composition and mode of operation, G.W. Canters
and E. Vijgenboom, editors, Kluwer Academic Publishers, Dordrecht,
The Netherlands, 1998, pp 9-27.
S.
Priyadarshy, S.M. Risser, and D.N. Beratan, "DNA-mediated electron
transfer," JBIC, 3, 196-200, 1998.
D.N.
Beratan and S.S. Skourtis, "Electron transfer mechanisms,"
Current opinions in chemical biology, 2, 235-243, 1998.
R.K.
Kondru, P. Wipf, and D.N. Beratan, "Theory assisted determination
of absolute stereochemistry for complex natural products via computation
of molar rotation angles." J. Am. Chem. Soc., 120, 2204-2205, 1998.
K.
Kumar, Z. Lin, I.V. Kurnikov, D.N. Beratan, D.H. Waldeck, and M.B.
Zimmt, "Use of modern theories to determine electronic coupling
matrix elements in intramolecular systems," J. Phys. Chem. A,
102, 5529-5541, 1998.
A.
Roitberg, M. Holden, M. Mayhew, I.V. Kurnikov, D.N. Beratan, and V.
Vilker, "Binding and electron transfer between putidaredoxin
and cytochrome P-450cam (cyp101). Theory and experiments," J.
Am. Chem. Soc., 120, 8927-932, 1998.
