BERATAN RESEARCH GROUP

 
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2011

Ben-Moshe V, Beratan DN, Nitzan A, Skourtis SS., Chiral control of current transfer in molecules. Top Curr Chem. 2011;298:259-78. PMID:21321805 [PubMed - in process] Related citations

Venkatramani R, Davis KL, Wierzbinski E, Bezer S, Balaeff A, Keinan S, Paul A, Kocsis L, Beratan DN, Achim C, Waldeck DH. Evidence for a near-resonant charge transfer mechanism for double-stranded peptide nucleic acid, J Am Chem Soc. 2011 Jan 12;133(1):62-72. Epub 2010 Dec 9. PMID: 21141966 [PubMed - in process] Related citations

 

2010

Skourtis SS, Waldeck DH, Beratan DN. Fluctuations in biological and bioinspired electron-transfer reactions. Annu Rev Phys Chem. 2010 Jan 19. [Epub ahead of print]PMID: 20192814 [PubMed - indexed for MEDLINE] Free PMC Article Free full text Related citations


Hu X, Hu H, Beratan DN, Yang W. A gradient-directed Monte Carlo approach for protein design. J Comput Chem. 2010 Feb 23. [Epub ahead of print]PMID: 20186860 [PubMed - indexed for MEDLINE] Related citations

Xing Y, Park TH, Venkatramani R, Keinan S, Beratan DN, Therien MJ, Borguet E. Optimizing single-molecule conductivity of conjugated organic oligomers with carbodithioate linkers. J Am Chem Soc. 2010 Jun 16;132(23):7946-56.PMID: 20433175 [PubMed - indexed for MEDLINE] Related citations

 

2009

Hu X, Beratan DN, Yang W., A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding. J Chem Phys. 2009 Oct 21;131(15):154117.PMID: 20568857 [PubMed - indexed for MEDLINE] Free PMC Article Free full text Related citations

Lin Z, Lawrence CM, Xiao D, Kireev VV, Skourtis SS, Sessler JL, Beratan DN, Rubtsov IV., Modulating unimolecular charge transfer by exciting bridge vibrations. J Am Chem Soc. 2009 Dec 23;131(50):18060-2.PMID: 19928957 [PubMed -indexed for MEDLINE] Related citations

Beratan DN, Skourtis SS, Balabin IA, Balaeff A, Keinan S, Venkatramani R, Xiao D. Steering electrons on moving pathways. Acc Chem Res. 2009 Oct 20;42(10):1669-78.PMID: 19645446 [PubMed - indexed for MEDLINE] Free PMC Article Free full text
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Yuan L, Seo JS, Kang NS, Keinan S, Steele SE, Michelotti GA, Wetsel WC, Beratan DN, Gong YD, Lee TH, Hong J. Identification of 3-hydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-ones as isoform-selective PKC-zeta inhibitors and potential therapeutics for psychostimulant abuse. Mol Biosyst. 2009 Sep;5(9):927-30. Epub 2009 May 8.PMID: 19668856 [PubMed - indexed for MEDLINE]

Balabin IA, Yang W, Beratan DN. Coarse-grained modeling of allosteric regulation in protein receptors. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14253-8. Epub 2009 Aug 12.PMID: 19706508 [PubMed - indexed for MEDLINE]Free PMC Article Free text

Xiao D, Skourtis SS, Rubtsov IV, Beratan DN. Turning charge transfer on and off in a molecular interferometer with vibronic pathways. Nano Lett. 2009 May;9(5):1818-23. PMID: 19435376 [PubMed]

Paul A, Bezer S, Venkatramani R, Kocsis L, Wierzbinski E, Balaeff A, Keinan S, Beratan DN, Achim C, Waldeck DH. "Role of nucleobase energetics and nucleobase interactions in single-stranded peptide nucleic acid charge transfer." J Am Chem Soc. 2009 May 13;131(18):6498-507. PMID: 19382798 [PubMed - indexed for MEDLINE] Related citations

Mukhopadhyay P, Wipf P, Beratan DN. "Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles." Acc Chem Res. 2009 Jun 16;42(6):809-19. PMID: 19378940 [PubMed - indexed for MEDLINE]
Free PMC Article Free full text Related citations

2008

Skourtis SS, Beratan DN, Naaman R, Nitzan A, Waldeck DH. "Chiral control of electron transmission through molecules." Phys Rev Lett. 2008 Dec 5;101(23):238103. Epub 2008 Dec 5. PMID: 19113598 [PubMed - indexed for MEDLINE] Related citations

 

Balamurugan D, Yang W, Beratan DN. "Exploring chemical space with discrete, gradient, and hybrid optimization methods." J Chem Phys. 2008 Nov 7;129(17):174105. PMID: 19045331 [PubMed - indexed for MEDLINE] Related citations

 

Balabin IA, Beratan DN, Skourtis SS. "Persistence of structure over fluctuations in biological electron-transfer reactions." Phys Rev Lett. 2008 Oct 10;101(15):158102. Epub 2008 Oct 8. PMID: 18999647 [PubMed - indexed for MEDLINE] Free full text
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Keinan S, Therien MJ, Beratan DN, Yang W. "Molecular design of porphyrin-based nonlinear optical materials." J Phys Chem A. 2008 Nov 27;112(47):12203-7. PMID: 18973325 [PubMed] Related citations

 

P. Mukhopadhyay, G. Zuber, D.N. Beratan. "Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computation."Biophys J. 2008 Dec 15;95(12):5574-86. [Epub ahead of print Sep 19.] PMID: 18805935 [PubMed - indexed for MEDLNE] Free full text Related citations

 

Keinan S, Paquette WD, Skoko JJ, Beratan DN, Yang W, Shinde S, Johnston PA, Lazo JS, Wipf P. "Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase Cdc25B." Org Biomol Chem. 2008 Sep 21;6(18):3256-63. Epub 2008 Jul 15 , PMID: 18802630 [PubMed - indexed for MEDLINE] Free full text
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He W, Hatcher E, Balaeff A, Beratan DN, Gil RR, Madrid M, Achim C. "Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations." J Am Chem Soc. 2008 Oct 8;130(40):13264-73
Epub 2008 Sep 10. PMID: 18781753 [PubMed - indexed for MEDLINE]

 

Hu X, Beratan DN, Yang W. "A gradient-directed Monte Carlo approach to molecular design." J Chem Phys. 2008 Aug 14;129(6):064102. PMID: 18715046 [PubMed] Related citations

 

Nano Lett. 2008 Sep;8(9):2814-8. Epub 2008 Aug 12. PMID: 18698728 [PubMed ] Related citations

 

Parks JM, Kondru RK, Hu H, Beratan DN, Yang W. "Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding." J Phys Chem B. 2008 Mar 13;112(10):3168-76. Epub 2008 Feb 14.
PMID: 18271573 [PubMed - indexed for MEDLINE] Related citations

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, Erratum in: Chemphyschem. 2008 Mar 14;9(4):504. PMID: 18219646 [PubMed]
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Beratan, D.N. and Balabin, I. "Heme-copper oxidases use tunneling pathways." Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):403-4. Epub 2008 Jan 7. No abstract available. PMID: 18180451 [PubMed - indexed for MEDLINE]

 

  • 2007

Skourtis S.S., Beratan, D.N., "Biochemistry. Photosynthesis from the protein's perspective." Science, 316(5825):703-4. No abstract available. 2007. PMID:17478711[PubMed - indexed for MEDLINE] Related citations

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. J Am Chem Soc. 2007 Apr 11;129(14):4206-16. Epub 2007 Mar 15. PMID: 17358057 [PubMed - indexed for MEDLINE] Related citations


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. PMID:17272715 [PubMed - indexed for MEDLINE] Free Article Related citations


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. Jan 16;104(3):802-7. Epub 2007 Jan 5. PMID: 17209014 [PubMed - indexed for MEDLINE] Free PMC Article Free full text Related citations


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. PMID: 17201401[PubMed]
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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. PMID:17645276 [PubMed] Related citations

 

  • 2006

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. PMID: 17072929 [PubMed - indexed for MEDLINE] Related citations

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. PMID: 16539520 [PubMed - indexed for MEDLINE]

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. Jan 7;8(1):63-7. Epub 2005 Nov 17. PMID: 16482245 [PubMed - indexed for MEDLINE] Free Article Related citations

M. Wang, X. Hu, D.N. Beratan and W. Yang. "Designing Molecules by Optimizing Potentials," J. Am. Chem. Soc., 128, 3228-3232, 2006. J Am Chem Soc. 2006 Mar 15;128(10):3228-32. PMID:16522103[PubMed] Related citations

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.

 

  • 2005

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. HopkinsG. Zuber, M. R. Goldsmith, T.D. Hopkins, D.N. Beratan and P. Wipf, ". "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.

  • 2004

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.

  • 2003

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.

  • 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.

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.

  • 2000
  • 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.

  • 1998

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.

 
 
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