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Multidimensional Spectroscopy; Peptides

370"Simulations of Two-Dimensional Femtosecond Infrared Photon-Echoes of Glycine Dipeptide," A. Piryatinski, S. Tretiak, V. Chernyak and S. Mukamel, J. Raman Spec. 31, 125-135 (2000). pdf
377"Two-Dimensional Coherent Infrared Spectroscopy of Vibrational Excitons in Polypeptides," A. Piryatinski, V. Chernyak, and S. Mukamel, in Ultrafast Infrared and Raman Spectroscopy, M. Fayer, Editor (Marcel Dekker Inc., New York), 349-382 (2001). no pdf
381"Two-Dimensional Infrared Femtosecond Spectroscopy of Cyclic Pentapeptides," A. Piryatinski, V. Chernyak, and S. Mukamel, AIP Conference Proceedings 503, 117-126 Y. Ozaki and I. Noda, Editors, (Melville, NY), (2000). pdf
398"Nonlinear Two-Dimensional IR Spectroscopy of Unfolding Processes in ?-Peptides," C. Scheurer, A. Piryatinski and S. Mukamel, in Ultrafast Phenomena XII, edited by T. Elsaesser, S. Mukamel, M. Murnane and N. Scherer, (Springer-Verlag, Berlin), 507-509 (2000). no pdf
403"Vibrational-Exciton Relaxation Probed by Three-Pulse Echoes in Polypeptides," A. Piryatinski, V. Chernyak and S. Mukamel, Chem. Phys. 266, 285-294 (2001). pdf
405"Two-Dimensional Correlation Spectroscopies of Localized Vibrations," A. Piryatinski, V. Chernyak and S. Mukamel, Chem. Phys. 266, 311-322 (2001). pdf
406"Signatures of -Peptide Unfolding in Two-Dimensional Vibrational Echo Spectroscopy: A Simulation Study," C. Scheurer, A. Piryatinski and S. Mukamel, J. Am. Chem. Soc. 123, 3114-3124 (2001). pdf
422"Intramoleuclar and Solvent Contributions to Amide-I Vibrational Echo Lineshapes of a Cyclic Dipeptide," R. Venkatramani, T. la Cour Jansen, J. Dreyer and S. Mukamel, TRVS XI Conference Proceedings (Submitted) (2003). no pdf
440"Two Dimensional Vibrational Spectroscopy of Antaminide; A Simulation Study," S. M. Park, C. Scheurer and S. Mukamel in Femtochemistry and Femtobiology: Ultrafast Dynamics in Molecular Science, 742-754, A. Douhal, Editor, (World Scientific, Singapore) (2002). pdf
453"Correlated Line Broadening in Three Pulse Multidimensional Spectroscopy of Coupled Vibrations", R. Venkatramani and S. Mukamel Ultrafast Phenomena XIII, R.J.Miller, M.M. Murnane, N.F. Scherer, and A.M. Wiener, Editors (Springer-Verlag, Berlin) 565-567 (2002). no pdf
456"Correlated Line Broadening in Multidimensional Vibrational Spectroscopy" R. Venkatramani and S. Mukamel, J. Chem. Phys., 117, 11089-11101 (2002). pdf
459"Ab initio Simulation of the Two-Dimensional Vibrational Spectrum of Dicarbonylacetylacetonato Rhodium(I)" A. M. Moran, J. Dreyer and S. Mukamel, J. Chem. Phys, 118, 1347-1355 (2002). pdf
465"Coherent Three-Pulse Spectroscopy of Couples Vibrations in a Rigid Dipeptide: DFT Simulations" J. Dreyer, A. M. Moran and S. Mukamel, J. Phys. Chem. B., 107, 5967-5985 (2003). pdf
470"Linear and Nonlinear IR Signatures of Local - and 310-Helical Structures in Alanine Polypeptides", A. Moran, S-M. Park, J. Dreyer and S. Mukamel, J. Chem. Phys. 118, 3651-3659 (2003). pdf
473"Infrared Photon Echo Signatures of Hydrogen Bond Connectivity in the Cyclic Decapeptide Antamanide" A. M. Moran, S.-M. Park, and S. Mukamel J. Chem. Phys. 118, 9971-9980 (2003). pdf
476"Arnoldi Algorithm for the Simulation of Multidimensional Infrared Spectroscopy", T. Hayashi and S. Mukamel, Bull Kor. Chem. Soc. 24, 1107-1110 (2003). pdf
480"Tensor Components in Three Pulse Vibrational Echoes of a Rigid Dipeptide ", J. Dreyer, A. Moran and S. Mukamel, Bull Kor. Chem. Soc. 24, 1091-1096 (2003). pdf
487"Many-Body Approaches For Simulating Coherent Nonlinear Spectroscopies of Electronic and Vibrational Excitons " D. Abramavicius and S. Mukamel, Chem. Rev., 104, 2073-2098 (2004). pdf
488"Multidimensional Infrared Signatures of Intramolecular Hydrogen-Bonding in Malonaldehyde", T. Hayashi and S. Mukamel, J. Phys. Chem.A, 107, 9113-9131 (2003). pdf
490"The Origin of Vibrational Mode Couplings in Various Secondary Structural Motifs of Polypeptides", A. Moran and S. Mukamel, Proc. Natl. Acad. Sci., 101, 506-510, (2004). pdf
499"Stochastic Liouville Equation Simulation of Multidimensional Vibrational Lineshapes of Trialanine," T. Jansen, W. Zhuang, and S. Mukamel, J. Chem. Phys. 121(21), 10577 (2004). pdf
503"Coherent Low-Frequency Motions of Hydrogen Bonded Acetic Acid Dimers in the Liquid Phase," K. Heyne, N. Huse, J. Dreyer, E.Nibbering, T. Elsaesser and S. Mukamel , J. Chem. Phys., 121, 902-913 (2004). pdf
505"Peptide Secondary Structure Determination by Three-Pulse Coherent Vibrational Spectroscopies; A Simulation Study," D. Abramavicius, W. Zhuang, S. Mukamel, J. Phys. Chem. B 108, 18034-18045 (2004). pdf
508"Collective Solvent Coordinates for the Infrared Spectrum of HOD in D2O Based on an Ab Initio Electrostatic Map," T. Hayashi, T. Jansen, W. Zhuang, S. Mukamel, J. Phys. Chem. A, 109 64-82 (2005). pdf
512"Dephasing-induced Vibronic Resonances in Difference Frequency Generation Spectroscopy," R. Venkatramani and S. Mukamel, J. Phys. Chem. B, 109 8132-8143 (2005)pdf
513"Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis," W. Zhuang, D. Abramavicius , and S. Mukamel, PNAS 102, 7443-7448 (2005)pdf
516"Stochastic Liouville Equations for Hydrogen-Bonding Fluctuations and their Signatures in Two Dimensional Vibrational Spectroscopy of Water" Thomas la Cour Jansen, Tomoyuki Hayashi, Wei Zhuang and Shaul Mukamel, J. Chem. Phys. 123, 114504 (2005)pdf
520"Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA" Tomoyuki Hayashi, Wei Zhuang and Shaul Mukamel, J. Phys. Chem. A 109, 9747-9759 (2005)pdf
521"Nonlinear Vibrational Response of the Amide I, II, III and A Bands of NMA: Simulation Study Based on an Electrostatic DFT Map," T. Hayashi, W. Zhuang, S. Mukamel, TRVS XII Conference Proceeding, (http://physics.nist.gov/Divisions/Div844/events/TRVS/trvs.html) (2005)pdf
525"Simulation Protocols for Coherent Femtosecond Vibrational Spectra of Peptides," W. Zhuang, D. Abramavicius, T. Hayashi, S. Mukamel, J. Chem. Phys. J. Phys. Chem. B 110, 3362-3374 (2006)pdf
539"Correlated Hydrogen Bonding Fluctuations and Vibrational Cross Peaks in NMA: Simulation Based on a Complete Electrostatic DFT Map", T. Hayashi, and S. Mukamel, J. Chem. Phys 125, 194510 (2006) (selected for the December 1, 2006 issue of Virtual Journal of Biological Physics Research)pdf
546"Three-Pulse Photon Echo in a Dense Potassium Vapor," V. Lorenz, S. Cundiff, W. Zhuang and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006).no pdf
547"Signatures of Chemical Exchange in 2D Vibrational Spectroscopy; Simulation Based on the Stochastic Liouville Equations", F. Sanda, W. Zhuang, T. La Cour Jansen, T. Hayashi and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006).no pdf
550"Lineshapes and Correlations in Two Dimensional Vibrational Signals of NMA", T. Hayashi, W. Zhuang and S. Mukamel. In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006).no pdf
551"Discrimination of Structural Models of Amyloid Fibrils Using Two Dimensional Infrared Response: A Simulation Study", W. Zhuang, D. Abramavicious and S. Mukamel, In preparation (2006).no pdf



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