2009
Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions S.T. Roberts, P.B. Petersen, K. Ramasesha, A. Tokmakoff, I.S. Ufimtsev, and T.J. Martinez, PNAS (2009).
Structural Rearrangements in Water Viewed Through Two-Dimensional Infrared Spectrscopy S.T. Roberts, K. Ramasesha, and A. Tokmakoff, Acc. Chem. Res. (2009).
Amide I'-II' 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity L.P. DeFlores, Z. Ganim, R.A. Nicodemus, and A. Tokmakoff, J. Am. Chem. Soc. 131, 3385-3391 (2009).
2008
Probing the Folding Transition State of Ubiquitin Mutants by Temperature-Jump-Induced Downhill Unfolding H.S. Chung, A. Shandiz, T.R. Sosnick, and A. Tokmakoff, Biochemistry 47, 13870-13877 (2008).
Ultrafast N-H Vibrational Dynamics of Cyclic Doubly Hydrogen-Bonded Homo- and Heterodimers P.B. Petersen, S.T. Roberts, K. Ramasesha, D.G. Nocera, and A. Tokmakoff, J. Phys. Chem. B 112, 13167-13171 (2008).
Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy H.S. Chung and A. Tokmakoff, Proteins 72, 474-487 (2008).
Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface H.S. Chung and A. Tokmakoff, Proteins 72, 488-497 (2008).
Amide I Two-Dimensional Infrared Spectroscopy of Proteins Z. Ganim, H.S. Chung, A. Smith, L.P. DeFlores, K.C. Jones and A. Tokmakoff, Acc. Chem. Res. 41, 432-441 (2008).
2007
Are Water Simulation Models Consistent with Steady-State and Ultrafast Vibrational Spectroscopy Experiments? J.R. Schmidt, S.T. Roberts, J.J. Loparo, A. Tokmakoff, M.D. Fayer, J.L. Skinner, Chem. Phys., 341, 143-157 (2007).
Infrared Spectroscopy of Tritiated Water R. A. Nicodemus and A. Tokmakoff, Chem. Phys. Lett., 449, 130-134 (2007).
Two-dimensional Fourier Transform Spectroscopy in the Pump-Probe Geometry L.P. DeFlores, R. A. Nicodemus and A. Tokmakoff, Opt. Lett., 32(20), 2966-2968 (2007).
Probing Local Structural Events in Beta-hairpin Unfolding with Transient Nonlinear Infrared Spectroscopy A. Smith and A. Tokmakoff, ACIE, 46(42), 7984-7987, (2007).
Variation of the transition dipole moment across the OH stretching band of water J.J. Loparo, S.T. Roberts, R. A. Nicodemus and A. Tokmakoff, Chem. Phys. 341, 218-229 (2007).
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics H.S. Chung, Z. Ganim, K.C. Jones and A. Tokmakoff, PNAS, 104, 14237-14242 (2007).
Shining light on the rapidly evolving structure of water A. Tokmakoff, Science, 317(5834), 54-55 (2007).
A Transient two-dimensional IR spectrometer for probing nanosecond temperature jump kinetics H.S. Chung, M. Khalil, A.W. Smith and A. Tokmakoff, Rev. Sci, Instr., 78(6), 063101 (2007).
Single-shot two-dimensional infrared spectroscopy M.F. DeCamp, L.P. DeFlores, K.C. Jones and A. Tokmakoff, Opt. Exp., 15(1), 233-241, (2007).
Amide I two-dimensional infrared spectroscopy of beta-hairpin peptides A. W. Smith and A. Tokmakoff, J. Chem. Phys, 126(4), 045109 (2007).
2006
Water Penetration into Protein Secondary Structure Revealed by Hydrogen-Deuterium Exchange Two-Dimensional Infrared Spectroscopy L.P. DeFlores and A. Tokmakoff, J. Am. Chem. Soc. 128(51) 16520-16521, (2006).
Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes J.J. Loparo, S.T. Roberts, and A. Tokmakoff, J. Chem. Phys. 125, 194521, (2006).
Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics J.J. Loparo, S.T. Roberts, and A. Tokmakoff, J. Chem. Phys. 125, 194522, (2006).
Characterization of spectral diffusion from two-dimensional line shapes S.T. Roberts, J.J. Loparo, and A. Tokmakoff, J.Chem. Phys., 125, 084502 (2006).
Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra Z. Ganim and A. Tokmakoff, Biophysical Journal 91, 2636-2646 (2006).
The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes of N-Methylacetamide L. P. DeFlores, Z. Ganim, S. F. Ackley, H. S. Chung, and A. Tokmakoff, J. Phys. Chem. A, 110(38), 18973-18980 (2006).
Single-shot two-dimensional spectrometer M. F. DeCamp, and A. Tokmakoff, Opt. Lett., 31, 113-115 (2006).
Visualization and Characterization of the Infrared Active Amide I Vibrations of Proteins H. S. Chung, and A. Tokmakoff, J. Phys. Chem. B, 110, 2888-2898 (2006).
2005
Hydrogen bonds in liquid water are broken only fleetingly J. D. Eaves*, J. J. Loparo*, C. J. Fecko, S. T. Roberts, A. Tokmakoff, and P. L. Geissler, PNAS, 102, 13019-13022 (2005).
Polarizable molecules in the vibrational spectroscopy of water E. Harder, J. D. Eaves, A. Tokmakoff, and B.J. Berne, PNAS 102(33), 11611-11616 (2005).
Electric Field Fluctuations Drive Vibrational Dephasing in Water J. D. Eaves, A. Tokmakoff, and P. L. Geissler, J. Phys. Chem. A 109(42), 9424-9436 (2005).
Residual Native Structure in a Thermally Denatured β-Hairpin A. W. Smith, H. S. Chung, Z. Ganim, and A. Tokmakoff, J. Phys. Chem. B 109, 17025-17027 (2005).
Upconversion multichannel infrared spectrometer M. F. DeCamp, and A. Tokmakoff, Opt. Lett., 30, 1818-1820 (2005).
Amide I Vibrational Dynamics of N-Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions M. F. DeCamp, L. P. DeFlores, J. M. McCracken, A. Tokmakoff, K. Kwac, and M. Cho, J. Phys. Chem. B, 109, 11016-11026 (2005).
Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin. H.S. Chung, M. Khalil, A.W. Smith, Z. Ganim, and A. Tokmakoff, PNAS, 102, 612-617 (2005).
Local hydrogen bonding dynamics and collective reorganization in water: Ultrafast infrared spectroscopy of HOD/D2O. C.J. Fecko, J. J. Loparo, S. T. Roberts, and A. Tokmakoff, J. Chem. Phys., 122, 054506 (2005).
2004
Reorientational and configurational fluctuations in water observed on the molecular length scales. J. J. Loparo, C.J. Fecko, J.D. Eaves, S. T. Roberts, and A. Tokmakoff, Phys. Rev. B, 70, 180201 (2004).
Nonlinear infrared spectroscopy of protein conformational change during thermal unfolding. H.S. Chung, M. Khalil and A. Tokmakoff, J. Phys. Chem. B, 108, 15332-15342 (2004).
Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure. N. Demirdöven, C. M. Cheatum, H. Chung, M. Khalil, J. Knoester and A. Tokmakoff, J. Am. Chem. Soc., 126, 7981-7990 (2004).
Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy. M. Khalil, N. Demirdšven and A. Tokmakoff, J. Chem. Phys., 121, 362-373 (2004).
Generation of 45 femtosecond pulses at 3 μm with a KNbO3 optical parametric amplifier. C. J. Fecko, J. J. Loparo and A. Tokmakoff, Optics Communications, 241, 521-528 (2004).
Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy. C. M. Cheatum, A. Tokmakoff, and J. Knoester, J. Chem. Phys., 120, 8201-8215 (2004).
2003
Coherent 2D IR Spectroscopy: Molecular Structure and Dynamics in Solution. M. Khalil, N. Demirdoven, A. Tokmakoff, J. Phys. Chem. A., 107, 5258-5279 (2003).
Polarization-selective femtosecond Raman spectroscopy of low-frequency motions in hydrated protein films. J. D. Eaves, C. J. Fecko, A. L. Stevens, P. Peng and A. Tokmakoff, Chem. Phys. Lett., 376, 20-25 (2003)
Ultrafast Hydrogen-Bond Dynamics in the Infrared Spectroscopy of Water. C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, P. L. Geissler, Science, 301, 1698-1702 (2003)
Obtaining absorptive line shapes in two-dimensional infrared vibrational correlation spectra. M. Khalil, N. Demirdoven, A. Tokmakoff, Phys. Rev. Lett., 90, 047401 (2003).
2002
Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy. N. Demirdoven, M. Khalil, A. Tokmakoff, Phys. Rev. Lett., 89, 237401 (2002).
Isotropic and anisotropic Raman scattering from molecular liquids measured by spatially masked optical Kerr effect spectroscopy. C. J. Fecko, J. D. Eaves, and A. Tokmakoff, J. Chem. Phys., 117, 1139-1154 (2002).
Dispersion compensation with optical materials for compression of intense sub-100-fs mid-infrared pulses. N. Demirdoven, M. Khalil, O. Golonzka, and A. Tokmakoff, Opt. Lett., 27, 433-435 (2002).
2001
Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibrational echo spectroscopy. O. Golonzka, M. Khalil, N. Demirdven and A. Tokmakoff, J. Chem. Phys., 115, 10814-10828 (2001).
Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations. N. Demirdven, M. Khalil, O. Golonzka and A. Tokmakoff, J. Phys. Chem. A, 105, 8025-8030 (2001).
Polarization-selective third-order spectroscopy of coupled vibronic states. O. Golonzka and A. Tokmakoff, J. Chem. Phys., 115, 297-309 (2001).
2000
Signatures of vibrational interactions in coherent two-dimensional infrared spectroscopy. M. Khalil and A. Tokmakoff, Chem. Phys., 266, 213-230 (2000).
Vibrational anharmonicities revealed by coherent two-dimensional infrared spectroscopy. O. Golonzka, M. Khalil, N. Demirdoven and A. Tokmakoff, Phys. Rev. Lett. 86, 2154-2157 (2000).
Separation of cascaded and direct fifth-order Raman signals using phase-sensitive intrinsic heterodyne detection. O. Golonzka, N. Demirdöven, M. Khalil, and A. Tokmakoff, J. Chem. Phys., 113, 9893-9896 (2000).
Polarization-selective femtosecond Raman spectroscopy of isotropic and anisotropic vibrational dynamics in liquids. M. Khalil, Oleg Golonzka, N. Demirdöven, C. J. Fecko, and A. Tokmakoff, Chem. Phys. Lett., 321, 231-237 (2000).
A phase-sensitive detection method using diffractive optics for polarization-selective femtosecond Raman spectroscopy. M. Khalil, N. Demirdöven, Oleg Golonzka, C.J. Fecko, and A. Tokmakoff, J. Phys. Chem. A, 104, 5711-5715 (2000).
Two-dimensional lineshapes derived from coherent third-order nonlinear spectroscopy. Andrei Tokmakoff, J. Phys. Chem. A, 104, 4247-4255 (2000).
1999
Two-dimensional lineshape analysis of photon echo signal. Ko Okumura, Andrei Tokmakoff, and Yoshitaka Tanimura, Chem. Phys. Lett, 314, 488-495 (1999).
Structural information from two-dimensional fifth order Raman spectroscopy. K. Okumura, A. Tokmakoff, and Y. Tanimura, J. Chem. Phys, 111, 492-503 (1999).
1998
The intermolecular interaction mechanisms in liquid CS2 at 299 K and 164 K probed with two-dimensional Raman spectroscopy. A. Tokmakoff, M. J. Lang, X. S. Jordanides and G. R. Fleming, Chem. Phys., 233, 231-242 (1998).
