Solvent and Conformation Dependence of Amide I Vibrations in Peptides and Proteins Containing Proline, S. Roy, J. Lessing, G. Meisl, Z. Ganim, A. Tokmakoff, J. Knoester, and T. L. C. Jansen, J. Chem. Phys. 135, 234507 (2011).

Vibrational excitons in ionophores: Experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels, Z. Ganim, A. Tokmakoff, and A. Vaziri, New Journal of Physics 13 113030 (2011).

A Fast-Scanning Fourier Transform 2D IR Interferometer S. T. Roberts, J. J. Loparo, K. Ramasesha, and A. Tokmakoff, Opt. Comm. 284 1062-1066 (2011).

Proton Transfer in Concentrated Aqueous Hydroxide Visualized using Ultrafast Infrared Spectroscopy S. T. Roberts, K. Ramasesha, P. B. Petersen, A. Mandal, and A. Tokmakoff, J. Phys. Chem. A 115 3957-3972 (2011).

Collective Hydrogen Bond Reorganization in Water Studied with Temperature-Dependent Ultrafast Infrared Spectroscopy R. A. Nicodemus, S. A. Corcelli, J. L. Skinner, and A. Tokmakoff, J. Phys. Chem. B 115 5604-5616 (2011).

Ultrafast 2D IR Anisotropy of Water Reveals Reorientation during Hydrogen-Bond Switching K. Ramasesha, S. T. Roberts, R. A. Nicodemus, A. Mandal, and A. Tokmakoff, J. Chem. Phys., 135, 054509 (2011).

Anharmonic Vibrational Modes of Nucleic Acid Bases Revealed by 2D IR Spectroscopy C. S. Peng, K. C. Jones, and A. Tokmakoff, J. Am. Chem. Soc. 133, 15650 (2011).

Melting of a β-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations A. W. Smith, J. Lessing, Z. Ganim, C. S. Peng, A. Tokmakoff, S. Roy, T. L. C. Jansen, and J. Knoester, J. Phys. Chem. B 114, 10913-10924 (2010).

Source for Ultrafast Continuum Infrared and Terahertz Radiation P. B. Petersen and A. Tokmakoff, Opt. Lett. 35(12), 1962-1964 (2010).

Hydrogen Bond Rearrangements in Water Probed with Temperature-Dependent 2D IR R. A. Nicodemus, K. Ramasesha, S. T. Roberts, and A. Tokmakoff, J. Phys. Chem. Lett 1, 1068-1072. (2010).

Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy Z. Ganim, K. C. Jones, and A. Tokmakoff, Phys. Chem. Chem. Phys. 12(14), 3579-3588 (2010).

2009

Heterodyne-Detected Dispersed Vibrational Echo Spectroscopy K. C. Jones, Z. Ganim, and A. Tokmakoff, J. Phys. Chem. A 113(51), 14060-14066 (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, Proc. Nat. Acad. Sci. 106(36), 15154-15159 (2009).

Structural Rearrangements in Water Viewed Through Two-Dimensional Infrared Spectroscopy S. T. Roberts, K. Ramasesha, and A. Tokmakoff, Acc. Chem. Res. 42(9), 1239-1249 (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(9), 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(52), 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(42), 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(1), 474-487 (2008).

Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface H. S. Chung and A. Tokmakoff, Proteins 72(1), 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(3), 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 β-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(1-3), 218-229 (2007).

Transient 2D IR spectroscopy of ubiquitin unfolding dynamics H. S. Chung, Z. Ganim, K. C. Jones and A. Tokmakoff, Proc. Nat. Acad. Sci. 104, 14237-14242 (2007).

Shining light on the rapidly evolving structure of water A. Tokmakoff, Science, 317(5834), 54-55 (2007).

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), 063101/1-063101/10 (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 β-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, Biophys. J. 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. B 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, Proc. Nat. Acad. Sci. 102, 13019-13022 (2005).

Polarizable molecules in the vibrational spectroscopy of water E. Harder, J. D. Eaves, A. Tokmakoff, and B. J. Berne, Proc. Nat. Acad. Sci. 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, Proc. Nat. Acad. Sci. 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 molecule 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. Demirdöven 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).

2003

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 (2003).

Coherent 2D IR Spectroscopy: Molecular Structure and Dynamics in Solution. M. Khalil, N. Demirdöven, 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. Demirdöven, and A. Tokmakoff, Phys. Rev. Lett. 90, 047401/1-047401/4 (2003).

2002

Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy. N. Demirdöven, M. Khalil, A. Tokmakoff, Phys. Rev. Lett. 89 237401/1-237401/4 (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. Demirdöven, 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. Demirdöven and A. Tokmakoff, J. Chem. Phys. 115, 10814-10828 (2001).

Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations. N. Demirdöven, M. Khalil, O. Golonzka and A. Tokmakoff, J. Phys. Chem. A 105, 8025-8030. (2001).

Polarization-sensitive 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. Demirdöven 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, O. 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, O. Golonzka, C. J. Fecko, and A. Tokmakoff, J. Phys. Chem. A 104, 5711-5715 (2000).

Two-dimensional line shapes derived from coherent third-order nonlinear spectroscopy. A. Tokmakoff, J. Phys. Chem. A 104, 4247-4255 (2000).

1999

Two-dimensional line-shape analysis of photon echo signal. K. Okumura, A. Tokmakoff, and Y. 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).