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Andrei Tokmakoff - Publications

Affiliations: 
1998-2012 Chemistry Massachusetts Institute of Technology, Cambridge, MA, United States 
 2013- Chemistry University of Chicago, Chicago, IL 
Area:
ultrafast vibrational spectroscopy to study the molecular dynamics of chemical reactions in solution and biological processes
Website:
https://chemistry.uchicago.edu/faculty/faculty/person/member/andrei-tokmakoff.html

171 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Whaley-Mayda L, Guha A, Penwell SB, Tokmakoff A. Fluorescence-Encoded Infrared Vibrational Spectroscopy with Single-Molecule Sensitivity. Journal of the American Chemical Society. PMID 33596055 DOI: 10.1021/jacs.1c00542  0.6
2020 Zhang XX, Brantley SL, Corcelli SA, Tokmakoff A. DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site. Communications Biology. 3: 525. PMID 32963293 DOI: 10.1038/s42003-020-01241-4  0.44
2020 Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, ... ... Tokmakoff A, et al. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chemical Reviews. PMID 32598850 DOI: 10.1021/acs.chemrev.9b00813  0.92
2020 Antoszewski A, Feng CJ, Vani BP, Thiede EH, Hong L, Weare J, Tokmakoff A, Dinner AR. Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding. The Journal of Physical Chemistry. B. PMID 32515958 DOI: 10.1021/acs.jpcb.0c03521  0.44
2020 Zhang XX, Tokmakoff A. Revealing the Dynamical Role of Co-Solvents in the Coupled Folding and Dimerization of Insulin. The Journal of Physical Chemistry Letters. PMID 32401513 DOI: 10.1021/acs.jpclett.0c00982  0.44
2019 Whaley-Mayda L, Penwell SB, Tokmakoff A. Fluorescence-Encoded Infrared Spectroscopy: Ultrafast Vibrational Spectroscopy on Small Ensembles of Molecules in Solution. The Journal of Physical Chemistry Letters. 1967-1972. PMID 30942587 DOI: 10.1021/acs.jpclett.9b00748  0.6
2018 Feng CJ, Dhayalan B, Tokmakoff A. Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala. Biophysical Journal. 114: 2820-2832. PMID 29925019 DOI: 10.1016/j.bpj.2018.05.003  0.44
2018 Penwell SB, Whaley-Mayda L, Tokmakoff A. Single-stage MHz mid-IR OPA using LiGaSand a fiber laser pump source. Optics Letters. 43: 1363-1366. PMID 29543236  0.6
2017 Mastron JN, Tokmakoff A. Fourier Transform Fluorescence-Encoded Infrared Spectroscopy. The Journal of Physical Chemistry. A. PMID 29251500 DOI: 10.1021/acs.jpca.7b10305  0.88
2017 Feng CJ, Tokmakoff A. The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study. The Journal of Chemical Physics. 147: 085101. PMID 28863528 DOI: 10.1063/1.4991871  0.44
2017 Ganim Z, Jones KC, Tokmakoff A. Correction: Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy. Physical Chemistry Chemical Physics : Pccp. PMID 28678231 DOI: 10.1039/c7cp90151h  1
2016 Mastron JN, Tokmakoff A. Two-Photon-Excited Fluorescence-Encoded Infrared Spectroscopy. The Journal of Physical Chemistry. A. PMID 27802385 DOI: 10.1021/acs.jpca.6b09158  0.88
2016 Reppert M, Roy AR, Tempkin JO, Dinner AR, Tokmakoff A. Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides. The Journal of Physical Chemistry. B. PMID 27736076 DOI: 10.1021/acs.jpcb.6b08678  0.48
2016 Zhang XX, Jones KC, Fitzpatrick A, Peng CS, Feng CJ, Baiz CR, Tokmakoff A. Studying Protein-Protein Binding Through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer. The Journal of Physical Chemistry. B. PMID 27203447 DOI: 10.1021/acs.jpcb.6b03246  0.96
2016 Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annual Review of Physical Chemistry. PMID 27023758 DOI: 10.1146/annurev-physchem-040215-112055  0.48
2015 Dhayalan B, Fitzpatrick A, Mandal K, Whittaker J, Weiss M, Tokmakoff A, Kent S. Efficient Total Chemical Synthesis of 13C=18O Isotopomers of Human Insulin for Isotope-Edited FTIR. Chembiochem : a European Journal of Chemical Biology. PMID 26715336 DOI: 10.1002/cbic.201500601  1
2015 Kent S, Mandal K, Dhayalan B, Avital-Shmilovici M, Tokmakoff A. Crystallization of enantiomerically pure proteins from quasi-racemic mixtures: structure determination by X-ray diffraction of isotope-labeled ester insulin and human insulin. Chembiochem : a European Journal of Chemical Biology. PMID 26707939 DOI: 10.1002/cbic.201500600  1
2015 Dai Q, Sanstead PJ, Peng CS, Han D, He C, Tokmakoff A. Weakened N3 hydrogen bonding by 5 formylcytosine and 5 carboxylcytosine reduces their base-pairing stability. Acs Chemical Biology. PMID 26641274 DOI: 10.1021/acschembio.5b00762  1
2015 Mandal A, Tokmakoff A. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy. The Journal of Chemical Physics. 143: 194501. PMID 26590536 DOI: 10.1063/1.4935174  1
2015 Biswas R, Tse YS, Tokmakoff A, Voth GA. Role of Pre-Solvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. The Journal of Physical Chemistry. B. PMID 26575795 DOI: 10.1021/acs.jpcb.5b09466  1
2015 Thämer M, De Marco L, Ramasesha K, Mandal A, Tokmakoff A. Ultrafast 2D IR spectroscopy of the excess proton in liquid water. Science (New York, N.Y.). 350: 78-82. PMID 26430117 DOI: 10.1126/science.aab3908  1
2015 Reppert M, Tokmakoff A. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy. The Journal of Chemical Physics. 143: 061102. PMID 26277120 DOI: 10.1063/1.4928637  1
2015 Stevenson P, Tokmakoff A. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons. The Journal of Chemical Physics. 142: 212424. PMID 26049444 DOI: 10.1063/1.4917321  1
2015 Baiz CR, Tokmakoff A. Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling. Biophysical Journal. 108: 1747-57. PMID 25863066 DOI: 10.1016/j.bpj.2014.12.061  1
2015 Stevenson P, Götz C, Baiz CR, Akerboom J, Tokmakoff A, Vaziri A. Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling. The Journal of Physical Chemistry. B. 119: 5824-31. PMID 25861001 DOI: 10.1021/acs.jpcb.5b02223  1
2015 Reppert M, Roy AR, Tokmakoff A. Isotope-enriched protein standards for computational amide I spectroscopy. The Journal of Chemical Physics. 142: 125104. PMID 25833611 DOI: 10.1063/1.4915271  1
2015 Peng CS, Fedeles BI, Singh V, Li D, Amariuta T, Essigmann JM, Tokmakoff A. Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity. Proceedings of the National Academy of Sciences of the United States of America. 112: 3229-34. PMID 25733867 DOI: 10.1073/pnas.1415974112  1
2014 Hummer G, Tokmakoff A. Preface: special topic on biological water. The Journal of Chemical Physics. 141: 22D101. PMID 25494771 DOI: 10.1063/1.4901337  1
2014 Eisele DM, Arias DH, Fu X, Bloemsma EA, Steiner CP, Jensen RA, Rebentrost P, Eisele H, Tokmakoff A, Lloyd S, Nelson KA, Nicastro D, Knoester J, Bawendi MG. Robust excitons inhabit soft supramolecular nanotubes. Proceedings of the National Academy of Sciences of the United States of America. 111: E3367-75. PMID 25092336 DOI: 10.1073/pnas.1408342111  1
2014 Baiz CR, Schach D, Tokmakoff A. Ultrafast 2D IR microscopy. Optics Express. 22: 18724-35. PMID 25089490 DOI: 10.1364/OE.22.018724  1
2014 Li D, Fedeles BI, Singh V, Peng CS, Silvestre KJ, Simi AK, Simpson JH, Tokmakoff A, Essigmann JM. Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2'-deoxycytidine. Proceedings of the National Academy of Sciences of the United States of America. 111: E3252-9. PMID 25071207 DOI: 10.1073/pnas.1405635111  1
2014 De Marco L, Thämer M, Reppert M, Tokmakoff A. Direct observation of intermolecular interactions mediated by hydrogen bonding. The Journal of Chemical Physics. 141: 034502. PMID 25053321 DOI: 10.1063/1.4885145  1
2014 Mandal A, Ramasesha K, De Marco L, Tokmakoff A. Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy. The Journal of Chemical Physics. 140: 204508. PMID 24880302 DOI: 10.1063/1.4878490  1
2014 Roberts ST, Mandal A, Tokmakoff A. Local and collective reaction coordinates in the transport of the aqueous hydroxide ion. The Journal of Physical Chemistry. B. 118: 8062-9. PMID 24666116 DOI: 10.1021/jp501145p  1
2014 Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. A molecular interpretation of 2D IR protein folding experiments with Markov state models. Biophysical Journal. 106: 1359-70. PMID 24655511 DOI: 10.1016/j.bpj.2014.02.008  1
2014 Singh V, Peng CS, Li D, Mitra K, Silvestre KJ, Tokmakoff A, Essigmann JM. Direct observation of multiple tautomers of oxythiamine and their recognition by the thiamine pyrophosphate riboswitch. Acs Chemical Biology. 9: 227-36. PMID 24252063 DOI: 10.1021/cb400581f  1
2013 Ramasesha K, De Marco L, Mandal A, Tokmakoff A. Water vibrations have strongly mixed intra- and intermolecular character. Nature Chemistry. 5: 935-40. PMID 24153371 DOI: 10.1038/nchem.1757  1
2013 Peng CS, Baiz CR, Tokmakoff A. Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 110: 9243-8. PMID 23690588 DOI: 10.1073/pnas.1303235110  1
2013 De Marco L, Ramasesha K, Tokmakoff A. Experimental evidence of Fermi resonances in isotopically dilute water from ultrafast broadband IR spectroscopy. The Journal of Physical Chemistry. B. 117: 15319-27. PMID 23638966 DOI: 10.1021/jp4034613  1
2013 Reppert M, Tokmakoff A. Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment. The Journal of Chemical Physics. 138: 134116. PMID 23574217 DOI: 10.1063/1.4798938  1
2013 Luan B, Shan B, Baiz C, Tokmakoff A, Raleigh DP. Cooperative cold denaturation: the case of the C-terminal domain of ribosomal protein L9. Biochemistry. 52: 2402-9. PMID 23461364 DOI: 10.1021/bi3016789  1
2013 Jones KC, Peng CS, Tokmakoff A. Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 110: 2828-33. PMID 23382249 DOI: 10.1073/pnas.1211968110  1
2013 Baiz CR, Reppert M, Tokmakoff A. Amide I two-dimensional infrared spectroscopy: methods for visualizing the vibrational structure of large proteins. The Journal of Physical Chemistry. A. 117: 5955-61. PMID 23228111 DOI: 10.1021/jp310689a  1
2012 Peng CS, Tokmakoff A. Identification of Lactam-Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy. The Journal of Physical Chemistry Letters. 3: 3302-3306. PMID 23227298 DOI: 10.1021/jz301706a  1
2012 Ramasesha K, De Marco L, Horning AD, Mandal A, Tokmakoff A. A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy. The Journal of Chemical Physics. 136: 134507. PMID 22482572 DOI: 10.1063/1.3700718  1
2012 Baiz CR, Peng CS, Reppert ME, Jones KC, Tokmakoff A. Coherent two-dimensional infrared spectroscopy: quantitative analysis of protein secondary structure in solution. The Analyst. 137: 1793-9. PMID 22398665 DOI: 10.1039/c2an16031e  1
2012 Lessing J, Roy S, Reppert M, Baer M, Marx D, Jansen TL, Knoester J, Tokmakoff A. Identifying residual structure in intrinsically disordered systems: a 2D IR spectroscopic study of the GVGXPGVG peptide. Journal of the American Chemical Society. 134: 5032-5. PMID 22356513 DOI: 10.1021/ja2114135  1
2012 Tokmakoff A. Watching time-evolving molecular structures with 2D IR spectroscopy International Conference On Ultrafast Structural Dynamics, Icusd 2012 1
2012 Jones KC, Ganim Z, Peng CS, Tokmakoff A. Transient two-dimensional spectroscopy with linear absorption corrections applied to temperature-jump two-dimensional infrared Journal of the Optical Society of America B: Optical Physics. 29: 118-129.  1
2011 Roy S, Lessing J, Meisl G, Ganim Z, Tokmakoff A, Knoester J, Jansen TL. Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline. The Journal of Chemical Physics. 135: 234507. PMID 22191886 DOI: 10.1063/1.3665417  1
2011 Peng CS, Jones KC, Tokmakoff A. Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy. Journal of the American Chemical Society. 133: 15650-60. PMID 21861514 DOI: 10.1021/ja205636h  1
2011 Ramasesha K, Roberts ST, Nicodemus RA, Mandal A, Tokmakoff A. Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching. The Journal of Chemical Physics. 135: 054509. PMID 21823714 DOI: 10.1063/1.3623008  1
2011 Nicodemus RA, Corcelli SA, Skinner JL, Tokmakoff A. Collective hydrogen bond reorganization in water studied with temperature-dependent ultrafast infrared spectroscopy. The Journal of Physical Chemistry. B. 115: 5604-16. PMID 21417373 DOI: 10.1021/jp111434u  1
2011 Roberts ST, Ramasesha K, Petersen PB, Mandal A, Tokmakoff A. Proton transfer in concentrated aqueous hydroxide visualized using ultrafast infrared spectroscopy. The Journal of Physical Chemistry. A. 115: 3957-72. PMID 21314148 DOI: 10.1021/jp108474p  1
2011 Ganim Z, Tokmakoff A, Vaziri A. Vibrational excitons in ionophores: Experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels New Journal of Physics. 13. DOI: 10.1088/1367-2630/13/11/113030  1
2011 Roberts ST, Loparo JJ, Ramasesha K, Tokmakoff A. A fast-scanning Fourier transform 2D IR interferometer Optics Communications. 284: 1062-1066. DOI: 10.1016/j.optcom.2010.10.049  1
2010 Smith AW, Lessing J, Ganim Z, Peng CS, Tokmakoff A, Roy S, Jansen TL, Knoester J. Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations. The Journal of Physical Chemistry. B. 114: 10913-24. PMID 20690697 DOI: 10.1021/jp104017h  1
2010 Petersen PB, Tokmakoff A. Source for ultrafast continuum infrared and terahertz radiation. Optics Letters. 35: 1962-4. PMID 20548353 DOI: 10.1364/OL.35.001962  1
2010 Ganim Z, Jones KC, Tokmakoff A. Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy. Physical Chemistry Chemical Physics : Pccp. 12: 3579-88. PMID 20336256 DOI: 10.1039/b923515a  1
2010 Nicodemus RA, Ramasesha K, Roberts ST, Tokmakoff A. Hydrogen bond rearrangements in water probed with temperature-dependent 2D IR Journal of Physical Chemistry Letters. 1: 1068-1072. DOI: 10.1021/jz100138z  1
2010 Ramasesha K, Nicodemus RA, Mandal A, Tokmakoff A. Orientational dynamics of water probed with 2D-IR anisotropy measurements Optics Infobase Conference Papers 1
2009 Jones KC, Ganim Z, Tokmakoff A. Heterodyne-detected dispersed vibrational echo spectroscopy. The Journal of Physical Chemistry. A. 113: 14060-6. PMID 19938867 DOI: 10.1021/jp906256s  1
2009 Roberts ST, Petersen PB, Ramasesha K, Tokmakoff A, Ufimtsev IS, Martinez TJ. Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions. Proceedings of the National Academy of Sciences of the United States of America. 106: 15154-9. PMID 19666493 DOI: 10.1073/pnas.0901571106  1
2009 Roberts ST, Ramasesha K, Tokmakoff A. Structural rearrangements in water viewed through two-dimensional infrared spectroscopy. Accounts of Chemical Research. 42: 1239-49. PMID 19585982 DOI: 10.1021/ar900088g  1
2009 Deflores LP, Ganim Z, Nicodemus RA, Tokmakoff A. Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity. Journal of the American Chemical Society. 131: 3385-91. PMID 19256572 DOI: 10.1021/ja8094922  1
2009 Alper J, Crespo M, Jones K, Tokmakoff A, Hamad-Schifferli K. Biomolecular activity switch actuated by ultrafast pulsed laser irradiation of gold nanorods Proceedings of the Asme Summer Bioengineering Conference, Sbc2008. 645-646.  1
2008 Chung HS, Shandiz A, Sosnick TR, Tokmakoff A. Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding. Biochemistry. 47: 13870-7. PMID 19053229 DOI: 10.1021/bi801603e  1
2008 Petersen PB, Roberts ST, Ramasesha K, Nocera DG, Tokmakoff A. Ultrafast N-H vibrational dynamics of cyclic doubly hydrogen-bonded homo- and heterodimers. The Journal of Physical Chemistry. B. 112: 13167-71. PMID 18821789 DOI: 10.1021/jp805338h  1
2008 Chung HS, Tokmakoff A. Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy. Proteins. 72: 474-87. PMID 18384151 DOI: 10.1002/prot.22043  1
2008 Chung HS, Tokmakoff A. Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface. Proteins. 72: 488-97. PMID 18384149 DOI: 10.1002/prot.22042  1
2008 Ganim Z, Chung HS, Smith AW, Deflores LP, Jones KC, Tokmakoff A. Amide I two-dimensional infrared spectroscopy of proteins. Accounts of Chemical Research. 41: 432-41. PMID 18288813 DOI: 10.1021/ar700188n  1
2008 Alper J, Wijaya A, Crespo M, DeFlores L, Tokmakoff A, Hamad-Schifferli K. Biomolecular activity switch: An application of metallic nanoparticle plasmon resonance Technical Proceedings of the 2008 Nsti Nanotechnology Conference and Trade Show, Nsti-Nanotech, Nanotechnology 2008. 2: 206-209.  1
2007 Decamp MF, Deflores LP, Jones KC, Tokmakoff A. Single-shot two-dimensional infrared spectroscopy. Optics Express. 15: 233-41. PMID 19532239 DOI: 10.1364/OE.15.000233  1
2007 Deflores LP, Nicodemus RA, Tokmakoff A. Two-dimensional Fourier transform spectroscopy in the pump-probe geometry. Optics Letters. 32: 2966-8. PMID 17938668 DOI: 10.1364/OL.32.002966  1
2007 Smith AW, Tokmakoff A. Probing local structural events in beta-hairpin unfolding with transient nonlinear infrared spectroscopy. Angewandte Chemie (International Ed. in English). 46: 7984-7. PMID 17853520 DOI: 10.1002/anie.200701172  1
2007 Tokmakoff A. Chemistry. Shining light on the rapidly evolving structure of water. Science (New York, N.Y.). 317: 54-5. PMID 17615330 DOI: 10.1126/science.1144515  1
2007 Chung HS, Khalil M, Smith AW, Tokmakoff A. Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics. The Review of Scientific Instruments. 78: 063101. PMID 17614599 DOI: 10.1063/1.2743168  1
2007 Chung HS, Ganim Z, Jones KC, Tokmakoff A. Transient 2D IR spectroscopy of ubiquitin unfolding dynamics. Proceedings of the National Academy of Sciences of the United States of America. 104: 14237-42. PMID 17551015 DOI: 10.1073/pnas.0700959104  1
2007 Smith AW, Tokmakoff A. Amide I two-dimensional infrared spectroscopy of beta-hairpin peptides. The Journal of Chemical Physics. 126: 045109. PMID 17286519 DOI: 10.1063/1.2428300  1
2007 Nicodemus RA, Tokmakoff A. Infrared spectroscopy of tritiated water Chemical Physics Letters. 449: 130-134. DOI: 10.1016/j.cplett.2007.10.055  1
2007 Loparo JJ, Roberts ST, Nicodemus RA, Tokmakoff A. Variation of the transition dipole moment across the OH stretching band of water Chemical Physics. 341: 218-229. DOI: 10.1016/j.chemphys.2007.06.056  1
2007 Schmidt JR, Roberts ST, Loparo JJ, Tokmakoff A, Fayer MD, Skinner JL. Are water simulation models consistent with steady-state and ultrafast vibrational spectroscopy experiments? Chemical Physics. 341: 143-157. DOI: 10.1016/j.chemphys.2007.06.043  1
2007 Smith AW, Chung HS, Ganim Z, Tokmakoff A. Multidimensional IR spectroscopy of site-specific hairpin folding Springer Series in Chemical Physics. 88: 350-352. DOI: 10.1007/978-3-540-68781-8-113  1
2007 Loparo JJ, Roberts ST, Tokmakoff A. 2D IR spectroscopy of hydrogen bond switching in liquid water Springer Series in Chemical Physics. 88: 341-343. DOI: 10.1007/978-3-540-68781-8-110  1
2006 DeFlores LP, Tokmakoff A. Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange two-dimensional infrared spectroscopy. Journal of the American Chemical Society. 128: 16520-1. PMID 17177399 DOI: 10.1021/ja067723o  1
2006 Loparo JJ, Roberts ST, Tokmakoff A. Multidimensional infrared spectroscopy of water. II. Hydrogen bond switching dynamics. The Journal of Chemical Physics. 125: 194522. PMID 17129138 DOI: 10.1063/1.2382896  1
2006 Loparo JJ, Roberts ST, Tokmakoff A. Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes. The Journal of Chemical Physics. 125: 194521. PMID 17129137 DOI: 10.1063/1.2382895  1
2006 DeFlores LP, Ganim Z, Ackley SF, Chung HS, Tokmakoff A. The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide. The Journal of Physical Chemistry. B. 110: 18973-80. PMID 16986892 DOI: 10.1021/jp0603334  1
2006 Roberts ST, Loparo JJ, Tokmakoff A. Characterization of spectral diffusion from two-dimensional line shapes. The Journal of Chemical Physics. 125: 084502. PMID 16965024 DOI: 10.1063/1.2232271  1
2006 Ganim Z, Tokmakoff A. Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra. Biophysical Journal. 91: 2636-46. PMID 16844758 DOI: 10.1529/biophysj.106.088070  1
2006 Chung HS, Tokmakoff A. Visualization and characterization of the infrared active amide I vibrations of proteins. The Journal of Physical Chemistry. B. 110: 2888-98. PMID 16471899 DOI: 10.1021/jp053956a  1
2006 DeCamp MF, Tokmakoff A. Single-shot two-dimensional spectrometer. Optics Letters. 31: 113-5. PMID 16419895 DOI: 10.1364/OL.31.000113  1
2006 DeCamp MF, Tokmakoff A. Single-shot two-dimensional spectroscopy Conference On Lasers and Electro-Optics and 2006 Quantum Electronics and Laser Science Conference, Cleo/Qels 2006. DOI: 10.1109/CLEO.2006.4627786  1
2006 DeCamp MF, Jones KC, Tokmakoff A. Two-dimensional infrared spectrometer Optics Infobase Conference Papers 1
2005 Eaves JD, Tokmakoff A, Geissler PL. Electric field fluctuations drive vibrational dephasing in water. The Journal of Physical Chemistry. A. 109: 9424-36. PMID 16866391 DOI: 10.1021/jp051364m  1
2005 Smith AW, Chung HS, Ganim Z, Tokmakoff A. Residual native structure in a thermally denatured beta-hairpin. The Journal of Physical Chemistry. B. 109: 17025-7. PMID 16853169 DOI: 10.1021/jp053949m  1
2005 DeCamp MF, DeFlores L, McCracken JM, Tokmakoff A, Kwac K, Cho M. Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions. The Journal of Physical Chemistry. B. 109: 11016-26. PMID 16852342 DOI: 10.1021/jp050257p  1
2005 Eaves JD, Loparo JJ, Fecko CJ, Roberts ST, Tokmakoff A, Geissler PL. Hydrogen bonds in liquid water are broken only fleetingly. Proceedings of the National Academy of Sciences of the United States of America. 102: 13019-22. PMID 16135564 DOI: 10.1073/pnas.0505125102  1
2005 DeCamp MF, Tokmakoff A. Upconversion multichannel infrared spectrometer. Optics Letters. 30: 1818-20. PMID 16092356  1
2005 Harder E, Eaves JD, Tokmakoff A, Berne BJ. Polarizable molecules in the vibrational spectroscopy of water. Proceedings of the National Academy of Sciences of the United States of America. 102: 11611-6. PMID 16081533 DOI: 10.1073/pnas.0505206102  1
2005 Fecko CJ, Loparo JJ, Roberts ST, Tokmakoff A. Local hydrogen bonding dynamics and collective reorganization in water: ultrafast infrared spectroscopy of HOD/D(2)O. The Journal of Chemical Physics. 122: 54506. PMID 15740338 DOI: 10.1063/1.1839179  1
2005 Garrett BC, Dixon DA, Camaioni DM, Chipman DM, Johnson MA, Jonah CD, Kimmel GA, Miller JH, Rescigno TN, Rossky PJ, Xantheas SS, Colson SD, Laufer AH, Ray D, Barbara PF, ... ... Tokmakoff A, et al. Role of water in electron-initiated processes and radical chemistry: issues and scientific advances. Chemical Reviews. 105: 355-90. PMID 15720157 DOI: 10.1021/cr030453x  1
2005 Chung HS, Khalil M, Smith AW, Ganim Z, Tokmakoff A. Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin. Proceedings of the National Academy of Sciences of the United States of America. 102: 612-7. PMID 15630083 DOI: 10.1073/pnas.0408646102  1
2005 Demchenko Y, Gommans L, De Laat C, Oudenaarde B, Tokmakoff A, Snijders M. Job-centric security model for open collaborative environment Proceedings - 2005 International Symposium On Collaborative Technologies and Systems. 2005: 69-77. DOI: 10.1109/ISCST.2005.1553296  0.01
2005 Chou SG, DeCamp MF, Jiang J, Samsonidze GG, Barros EB, Plentz F, Jorio A, Zheng M, Onoa GB, Semke ED, Tokmakoff A, Saito R, Dresselhaus G, Dresselhaus MS. Phonon-assisted exciton relaxation dynamics for a (6,5)-enriched DNA-wrapped single-walled carbon nanotube sample Physical Review B - Condensed Matter and Materials Physics. 72. DOI: 10.1103/PhysRevB.72.195415  1
2004 Cheatum CM, Tokmakoff A, Knoester J. Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy. The Journal of Chemical Physics. 120: 8201-15. PMID 15267740 DOI: 10.1063/1.1689637  1
2004 Khalil M, Demirdöven N, Tokmakoff A. Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy. The Journal of Chemical Physics. 121: 362-73. PMID 15260555 DOI: 10.1063/1.1756870  1
2004 Demirdöven N, Cheatum CM, Chung HS, Khalil M, Knoester J, Tokmakoff A. Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure. Journal of the American Chemical Society. 126: 7981-90. PMID 15212548 DOI: 10.1021/ja049811j  1
2004 Loparo JJ, Fecko CJ, Eaves JD, Roberts ST, Tokmakoff A. Reorientational and configurational fluctuations in water observed on molecular length scales Physical Review B - Condensed Matter and Materials Physics. 70: 1-4. DOI: 10.1103/PhysRevB.70.180201  1
2004 Chung HS, Khalil M, Tokmakoff A. Nonlinear infrared spectroscopy of protein conformational change during thermal unfolding Journal of Physical Chemistry B. 108: 15332-15342. DOI: 10.1021/jp0479926  1
2004 Fecko CJ, Loparo JJ, Tokmakoff A. Generation of 45 femtosecond pulses at 3 μm with a KNbO3 optical parametric amplifier Optics Communications. 241: 521-528. DOI: 10.1016/j.optcom.2004.07.038  1
2004 Fecko CJ, Eaves JD, Loparo JJ, Roberts ST, Tokmakoff A, Geissler PL. Dynamics of hydrogen bonds in water: Vibrational echoes and two-dimensional infrared spectroscopy Springer Series in Chemical Physics. 79: 535-538.  1
2004 Loparo JJ, Fecko CJ, Eaves JD, Roberts ST, Tokmakoff A. A unified analysis of ultrafast vibrational and orientational dynamics of HOD in D2O Springer Series in Chemical Physics. 79: 410-412.  1
2004 Chung HS, Khalil M, Smith AW, Ganim Z, Tokmakoff A. Thermal denaturing of proteins: Equilibrium and transient studies using nonlinear infrared probes Springer Series in Chemical Physics. 79: 551-553.  1
2004 DeCamp MF, DeFlores LP, McCracken JM, Tokmakoff A. Solvation dynamics of N-methylacetamide in D2O, CDCl3 and DMSO-d6 Springer Series in Chemical Physics. 79: 422-424.  1
2003 Fecko CJ, Eaves JD, Loparo JJ, Tokmakoff A, Geissler PL. Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water. Science (New York, N.Y.). 301: 1698-702. PMID 14500975 DOI: 10.1126/science.1087251  1
2003 Khalil M, Demirdöven N, Tokmakoff A. Obtaining absorptive line shapes in two-dimensional infrared vibrational correlation spectra. Physical Review Letters. 90: 047401. PMID 12570457  1
2003 Khalil M, Demirdöven N, Tokmakoff A. Coherent 2D IR spectroscopy: Molecular structure and dynamics in solution Journal of Physical Chemistry A. 107: 5258-5279. DOI: 10.1021/jp0219247  1
2003 Eaves JD, Fecko CJ, Stevens AL, Peng P, Tokmakoff A. Polarization-selective femtosecond Raman spectroscopy of low-frequency motions in hydrated protein films Chemical Physics Letters. 376: 20-25. DOI: 10.1016/S0009-2614(03)00890-X  1
2003 Khalil M, Demirdöven N, Tokmakoff A. Coherent two-dimensional fourier transform infrared spectroscopy Springer Series in Chemical Physics. 71: 583-585.  1
2003 Demirdöven N, Khalil M, Tokmakoff A. Correlated vibrational dynamics in solution studied by two-dimensional Fourier transform infrared spectroscopy Springer Series in Chemical Physics. 71: 589-591.  1
2002 Demirdöven N, Khalil M, Golonzka O, Tokmakoff A. Dispersion compensation with optical materials for compression of intense sub-100-fs mid-infrared pulses. Optics Letters. 27: 433-5. PMID 18007825  1
2002 Demirdöven N, Khalil M, Tokmakoff A. Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy. Physical Review Letters. 89: 237401. PMID 12485039  1
2002 Fecko CJ, Eaves JD, Tokmakoff A. Isotropic and anisotropic Raman scattering from molecular liquids measured by spatially masked optical Kerr effect spectroscopy Journal of Chemical Physics. 117: 1139-1154. DOI: 10.1063/1.1485070  1
2002 Golonzka O, Khalil M, Demirdöven N, Tokmakoff A. Third-order nonlinear spectroscopy of coupled vibrations Acs Symposium Series. 820: 169-181.  1
2002 Tokmakoff A. Coherent two-dimensional vibrational spectroscopy of molecular dynamics in solution Conference On Quantum Electronics and Laser Science (Qels) - Technical Digest Series. 74: 243.  1
2001 Golonzka O, Khalil M, Demirdöven N, Tokmakoff A. Vibrational anharmonicities revealed by coherent two-dimensional infrared spectroscopy. Physical Review Letters. 86: 2154-7. PMID 11289878 DOI: 10.1103/PhysRevLett.86.2154  1
2001 Golonzka O, Khalil M, Demirdöven N, Tokmakoff A. Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibration echo spectroscopy Journal of Chemical Physics. 115: 10814-10828. DOI: 10.1063/1.1417504  1
2001 Golonzka O, Tokmakoff A. Polarization-selective third-order spectroscopy of coupled vibronic states Journal of Chemical Physics. 115: 297-309. DOI: 10.1063/1.1376144  1
2001 Demirdöven N, Khalil M, Golonzka O, Tokmakoff A. Correlation effects in the two-dimensional vibrational spectroscopy of coupled vibrations Journal of Physical Chemistry A. 105: 8025-8030. DOI: 10.1021/jp011215d  1
2001 Khalil M, Tokmakoff A. Signatures of vibrational interactions in coherent two-dimensional infrared spectroscopy Chemical Physics. 266: 213-230. DOI: 10.1016/S0301-0104(01)00230-0  1
2001 Golonzka O, Demirdöven N, Tokmakoff A. Separating the direct and cascaded contributions to two-dimensional Raman signals using phase-sensitive detection Springer Series in Chemical Physics. 66: 516-518.  1
2001 Khalil M, Golonzka O, Demirdöven N, Tokmakoff A. Phase-sensitive detection for polarization-selective femtosecond Raman spectroscopy Springer Series in Chemical Physics. 66: 545-547.  1
2000 Golonzka O, Demirdöven N, Khalil M, Tokmakoff A. Separation of cascaded and direct fifth-order Raman signals using phase-sensitive intrinsic heterodyne detection Journal of Chemical Physics. 113: 9893-9896. DOI: 10.1063/1.1330236  1
2000 Khalil M, Demirdoven N, Golonzka O, Fecko CJ, Tokmakoff A. A phase-sensitive detection method using diffractive optics for polarization-selective femtosecond raman spectroscopy Journal of Physical Chemistry A. 104: 5711-5715.  1
2000 Tokmakoff A. Two-dimensional line shapes derived from coherent third-order nonlinear spectroscopy Journal of Physical Chemistry A. 104: 4247-4255.  1
2000 Khalil M, Golonzka O, Demirdöven N, Fecko CJ, Tokmakoff A. Polarization-selective femtosecond Raman spectroscopy of isotropic and anisotropic vibrational dynamics in liquids Chemical Physics Letters. 321: 231-237.  1
1999 Tokmakoff A, Billingtont J. An approach to the analysis of interworking traders Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1639: 127-146. DOI: 10.1007/3-540-48745-X_9  1
1999 Okumura K, Tokmakoff A, Tanimura Y. Two-dimensional line-shape analysis of photon-echo signal Chemical Physics Letters. 314: 488-495.  1
1999 Okumura K, Tokmakoff A, Tanimura Y. Structural information from two-dimensional fifth-order Raman spectroscopy Journal of Chemical Physics. 111: 492-503.  1
1998 Tokmakoff A, Lang MJ, Larsen DS, Jordanides XJ, Fleming GR. Studies of molecular interactions and collective liquid motions with two-dimensional Raman spectroscopy Springer Series in Chemical Physics. 63: 538-540.  1
1998 Tokmakoff A, Lang MJ, Jordanides XJ, Fleming GR. The intermolecular interaction mechanisms in liquid CS2 at 295 and 165 K probed with two-dimensional Raman spectroscopy Chemical Physics. 233: 231-242.  1
1997 Tokmakoff A, Lang MJ, Larsen DS, Fleming GR, Chernyak V, Mukamel S. Two-dimensional Raman spectroscopy of vibrational interactions in liquids Physical Review Letters. 79: 2702-2705.  1
1997 Rector KD, Kwok AS, Ferrante C, Tokmakoff A, Rella CW, Fayer MD. Vibrational anharmonicity and multilevel vibrational dephasing from vibrational echo beats Journal of Chemical Physics. 106: 10027-10036.  1
1997 Tokmakoff A, Lang MJ, Larsen DS, Fleming GR. Intrinsic optical heterodyne detection of a two-dimensional fifth order Raman response Chemical Physics Letters. 272: 48-54.  1
1997 Tokmakoff A, Fleming GR. Two-dimensional Raman spectroscopy of the intermolecular modes of liquid CS2 Journal of Chemical Physics. 106: 2569-2582.  1
1996 Tokmakoff A. Orientational correlation functions and polarization selectivity for nonlinear spectroscopy of isotropic media. I. Third order Journal of Chemical Physics. 105: 1-12.  1
1996 Tokmakoff A. Orientational correlation functions and polarization selectivity for nonlinear spectroscopy of isotropic media. II. Fifth order Journal of Chemical Physics. 105: 13-21.  1
1995 Tokmakoff A, Kowk A, Urhdal R, Zimdars DA, Fayer MD. Vibrational dynamics in condensed matter probed with linac based FELs Nuclear Inst. and Methods in Physics Research, A. 358: 540-543. DOI: 10.1016/0168-9002(94)01598-8  1
1995 Tokmakoff A, Kwok AS, Urdahl RS, Francis RS, Fayer MD. Multilevel vibrational dephasing and vibrational anharmonicity from infrared photon echo beats Chemical Physics Letters. 234: 289-295. DOI: 10.1016/0009-2614(95)00068-F  1
1995 Tokmakoff A, Fayer MD. Infrared Photon Echo Experiments: Exploring Vibrational Dynamics in Liquids and Glasses Accounts of Chemical Research. 28: 437-444.  1
1995 Tokmakoff A, Zimdars D, Urdahl RS, Francis RS, Kwok AS, Fayer MD. Infrared vibrational photon echo experiments in liquids and glasses Journal of Physical Chemistry. 99: 13310-13320.  1
1995 Tokmakoff A, Urdahl RS, Zimdars D, Francis RS, Kwok AS, Fayer MD. Vibrational spectral diffusion and population dynamics in a glass-forming liquid: Variable bandwidth picosecond infrared spectroscopy The Journal of Chemical Physics. 102: 3919-3931.  1
1995 Tokmakoff A, Fayer MD. Homogeneous vibrational dynamics and inhomogeneous broadening in glass-forming liquids: Infrared photon echo experiments from room temperature to 10 K The Journal of Chemical Physics. 103: 2810-2826.  1
1995 Moore P, Tokmakoff A, Keyes T, Fayer MD. The low frequency density of states and vibrational population dynamics of polyatomic molecules in liquids The Journal of Chemical Physics. 103: 3325-3334.  1
1995 Moore P, Tokmakoff A, Keyes T, Fayer MD. The low frequency density of states and vibrational population dynamics of polyatomic molecules in liquids The Journal of Chemical Physics. 103: 3325-3334.  1
1994 Tokmakoff A, Sauter B, Kwok AS, Fayer MD. Phonon-induced scattering between vibrations and multiphoton vibrational up-pumping in liquid solution Chemical Physics Letters. 221: 412-418. DOI: 10.1016/0009-2614(94)00276-2  1
1994 Haynes DR, Tokmakoff A, George SM. Distance dependence of electronic energy transfer between donor and acceptor adlayers: p-terphenyl and 9,10-diphenylanthracene The Journal of Chemical Physics. 100: 1968-1980.  1
1994 Tokmakoff A, Sauter B, Fayer MD. Temperature-dependent vibrational relaxation in polyatomic liquids: Picosecond infrared pump-probe experiments The Journal of Chemical Physics. 100: 9035-9043.  1
1994 Kenkre VM, Tokmakoff A, Fayer MD. Theory of vibrational relaxation of polyatomic molecules in liquids The Journal of Chemical Physics. 101: 10618-10629.  1
1994 Hill JR, Tokmakoff A, Peterson KA, Sauter B, Zimdars D, Dlott DD, Fayer MD. Vibrational dynamics of carbon monoxide at the active site of myoglobin: Picosecond infrared free-electron laser pump-probe experiments Journal of Physical Chemistry. 98: 11213-11219.  1
1994 Tokmakoff A, Zimdars D, Sauter B, Francis RS, Kwok AS, Fayer MD. Vibrational photon echoes in a liquid and glass: Room temperature to 10 K The Journal of Chemical Physics. 101: 1741-1744.  1
1993 Zimdars D, Tokmakoff A, Chen S, Greenfield SR, Fayer MD, Smith TI, Schwettman HA. Picosecond infrared vibrational photon echoes in a liquid and glass using a free electron laser. Physical Review Letters. 70: 2718-2721. PMID 10053635 DOI: 10.1103/PhysRevLett.70.2718  1
1993 Tokmakoff A, Marshall CD, Fayer MD. Optical parametric amplification of 1-kHz high-energy picosecond midinfrared pulses and application to infrared transient-grating experiments on diamond Journal of the Optical Society of America B: Optical Physics. 10: 1785-1791. DOI: 10.1364/JOSAB.10.001785  1
1993 Fishman IM, Marshall CD, Tokmakoff A, Fayer MD. Transient grating diffraction from an interface between two materials: Theory and experimental application Journal of the Optical Society of America B: Optical Physics. 10: 1006-1016. DOI: 10.1364/JOSAB.10.001006  1
1993 Marshall CD, Tokmakoff A, Fishman IM, Eom CB, Phillips JM, Fayer MD. Thermal boundary resistance and diffusivity measurements on thin YBa 2Cu3O7-x films with MgO and SrTiO3 substrates using the transient grating method Journal of Applied Physics. 73: 850-857. DOI: 10.1063/1.353296  1
1993 Haynes DR, Tokmakoff A, George SM. Temperature-dependent absolute fluorescence quantum yield of C60 multilayers Chemical Physics Letters. 214: 50-56. DOI: 10.1016/0009-2614(93)85454-V  1
1993 Tokmakoff A, Banholzer WF, Fayer MD. Thermal diffusivity measurements of natural and isotopically enriched diamond by picosecond infrared transient grating experiments Applied Physics a Solids and Surfaces. 56: 87-90. DOI: 10.1007/BF00351908  1
1993 Tokmakoff A, Fayer MD, Dlott DD. Chemical reaction initiation and hot-spot formation in shocked energetic molecular materials Journal of Physical Chemistry. 97: 1901-1913.  1
1992 Stankus JJ, Torre R, Marshall CD, Greenfield SR, Sengupta A, Tokmakoff A, Fayer MD. Nanosecond time scale dynamics of pseudo-nematic domains in the isotropic phase of liquid crystals Chemical Physics Letters. 194: 213-216. DOI: 10.1016/0009-2614(92)85537-K  1
1991 Tokmakoff A, Haynes DR, George SM. Desorption kinetics of C60 multilayers from Al2O3 (0001) Chemical Physics Letters. 186: 450-455. DOI: 10.1016/0009-2614(91)90207-P  1
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