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Journal Publications

2024

• Generation and Implementation of Continuum Infrared Pulses for Broadband Detection in 2D IR Spectroscopy, John H. Hack, Nicholas H. C. Lewis, Samuel Knight, William B. Carpenter, Luigi DeMarco, Krupa Ramasesha and Andrei Tokmakoff, J. Phys. Chem. A. (2024).
• Molecular Tuning of Reactivity of Zeolite Protons in HZSM-5, Yaxin Chen, Xinyou Ma, John H. Hack, Shuhao Zhang, Anyang Peng, James P. Dombrowski, Gregory A. Voth, Andrei Tokmakoff, Mayfair C. Kung, Harold H. Kung, J. Ameri. Chem. Soc. (2024).
• Molecular factors determining brightness in fluorescence-encoded infrared vibrational spectroscopy, Abhirup Guha, Lukas Whaley-Mayda, Seung Yeon Lee, Andrei Tokmakoff, J. Chem. Phys. 160: 104202 (2024).
• Anomalously enhanced ion transport and uptake in functionalized angstrom-scale two-dimensional channels, Mingzhan Wang, Tumpa Sadhukhan, Nicholas H. C. Lewis, Maoyu Wang, Xiang He, Gangbin Yan, Dongchen Ying, Eli Hoenig, Yu Han, Guiming Peng, One-Sun Lee, Fengyuan Shi, David M. Tiede, Hua Zhou, Andrei Tokmakoff, George C. Schatz and Chong Liu, Proc. Natl. Acad. Sci. 121(2): e2313616121 (2024).

2023

• Strong H-bonding from Zeolite Bro̷nsted Acid Site to Water: Origin of the Broad IR Doublet, John H. Hack, Yaxin Chen, Nicholas H. C. Lewis, Harold H. Kung and Andrei Tokmakoff, J. Phys. Chem. B. 127(51): 11054–11063 (2023).
• Vibrational Probe at the Electrochemical Interface: Dependence on Plasmon Coupling and Potential of the Lineshape in Two-Dimensional Infrared Spectroscopy, Melissa Bodine, Vepa Rozyyev, Jeffrey W. Elam, Andrei Tokmakoff and Nicholas H. C. Lewis, J. Phys. Chem. Lett. 14: 11092-11099 (2023).

• Development and Characterization of Electrodes for Surface-Specific Attenuated Total Reflection Two-Dimensional Infrared Spectroelectrochemistry, Melissa Bodine, Vepa Rozyyev, Jeffrey W. Elam, Andrei Tokmakoff and Nicholas H. C. Lewis, J. Phys. Chem. C 127: 23199–23211 (2023).

• Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory, Lukas Whaley-Mayda, Abhirup Guha, and Andrei Tokmakoff, J. Chem. Phys. 159: 194201 (2023).
• Multimode Vibrational Dynamics and Orientational Effects in Fluorescence-Encoded Infrared Spectroscopy. II. Analysis of Early-Time Signals, Lukas Whaley-Mayda, Abhirup Guha, and Andrei Tokmakoff, J. Chem. Phys. 159: 194202 (2023).
• Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs , Brennan Ashwood, Michael S. Jones, Aleksandar Radakovic, Smayan Khanna, Yumin Lee, Joseph R. Sachleben, Jack W. Szostak, Andrew L. Ferguson, and Andrei Tokmakoff, Biophys. J. 122(16): 3323-3339 (2023).
• Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5, John H. Hack, Xinyou Ma, Yaxin Chen, James P. Dombrowski, Nicholas H. C. Lewis, Chenghan Li, Harold H. Kung, Gregory A. Voth, and Andrei Tokmakoff. J. of Phys. Chem. C. 127 (32): 16175-16186 (2023).
• Disruption of Energetic and Dynamic Base Pairing Cooperativity in DNA Duplexes by an Abasic Site, Brennan Ashwood, Michael S. Jones, Andrew L. Ferguson, and Andrei Tokmakoff, Proc. Natl. Acad. Sci. U. S. A. 120 (14): e2219124120 (2023).
• Infrared Compatible Rapid Mixer to Probe Millisecond Chemical Kinetics, Ram C. Itani, Max M. Cohen, and Andrei Tokmakoff, Rev. Sci. Instrum. 94 (3): 034102 (2023).
• Amplification of Mid-IR Continuum for Broadband 2D IR Spectroscopy, John H. Hack, Nicholas H. C. Lewis, William B. Carpenter, and Andrei Tokmakoff, Opt. Lett. 48: 960-963 (2023).

2022

• From Networked to Isolated: Observing Water Hydrogen Bonds in Concentrated Electrolytes with Two-Dimensional Infrared Spectroscopy, Nicholas H. C. Lewis, Bogdan Dereka Yong Zhang, Edward J. Maginn, and Andrei Tokmakoff, J. Phys. Chem. B. 126: 5305-5319 (2022).
• Resonance Conditions, Detection Quality, and Single-Molecule Sensitivity in Fluorescence-Encoded Infrared Vibrational Spectroscopy, Lukas Whaley-Mayda, Abhirup Guha, and Andrei Tokmakoff, J. Phys. Chem. Phys. 156: 174202 (2022).
• Exchange-Mediated Transport in Battery Electrolytes: Ultrafast or Ultraslow, Bogdan Dereka, Nicholas H. C. Lewis, Jonathan H. Keim,  Scott A. Snyder, Edward Maginn, and Andrei Tokmakoff, J. Am. Chem. Soc. 144: 8591-8604 (2022).
• Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes, Bogdan Dereka, Nicholas H. C. Lewis, Jonathan H. Keim,  Scott A. Snyder, and Andrei Tokmakoff, J. Phys. Chem. B. 126: 278-291 (2022).

2021

• Lineshape Distortions in Internal Reflection Two-Dimensional Infrared Spectroscopy: Tuning across the Critical Angle, Nicholas H. C. Lewis, and Andrei Tokmakoff, J. Phys. Chem Lett. 12: 11843–11849 (2021).
• Structural Ensemble of the Insulin Monomer, Luis Busto-Moner, Chi-Jui Feng, Adam Antoszewski, Andrei Tokmakoff, and Aaron R. Dinner,  Biochem. 60: 3125–3136 (2021).
• Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy, Michael S. Jones, Brennan Ashwood, Andrei Tokmakoff, and Andrew L. Ferguson,  J. Am. Chem. Soc. 143: 17395–17411 (2021).
• Water or Anion? Uncovering the Zn2+ Solvation Environment in Mixed Zn(TFSI)2 and LiTFSI Water-in-Salt Electrolytes, Yong Zhang, Gang Wan, Nicholas H. C. Lewis, Julian Mars, Sharon E. Bone, Hans-Georg Steinrück, Maria R. Lukatskaya, Nicholas J. Weadock, Michal Bajdich, Oleg Borodin, Andrei Tokmakoff, Michael F. Toney, and Edward J. Maginn,  ACS. Energy. Lett. 6: 3458–3463 (2021).
• Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport, Edward Barry, Raelyn Burns, Wei Chen, Guilhem X. De Hoe, Barry, Joan Manuel Montes De Oca, Juan J. de Pablo, James Dombrowski, Jeffrey W. Elam, Alanna M. Felts, Giulia Galli, John Hack, Qiming He, Xiang He, Eli Hoenig, Aysenur Iscen, Benjamin Kash, Harold H. Kung, Nicholas H. C. Lewis, Chong Liu, Xinyou Ma, Anil Mane, Alex B. F. Martinson, Karen L. Mulfort, Julia Murphy, Kristian Mølhave, Paul Nealey, Yijun Qiao, Vepa Rozyyev, George C. Schatz, Steven J. Sibener, Dmitri Talapin, David M. Tiede, Matthew V. Tirrell, Andrei Tokmakoff, Gregory A. Voth, Zhongyang Wang, Zifan Ye, Murat Yesibolati, Nestor J. Zaluzec, Seth B. Darling., Chem. Rev. 121: 9450–9501 (2021).
• Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites, John H. Hack, James P. Dombrowski, Xinyou Ma, Yaxin Chen, Nicholas H. C. Lewis, William B. Carpenter, Chenghan Li, Gregory A. Voth, Harold H. Kung, and Andrei Tokmakoff, J. Am. Chem. Soc. 143: 10203–10213 (2021).
• Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity, Chi-Jui Feng, Anton Sinitskiy, Vijay Pande, and Andrei Tokmakoff, J. Phys. Chem. B. 125: 4620–4633 (2021).
• Fluorescence-Encoded Infrared Vibrational Spectroscopy with Single-Molecule Sensitivity, Lukas Whaley-Mayda, Abhirup Guha, Samuel B. Penwell, and Andrei Tokmakoff, J. Am. Chem. Soc. 143: 3060–64 (2021).
• Water-in-Salt LiTFSI Aqueous Electrolytes. 1. Liquid Structure from Combined Molecular Dynamics Simulation and Experimental Studies, Yong Zhang, Nicholas H. C. Lewis, Julian Mars, Gang Wan, Nichloas J. Weadock, Christopher J. Takacs, Maria R. Lukatskaya, Hans-Georg Steinrück, Michael F. Toney, Andrei Tokmakoff, and Edward J. Maginn, J. Phys. Chem. B. 125: 4501–4513 (2021).
• Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations, Ryan J. Menssen, Gregory J. Kimmel, and Andrei Tokmakoff, J. Chem. Phys. 154: 045101 (2021).
• Crossover from hydrogen bonding to chemical bonding, Bogdan Dereka, Qi Yu, Nicholas H. C. Lewis, William B. Carpenter, Joel M. Bowman, and Andrei Tokmakoff, Science. 371: 160-164 (2021).
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2020

• Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations, William B. Carpenter, Qi Yu, John H. Hack, Bogdan Dereka, Joel M. Bowman, and Andrei Tokmakoff, J. Chem. Phys. 153, 124506 (2020).
• DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site, Xin-Xing Zhang, Shelby Brantley, Steven Corcelli, and Andrei Tokmakoff, Commun. Biol. 3, 525 (2020).
• Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding, Adam Antoszewski, Chi-Jui Feng, Bodhi P. Vani, Erik H. Thiede, Lu Hong, Jonathan Weare, Andrei Tokmakoff, and Aaron R. Dinner, J. Phys. Chem. B 27, 5571-5587 (2020).
• Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating, Brennan Ashwood, Nicholas H.C. Lewis, Paul J. Sanstead, and Andrei Tokmakoff, J. Phys. Chem. B 124, 8665-8677 (2020).
• Vibrational Probe of Aqueous Electrolytes: The Field Is Not Enough, Nicholas H. C. Lewis, Aysenur Iscen, Alanna Felts, Bogdan Dereka, George C. Schatz, and Andrei Tokmakoff, J. Phys. Chem. B 124, 7013-7026 (2020).
• Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction, Carlos R. Baiz, Bartosz Błasiak, Jens Bredenbeck, Minhaeng Cho, Jun-Ho Choi, Steven A. Corcelli, Arend G. Dijkstra, Chi-Jui Feng, Sean Garrett-Roe, Nien-Hui Ge, Magnus W. D. Hanson-Heine, Jonathan D. Hirst, Thomas L. C. Jansen, Kijeong Kwac, Kevin J. Kubarych, Casey H. Londergan, Hiroaki Maekawa, Mike Reppert, Shinji Saito, Santanu Roy, James L. Skinner, Gerhard Stock, John E. Straub, Megan C. Thielges, Keisuke Tominaga, Andrei Tokmakoff, Hajime Torii, Lu Wang, Lauren J. Webb, and Martin T. Zanni, Chem. Rev. 120, 7152-7218 (2020).
• Revealing the Dynamical Role of Co-solvents in the Coupled Folding and Dimerization of Insulin, Xin-Xing Zhang and Andrei Tokmakoff, J. Phys. Chem. Lett. 11, 4353-4358 (2020).
• Dynamic and programmable cellular-scale granules enable tissue-like materials, Yin Fang, Endao Han, Xin-Xing Zhang, Yuanwen Jiang, Yiliang Lin, Jiuyun Shi, Jiangbo Wu, Lingyuan Meng, Xiang Gao, Philip J. Griffin, Xianghui Xiao, Hsiu-Ming Tsai, Hua Zhou, Xiaobing Zuo, Qing Zhang, Miaoqi Chu, Qingteng Zhang, Ya Gao, Leah K. Roth, Reiner Bleher, Zhiyuan Ma, Zhang Jiang, Jiping Yue, Chien-Min Kao, Chin-Tu Chen, Andrei Tokmakoff, Jin Wang, Heinrich M. Jaeger, Bozhi Tian, Matter 2, 948-964 (2020).
• Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA, Paul Sanstead, Brennan Ashwood, Qing Dai, Chuan He, Andrei Tokmakoff, J. Phys. Chem. B 124, 1160-1174 (2020).
• Signatures of Ion-Pairing and Aggregation in the Vibrational Spectroscopy of Super-Concentrated Aqueous Lithium Bistriflimide Solutions, Nicholas H.C. Lewis, Yong Zhang, Bogdan Dereka, Emily V. Carino, Edward J. Maginn, and Andrei Tokmakoff, J. Phys. Chem. C 124, 3470-3481 (2020).
• 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex, Brennan Ashwood, Paul J. Sanstead, Qing Dai, Chuan He, and Andrei Tokmakoff, J. Phys. Chem. B 124, 627-640 (2020).

2019

• High-Level VSCF/VCI Calculations Decode the Vibrational Spectrum of the Aqueous Proton, Qi Yu, William B. Carpenter, Nicholas H. C. Lewis, Andrei Tokmakoff, and Joel M. Bowman, J. Phys. Chem. B 123, 7214-7224 (2019).
• Entropic barriers in the kinetics of aqueous proton transfer, William B. Carpenter, Nicholas H. C. Lewis, Joseph A. Fournier, and Andrei Tokmakoff, J. Chem. Phys. 151, 034501 (2019).
• A lattice model for the interpretation of oligonucleotide hybridization experiments, Paul J. Sanstead and Andrei Tokmakoff, J. Chem. Phys. 150, 185104 (2019).
• Fluorescence-Encoded Infrared Spectroscopy: Ultrafast Vibrational Spectroscopy on Small Ensembles of Molecules in Solution, Lukas Whaley-Mayda, Samuel B. Penwell, and Andrei Tokmakoff, J. Phys. Chem. Lett. 10, 1967-1972 (2019).
• Length-Dependent Melting Kinetics of Short DNA Oligonucleotides Using Temperature-Jump IR Spectroscopy, Ryan J. Menssen and Andrei Tokmakoff, J. Phys. Chem. B 123, 756-767 (2019).
• Direct Observation of Ion Pairing in Aqueous Nitric Acid Using 2D Infrared Spectroscopy, Nicholas H. C. Lewis, Joseph A. Fournier, William B. Carpenter, and Andrei Tokmakoff, J. Phys. Chem. B 123, 225-238 (2019).

2018

• Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala-Ala-Ala, Chi-Jui Feng, Balamurugan Dhayalan, and Andrei Tokmakoff, Biophys. J. 114, 2820-2832 (2018).
• Single-stage MHz mid-IR OPA using LiGaS₂ and a fiber laser pump source, Samuel Penwell, Lukas Whaley-Mayda, and Andrei Tokmakoff, Opt. Lett. 43, 1363-1366 (2018).
• Direct Observation of Activated Kinetics and Downhill Dynamics in DNA Dehybridization, Paul J. Sanstead and Andrei Tokmakoff, J. Phys. Chem. B 122, 3088-3100 (2018).
• Broadband 2D IR spectroscopy reveals dominant asymmetric H₅O₂⁺ proton hydration structures in acid solutions, Joseph A. Fournier, William B. Carpenter, Nicholas H.C. Lewis, and Andrei Tokmakoff, Nat. Chem. 10, 932-937 (2018).
• Infrared Insights into the Effect of Cholesterol on Lipid Membranes, Paul Stevenson and Andrei Tokmakoff, Chem. Phys. 512, 146-153 (2018).
• Picosecond Proton Transfer Kinetics in Water Revealed with Ultrafast IR Spectroscopy, William B. Carpenter, Joseph A. Fournier, Nicholas H.C. Lewis, and Andrei Tokmakoff, J. Phys. Chem. B 122, 2792-2802 (2018).
• Fourier Transform Fluorescence-Encoded Infrared Spectroscopy, Joseph N. Mastron and Andrei Tokmakoff, J. Phys. Chem. A 122, 554-562 (2018).

2017

• The Dynamics of Peptide-Water Interactions in Dialanine: An Ultrafast Amide I 2D IR and Computational Spectroscopy Study, Chi-Jui Feng and Andrei Tokmakoff, J. Chem. Phys. 147, 085101-1-11 (2017).
• Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water, William B. Carpenter, Joseph A. Fournier, Rajib Biswas, Gregory A. Voth, and Andrei Tokmakoff, J. Chem. Phys. 147, 084503-1-10 (2017).
• Time-Resolved Measurements of an Ion Channel Conformational Change Driven by a Membrane Phase Transition, Paul Stevenson and Andrei Tokmakoff, Proc. Natl. Acad. Sci. U. S. A. 114, 10840-10845 (2017).
• IR spectral assignments for the hydrated excess proton in liquid water, Rajib Biswas, William Carpenter, Joseph A. Fournier, Gregory A. Voth, and Andrei Tokmakoff, J. Chem. Phys. 146, 154507 (2017).
• Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes, Paul Stevenson and Andrei Tokmakoff, J. Am. Chem. Soc. 139, 4743-4752 (2017).

2016

• Two-Photon-Excited Fluorescence-Encoded Spectroscopy, Joseph N. Mastron and Andrei Tokmakoff, J. Phys. Chem. A 120, 9178-9187 (2016).
• Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water, Rajib Biswas, William Carpenter, Gregory Voth, and Andrei Tokmakoff, J. Chem. Phys. 145, 154504-1-12 (2016).
• Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides, Mike Reppert, Anish R. Roy, Jeremy O. B. Tempkin, Aaron R. Dinner, and Andrei Tokmakoff, J. Phys. Chem. B 120, 11395-11404 (2016).
• Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy, Luigi De Marco, Joseph A. Fournier, Martin Thämer, William Carpenter, and Andrei Tokmakoff, J. Chem. Phys. 145, 094501-1-13 (2016).
• “Sequence-Dependent Mechanism of DNA Oligonucleotide Dehybridization Resolved through Infrared Spectroscopy, Paul J. Sanstead, Paul Stevenson, and Andrei Tokmakoff, J. Am. Chem. Soc. 138, 11792-11801 (2016).
• Interplay of Ion–Water and Water–Water Interactions within the Hydration Shells of Nitrate and Carbonate Directly Probed with 2D IR Spectroscopy, Joseph A. Fournier, William Carpenter, Luigi De Marco, and Andrei Tokmakoff, J. Am. Chem. Soc. 138, 9634-9645 (2016).
• Studying Protein–Protein Binding through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer, Xin-Xing Zhang, Kevin C. Jones, Ann Fitzpatrick, Chunte Sam Peng, Chi-Jui Feng, Carlos Baiz, and Andrei Tokmakoff, J. Phys. Chem. B 120, 5134-5145 (2016).
• Differences in the Vibrational Dynamics of H₂O and D₂O: Observation of Symmetric and Antisymmetric Stretching Vibrations in Heavy Water, Luigi De Marco, William Carpenter, Hanchao Liu, Rajib Biswas, Joel M. Bowman, and Andrei Tokmakoff, J. Phys. Chem. Lett. 7, 1769-1774 (2016).
• Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics, Mike Reppert and Andrei Tokmakoff, Annu. Rev. Phys. Chem. 67, 359-386 (2016).
• Efficient Total Chemical Synthesis of ¹³C=¹⁸O Isotopomers of Human Insulin for Isotope-Edited FTIR, Balamurugan Dhayalan, Ann Fitzpatrick, Kalyaneswar Mandal, Jonathan Whittaker, Michael A. Weiss, Andrei Tokmakoff, and Stephen B. H. Kent, ChemBioChem 17, 421-425 (2016).
• Crystallization of Enantiomerically Pure Proteins from Quasi-Racemic Mixtures: Structure Determination by X-Ray Diffraction of Isotope-Labeled Ester Insulin and Human Insulin, Kalyaneswar Mandal, Balamurugan Dhayalan, Michal Avital-Shmilovici, Andrei Tokmakoff, and Stephen B. H. Kent, ChemBioChem 17, 415-420 (2016).
• Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability, Qing Dai, Paul J. Sanstead, Chunte Sam Peng, Dali Han, Chuan He, and Andrei Tokmakoff, ACS Chem. Bio. 11, 470-477 (2016).
• Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport, Rajib Biswas, Ying-Lung Steve Tse, Andrei Tokmakoff, and Gregory A. Voth, J. Phys. Chem. B 120, 1793-1804 (2016).

2015

• Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy, Aritra Mandal and Andrei Tokmakoff, J. Chem. Phys. 143, 194501 (2015).
• Ultrafast 2D IR spectroscopy of the excess proton in liquid water, Martin Thämer, Luigi De Marco, Krupa Ramasesha, Aritra Mandal, and Andrei Tokmakoff, Science 350, 78-82 (2015).
• Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy, Mike Reppert and Andrei Tokmakoff, J. Chem. Phys. 143, 061102 (2015).
• Distinguishing Gramicidin D Conformers through Two-Dimensional Infrared Spectroscopy of Vibrational Excitons, Paul Stevenson and Andrei Tokmakoff, J. Chem. Phys. 142, 212424 (2015).
• Isotope-Enriched Protein Standards for Computational Amide I Spectroscopy, Mike Reppert, Anish R. Roy, and Andrei Tokmakoff, J. Chem. Phys. 142, 125104-1-10 (2015).
• Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling, P. Stevenson, C. Götz, C. R. Baiz, J. Akerboom, A. Tokmakoff, and A. Vaziri, J. Phys. Chem. B 119, 5824-5831 (2015).
• Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity, C. S. Peng, B. I. Fedeles, V. Singh, D. Li, T. Amariuta, J. M. Essigmann and A. Tokmakoff, Proc. Nat. Acad. Sci. 112, 3229-3234 (2015).
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2014

• Preface: Special Topic on Biological Water, Gerhard Hummer and Andrei Tokmakoff, J. Chem. Phys. 141, 22D101-1-2 (2014).
• Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2′-deoxycytidine, D. Li, B. I. Fedeles, V. Singh, C. S. Peng, K. J. Silvestre, A. K. Simi, J. H. Simpson, A. Tokmakoff, and J. M. Essigmann, Proc. Nat. Acad. Sci. 111, E3252-E3259 (2014).
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• Ultrafast 2D IR microscopy, C. R. Baiz, D. Schach, and A. Tokmakoff, Opt. Express 22, 18724-18735 (2014).
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• Direct observation of intermolecular interactions mediated by hydrogen bonding, L. De Marco, M. Thämer, M. Reppert, and A. Tokmakoff, J. Chem. Phys. 141, 034502 (2014).
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• Robust excitons inhabit soft supramolecular nanotubes, D. M. Eisele, D. H. Arias, X. Fu, E. A. Bloemsma, C. P. Steiner, R. A. Jensen, P. Rebentrost, H. Eisele, A. Tokmakoff, S. Lloyd, K. A. Nelson, D. Nicastro, J. Knoester, and M. G. Bawendi, Proc. Nat. Acad. Sci. 111, E3367-E3375 (2014).
• Collective vibrations of water-solvated hydroxide ions investigated with broadband 2DIR spectroscopy, A. Mandal, K. Ramasesha, L. De Marco, and A. Tokmakoff, J. Chem. Phys. 140, 204508 (2014).
• Local and Collective Reaction Coordinates in the Transport of the Aqueous Hydroxide Ion, S. T. Roberts, A. Mandal, and A. Tokmakoff, J. Phys. Chem. B 118, 8062-8069 (2014).
• A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models, C. R. Baiz, Y. Lin, C. S. Peng, K. A. Beauchamp, V. A. Voelz, V. S. Pande, and A. Tokmakoff, Biophys. J. 106, 1359-1370 (2014).
• Direct Observation of Multiple Tautomers of Oxythiamine and their Recognition by the Thiamine Pyrophosphate Riboswitch, V. Singh, C. S. Peng, D. Li, K. Mitra, K. J. Silvestre, A. Tokmakoff, and J. M. Essigmann, ACS Chem. Biol. 9, 227-236 (2014).

2013

• Water Vibrations have Strongly Mixed Intra- and Intermolecular Character, K. Ramasesha, L. De Marco, A. Mandal, and A. Tokmakoff, Nature Chem. 5, 935-940 (2013).
• Experimental Evidence of Fermi Resonances in Isotopically Dilute Water from Ultrafast Broadband IR Spectroscopy, L. De Marco, K. Ramasesha, and A. Tokmakoff, J. Phys. Chem. B. 117, 15319-15327 (2013).
• Direct observation of ground-state lactam-lactim tautomerization using temperature-jump transient 2D IR spectroscopy, C. S. Peng, C. R. Baiz, and A. Tokmakoff, Proc. Nat. Acad. Sci. 110, 9243-9248 (2013).
• Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment, M. Reppert and A. Tokmakoff, J. Chem. Phys. 138, 134116-1-11 (2013).
• Cooperative cold denaturation: The case of the C-terminal domain of ribosomal protein L9, B. Luan, B. Shan, C. Baiz, A. Tokmakoff, and D.P. Raleigh, Biochem. 52, 2402-2409 (2013).
• Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy, K. C. Jones, C. S. Peng, and A. Tokmakoff, Proc. Nat. Acad. Sci. 110, 2828-2833 (2013).
• Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins, C. R. Baiz, M. Reppert, and A. Tokmakoff, J Phys. Chem A. 117, 5955-5961 (2013).
• An Introduction to Protein 2D IR Spectroscopy, Carlos Baiz, Mike Reppert, Andrei Tokmakoff, Ch. 12 in Ultrafast Infrared Vibrational Spectroscopy, ed. by Michael D. Fayer (Taylor & Francis, New York, 2013), pp. 361-404.

2012

• Identification of Lactam-Lactim Tautomers of Aromatic Heterocycles in Aqueous Solution Using 2D IR Spectroscopy, C. S. Peng, and A. Tokmakoff, J. Phys. Chem. Lett. 3, 3302-3306 (2012).
• Transient Two-Dimensional Spectroscopy with Linear Absorption Corrections Applied to Temperature-jump Two-dimensional Infrared, K. C. Jones, Z. Ganim, C. Sam Peng, and A. Tokmakoff, J. Opt. Soc. Am. B 29, 118-129 (2012).
• Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution, C. Baiz, C. Sam Peng, M. E. Reppert, K. C. Jones, and A. Tokmakoff, Analyst 137, 1793-1799 (2012).
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• Identifying residual structure in intrinsically disordered systems: A 2D IR spectroscopic study of the GVGXPGVG peptide, J. Lessing, S. Roy, M. Reppert, M. Baer, D. Marx, T. La Cour Jansen, J. Knoester, and A. Tokmakoff, J. Am. Chem. Soc. 134, 5032-5035 (2012).
• A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy, K. Ramasesha, L. De Marco, A. D. Horning, A. Mandal and A. Tokmakoff, J. Chem. Phys. 136, 134507-1-11 (2012).

2011

• 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).

2010

• Orientational Dynamics of Water Probed with 2D-IR Anisotropy Measurements, K. Ramasesha, R. A. Nicodemus, S. T. Roberts, A. Mandal and A. Tokmakoff, in Ultrafast Phenomena XVII, Ed. by E. Riedle, R.W. Schoenlein, M. Chergui, and A. Taylor, (Oxford University Press, New York, 2010), pp 454-456.
• 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, 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, 3579-3588 (2010).

2009

• Heterodyne-Detected Dispersed Vibrational Echo Spectroscopy, K. C. Jones, Z. Ganim, and A. Tokmakoff, J. Phys. Chem. A 113, 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, 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, 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, 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, 2966-2968 (2007).
• Probing Local Structural Events in β-hairpin Unfolding with Transient Nonlinear Infrared Spectroscopy, A. Smith and A. Tokmakoff, ACIE 46, 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, Proc. Nat. Acad. Sci. 104, 14237-14242 (2007).
• Shining light on the rapidly evolving structure of water, A. Tokmakoff, Science 317, 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, 063101 (2007).
• Single-shot two-dimensional infrared spectroscopy, M. F. DeCamp, L. P. DeFlores, K. C. Jones and A. Tokmakoff, Opt. Exp. 15, 233-241, (2007).
• Amide I two-dimensional infrared spectroscopy of β-hairpin peptides, A. W. Smith and A. Tokmakoff, J. Chem. Phys. 126, 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, 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, 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

• Phonon-assisted exciton relaxation dynamics for a (6,5)-enriched DNA-wrapped single-walled carbon nanotube sample, S. G. Chou, M. F. DeCamp, J. Jiang, Ge. G. Samsonidze, E. B. Barros, F. Plentz, A. Jorio, M. Zheng, G. B. Onoa, E. D. Semke, A. Tokmakoff, R. Saito, G. Dresselhaus, and M. S. Dresselhaus, Phys. Rev. B 72, 195415 (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, 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, 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

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).