Abstract

Multidimensional spectroscopies provide increased spectral information but time resolution is often limited by the picosecond lifetimes of the transitions they probe. At the expense of additional complexity, transient multidimensional techniques extend the accessible timescales for studying nonequilibrium chemical and biophysical phenomena. Transient temperature-jump (T-jump) experiments are particularly versatile, since they can be applied to any temperature-dependent change of state. We have developed a method to correct transient nonlinear techniques for distortions resulting from transient linear absorption of the probing pulses, distortions which can lead to false interpretations of the data. We apply these corrections in the collection of T-jump transient two- dimensional infrared spectra for the peptides diglycine and the β-hairpin peptide trpzip2. For diglycine, the T-jump induces changes in H-bonding, a response which is inherent to all aqueous systems. The trpzip2 results probe the hairpin unfolding kinetics and reveal two time scales: <10ns increased flexibility and 1.1μs β-hairpin disordering.

© 2011 Optical Society of America

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  1. S. Woutersen and P. Hamm, “Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy,” J. Phys. Chem. B 104, 11316–11320 (2000).
    [CrossRef]
  2. A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
    [CrossRef] [PubMed]
  3. C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
    [CrossRef] [PubMed]
  4. H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
    [CrossRef] [PubMed]
  5. J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
    [CrossRef] [PubMed]
  6. J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
    [CrossRef] [PubMed]
  7. Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
    [CrossRef] [PubMed]
  8. A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
    [CrossRef]
  9. T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
    [CrossRef] [PubMed]
  10. M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
    [CrossRef]
  11. M. D. Fayer, “Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy,” Annu. Rev. Phys. Chem. 60, 21–38 (2009).
    [CrossRef]
  12. J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
    [CrossRef] [PubMed]
  13. C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
    [CrossRef]
  14. J. M. Anna, M. R. Ross, and K. J. Kubarych, “Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy,” J. Phys. Chem. A 113, 6544–6547 (2009).
    [CrossRef] [PubMed]
  15. J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
    [CrossRef]
  16. J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
    [CrossRef] [PubMed]
  17. C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
    [CrossRef] [PubMed]
  18. R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
    [CrossRef] [PubMed]
  19. C. R. Baiz, M. J. Nee, R. McCanne, and K. J. Kubarych, “Ultrafast nonequilibrium Fourier-transform two-dimensional infrared spectroscopy,” Opt. Lett. 33, 2533–2535 (2008).
    [CrossRef] [PubMed]
  20. W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
    [CrossRef] [PubMed]
  21. H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
    [CrossRef] [PubMed]
  22. H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
    [CrossRef] [PubMed]
  23. E. R. Andresen and P. Hamm, “Site-specific difference 2D-IR spectroscopy of Bacteriorhodopsin,” J. Phys. Chem. B 113, 6520–6527 (2009).
    [CrossRef] [PubMed]
  24. H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
    [CrossRef] [PubMed]
  25. C. R. Baiz, R. McCanne, and K. J. Kubarych, “Transient vibrational echo versus transient absorption spectroscopy: a direct experimental and theoretical comparison,” Appl. Spectrosc. 64, 1037–1044 (2010).
    [CrossRef] [PubMed]
  26. K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
    [CrossRef] [PubMed]
  27. Although the transient absorption signal is formally 3rd order, here we take a phenomenological approach in which the T-jump pulse is not considered in the nonlinear spectral response.
  28. J. Wang and M. A. El-Sayed, “Temperature jump-induced secondary structural change of the membrane protein bacteriorhodopsin in the premelting temperature region: a nanosecond time-resolved fourier transform infrared study,” Biophys. J. 76, 2777–2783 (1999).
    [CrossRef] [PubMed]
  29. S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
    [CrossRef] [PubMed]
  30. C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
    [CrossRef] [PubMed]
  31. K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
    [CrossRef] [PubMed]
  32. H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
    [CrossRef]
  33. A. W. Smith, J. Lessing, Z. Ganim, C. S. Peng, A. Tokmakoff, S. Roy, T. L. C. Jansen, and J. Knoester, “Melting of a β-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations,” J. Phys. Chem. B 114, 10913–10924 (2010).
    [CrossRef] [PubMed]
  34. J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
    [CrossRef]
  35. N. Belabas and D. M. Jonas, “Three-dimensional view of signal propagation in femtosecond four-wave mixing with application to the boxcars geometry,” J. Opt. Soc. Am. B 22, 655–674(2005).
    [CrossRef]
  36. M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
    [CrossRef] [PubMed]
  37. S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
    [CrossRef]
  38. Adam W. Smith and A. Tokmakoff, “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy,” Angew. Chem.. Int. Ed. Engl., Suppl. 46, 7984–7987 (2007).
    [CrossRef]
  39. K. E. Amunson and J. Kubelka, “On the temperature dependence of amide I frequencies of peptides in solution,” J. Phys. Chem. B 111, 9993–9998 (2007).
    [CrossRef] [PubMed]
  40. J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
    [CrossRef]
  41. R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
    [CrossRef] [PubMed]
  42. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
    [CrossRef] [PubMed]
  43. N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
    [CrossRef] [PubMed]
  44. A. Barth and C. Zscherp, “What vibrations tell us about proteins,” Q. Rev. Biophys. 35, 369–430 (2002).
    [CrossRef]

2011

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
[CrossRef]

2010

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

C. R. Baiz, R. McCanne, and K. J. Kubarych, “Transient vibrational echo versus transient absorption spectroscopy: a direct experimental and theoretical comparison,” Appl. Spectrosc. 64, 1037–1044 (2010).
[CrossRef] [PubMed]

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

2009

E. R. Andresen and P. Hamm, “Site-specific difference 2D-IR spectroscopy of Bacteriorhodopsin,” J. Phys. Chem. B 113, 6520–6527 (2009).
[CrossRef] [PubMed]

K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
[CrossRef] [PubMed]

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

M. D. Fayer, “Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy,” Annu. Rev. Phys. Chem. 60, 21–38 (2009).
[CrossRef]

J. M. Anna, M. R. Ross, and K. J. Kubarych, “Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy,” J. Phys. Chem. A 113, 6544–6547 (2009).
[CrossRef] [PubMed]

2008

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

C. R. Baiz, M. J. Nee, R. McCanne, and K. J. Kubarych, “Ultrafast nonequilibrium Fourier-transform two-dimensional infrared spectroscopy,” Opt. Lett. 33, 2533–2535 (2008).
[CrossRef] [PubMed]

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

2007

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

Adam W. Smith and A. Tokmakoff, “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy,” Angew. Chem.. Int. Ed. Engl., Suppl. 46, 7984–7987 (2007).
[CrossRef]

K. E. Amunson and J. Kubelka, “On the temperature dependence of amide I frequencies of peptides in solution,” J. Phys. Chem. B 111, 9993–9998 (2007).
[CrossRef] [PubMed]

2006

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

2005

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

N. Belabas and D. M. Jonas, “Three-dimensional view of signal propagation in femtosecond four-wave mixing with application to the boxcars geometry,” J. Opt. Soc. Am. B 22, 655–674(2005).
[CrossRef]

2004

H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
[CrossRef]

J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
[CrossRef] [PubMed]

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

2003

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
[CrossRef]

A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
[CrossRef]

2002

A. Barth and C. Zscherp, “What vibrations tell us about proteins,” Q. Rev. Biophys. 35, 369–430 (2002).
[CrossRef]

2001

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
[CrossRef]

2000

S. Woutersen and P. Hamm, “Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy,” J. Phys. Chem. B 104, 11316–11320 (2000).
[CrossRef]

1999

J. Wang and M. A. El-Sayed, “Temperature jump-induced secondary structural change of the membrane protein bacteriorhodopsin in the premelting temperature region: a nanosecond time-resolved fourier transform infrared study,” Biophys. J. 76, 2777–2783 (1999).
[CrossRef] [PubMed]

1996

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
[CrossRef] [PubMed]

Amunson, K. E.

K. E. Amunson and J. Kubelka, “On the temperature dependence of amide I frequencies of peptides in solution,” J. Phys. Chem. B 111, 9993–9998 (2007).
[CrossRef] [PubMed]

Andresen, E. R.

E. R. Andresen and P. Hamm, “Site-specific difference 2D-IR spectroscopy of Bacteriorhodopsin,” J. Phys. Chem. B 113, 6520–6527 (2009).
[CrossRef] [PubMed]

Anna, J. M.

J. M. Anna, M. R. Ross, and K. J. Kubarych, “Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy,” J. Phys. Chem. A 113, 6544–6547 (2009).
[CrossRef] [PubMed]

Arnold, E.

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

Asbury, J.

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Baiz, C. R.

Ballew, R. M.

R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
[CrossRef] [PubMed]

Bandaria, J. N.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

Barth, A.

A. Barth and C. Zscherp, “What vibrations tell us about proteins,” Q. Rev. Biophys. 35, 369–430 (2002).
[CrossRef]

Bauman, J. D.

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

Behrendt, R.

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Belabas, N.

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

N. Belabas and D. M. Jonas, “Three-dimensional view of signal propagation in femtosecond four-wave mixing with application to the boxcars geometry,” J. Opt. Soc. Am. B 22, 655–674(2005).
[CrossRef]

Blankenship, R. E.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

Bour, P.

J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
[CrossRef]

Bredenbeck, J.

J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Brixner, T.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

Cahoon, J. F.

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

Callender, R. H.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Causgrove, T. P.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Cheatum, C. M.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

Chen, X.

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Cho, M.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

Chung, H. S.

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

Chung, J. K.

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

Clark, I. P.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Das, K.

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

DeFlores, L. P.

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

DeGrado, W. F.

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

Demirdoven, N.

M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
[CrossRef]

Demirdöven, N.

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

Du, D.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

Dutta, S.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

Dyer, R. B.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Eaves, J. D.

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
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El-Sayed, M. A.

J. Wang and M. A. El-Sayed, “Temperature jump-induced secondary structural change of the membrane protein bacteriorhodopsin in the premelting temperature region: a nanosecond time-resolved fourier transform infrared study,” Biophys. J. 76, 2777–2783 (1999).
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Ervin, J.

H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
[CrossRef]

Fang, C.

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

Fang, K. S.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Fayer, M. D.

M. D. Fayer, “Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy,” Annu. Rev. Phys. Chem. 60, 21–38 (2009).
[CrossRef]

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Fecko, C. J.

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

Ferro, A. Albrecht

J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
[CrossRef]

Fleming, G. R.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

Franking, R. A.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Gai, F.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

Ganim, Z.

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

K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
[CrossRef] [PubMed]

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

Geissler, P. L.

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

Getahun, Z.

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

Gilmanshin, R.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Gopalan, P.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Greetham, G. M.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Gruebele, M.

H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
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R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
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Hagen, S. J.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

Ham, S.

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

Hamers, R. J.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Hamm, P.

E. R. Andresen and P. Hamm, “Site-specific difference 2D-IR spectroscopy of Bacteriorhodopsin,” J. Phys. Chem. B 113, 6520–6527 (2009).
[CrossRef] [PubMed]

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

S. Woutersen and P. Hamm, “Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy,” J. Phys. Chem. B 104, 11316–11320 (2000).
[CrossRef]

Harris, C. B.

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

Hauser, K.

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

Helbing, J.

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Hochstrasser, R. M.

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

Huang, C.-Y.

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

Huang, R.

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

Hunt, N. T.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Hybl, J. D.

J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
[CrossRef]

Ishikawa, H.

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

Jansen, T. L. C.

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

Jonas, D. M.

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

N. Belabas and D. M. Jonas, “Three-dimensional view of signal propagation in femtosecond four-wave mixing with application to the boxcars geometry,” J. Opt. Soc. Am. B 22, 655–674(2005).
[CrossRef]

J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
[CrossRef]

Jones, K. C.

K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
[CrossRef] [PubMed]

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

Kaminsky, J.

J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
[CrossRef]

Kania, R.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Keiderling, T. A.

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

Khalil, M.

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
[CrossRef]

Kim, J.-H.

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

Kim, S.

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

Kitney, K. A.

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

Klemke, J. W.

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

Knoester, J.

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

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

Kohen, A.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

Kolano, C.

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

Korendovych, I. V.

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

Kozinski, M.

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

Krejtschi, C.

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

Krummel, A. T.

A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
[CrossRef]

Kubarych, K. J.

Kubelka, J.

J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
[CrossRef]

K. E. Amunson and J. Kubelka, “On the temperature dependence of amide I frequencies of peptides in solution,” J. Phys. Chem. B 111, 9993–9998 (2007).
[CrossRef] [PubMed]

Kwak, K.

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Laaser, J. E.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Lee, H.

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

Lessing, J.

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

Loparo, J. J.

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

Ma, H.

H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
[CrossRef]

McCanne, R.

Moroder, L.

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Mukherjee, P.

A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
[CrossRef]

Nee, M. J.

Nydegger, M. W.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

Pande, V. S.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

Paoprasert, P.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Parker, A. W.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Peng, C. S.

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

Piletic, I. R.

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Qiu, L.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

Remorino, A.

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

Renner, C.

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Rock, W.

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

Ross, M. R.

J. M. Anna, M. R. Ross, and K. J. Kubarych, “Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy,” J. Phys. Chem. A 113, 6544–6547 (2009).
[CrossRef] [PubMed]

Roy, S.

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

Sabelko, J.

R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
[CrossRef] [PubMed]

Sander, W.

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

Sawyer, K. R.

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

Schlegel, J. P.

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

Smith, A. W.

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

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

Smith, Adam W.

Adam W. Smith and A. Tokmakoff, “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy,” Angew. Chem.. Int. Ed. Engl., Suppl. 46, 7984–7987 (2007).
[CrossRef]

Snow, C. D.

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

Stenger, J.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

Stewart, A. I.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Tokmakoff, A.

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

K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
[CrossRef] [PubMed]

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

Adam W. Smith and A. Tokmakoff, “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy,” Angew. Chem.. Int. Ed. Engl., Suppl. 46, 7984–7987 (2007).
[CrossRef]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
[CrossRef]

Towrie, M.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Vaswani, H. M.

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

Wachtveitl, J.

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

Wang, J.

J. Wang and M. A. El-Sayed, “Temperature jump-induced secondary structural change of the membrane protein bacteriorhodopsin in the premelting temperature region: a nanosecond time-resolved fourier transform infrared study,” Biophys. J. 76, 2777–2783 (1999).
[CrossRef] [PubMed]

Williams, S.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Woodruff, W. H.

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Woutersen, S.

S. Woutersen and P. Hamm, “Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy,” J. Phys. Chem. B 104, 11316–11320 (2000).
[CrossRef]

Wu, L.

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

Wu, Y.

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

Xiong, W.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

Yetzbacher, M. K.

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

Zanni, M. T.

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
[CrossRef]

Zheng, J. R.

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

Zscherp, C.

A. Barth and C. Zscherp, “What vibrations tell us about proteins,” Q. Rev. Biophys. 35, 369–430 (2002).
[CrossRef]

Acc. Chem. Res.

Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, “Amide I two-dimensional infrared spectroscopy of proteins,” Acc. Chem. Res. 41, 432–441 (2008).
[CrossRef] [PubMed]

Angew. Chem.. Int. Ed. Engl., Suppl.

Adam W. Smith and A. Tokmakoff, “Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy,” Angew. Chem.. Int. Ed. Engl., Suppl. 46, 7984–7987 (2007).
[CrossRef]

Annu. Rev. Phys. Chem.

M. D. Fayer, “Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy,” Annu. Rev. Phys. Chem. 60, 21–38 (2009).
[CrossRef]

Appl. Spectrosc.

Biochemistry

S. Williams, T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer, “Fast events in protein folding: helix melting and formation in a small peptide,” Biochemistry 35, 691–697 (1996).
[CrossRef] [PubMed]

Biophys. J.

J. Wang and M. A. El-Sayed, “Temperature jump-induced secondary structural change of the membrane protein bacteriorhodopsin in the premelting temperature region: a nanosecond time-resolved fourier transform infrared study,” Biophys. J. 76, 2777–2783 (1999).
[CrossRef] [PubMed]

J. Am. Chem. Soc.

C.-Y. Huang, J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai, “Temperature-dependent helix-coil transition of an alanine based peptide,” J. Am. Chem. Soc. 123, 9235–9238 (2001).
[CrossRef] [PubMed]

K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, “Site-specific relaxation kinetics of a tryptophan zipper hairpin peptide using temperature-jump IR spectroscopy and isotopic labeling,” J. Am. Chem. Soc. 130, 2984–2992 (2008).
[CrossRef] [PubMed]

J. Bredenbeck, J. Helbing, and P. Hamm, “Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer,” J. Am. Chem. Soc. 126, 990–991 (2004).
[CrossRef] [PubMed]

W. Xiong, J. E. Laaser, P. Paoprasert, R. A. Franking, R. J. Hamers, P. Gopalan, and M. T. Zanni, “Transient 2D IR spectroscopy of charge injection in dye-sensitized nanocrystalline thin films,” J. Am. Chem. Soc. 131, 18040–18041 (2009).
[CrossRef] [PubMed]

N. Demirdöven, C. M. Cheatum, H. S. Chung, M. Khalil, J. Knoester, and A. Tokmakoff, “Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure,” J. Am. Chem. Soc. 126, 7981–7990 (2004).
[CrossRef] [PubMed]

J. Chem. Phys.

J. D. Hybl, A. Albrecht Ferro, and D. M. Jonas, “Two-dimensional fourier transform electronic spectroscopy,” J. Chem. Phys. 115, 6606–6622 (2001).
[CrossRef]

M. K. Yetzbacher, N. Belabas, K. A. Kitney, and D. M. Jonas, “Propagation, beam geometry, and detection distortions of peak shapes in two-dimensional Fourier transform spectra,” J. Chem. Phys. 126, 044511 (2007).
[CrossRef] [PubMed]

S. Ham, J.-H. Kim, H. Lee, and M. Cho, “Correlation between electronic and molecular structure distortions and vibrational properties. II. amide I modes of NMA-nD2O complexes,” J. Chem. Phys. 118, 3491–3498 (2003).
[CrossRef]

J. Opt. Soc. Am. B

J. Phys. Chem. A

K. C. Jones, Z. Ganim, and A. Tokmakoff, “Heterodyne-detected dispersed vibrational echo spectroscopy,” J. Phys. Chem. A 113, 14060–14066 (2009).
[CrossRef] [PubMed]

M. Khalil, N. Demirdoven, and A. Tokmakoff, “Coherent 2D IR spectroscopy: molecular structure and dynamics in solution,” J. Phys. Chem. A 107, 5258–5279 (2003).
[CrossRef]

J. M. Anna, M. R. Ross, and K. J. Kubarych, “Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy,” J. Phys. Chem. A 113, 6544–6547 (2009).
[CrossRef] [PubMed]

J. Kaminsky, P. Bour, and J. Kubelka, “Simulations of the temperature dependence of the amide I vibration,” J. Phys. Chem. A 115, 30–34 (2011).
[CrossRef]

J. Phys. Chem. B

J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, “Transient 2D-IR spectroscopy: snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide.,” J. Phys. Chem. B 107, 8654–8660 (2003).
[CrossRef]

A. T. Krummel, P. Mukherjee, and M. T. Zanni, “Inter and intrastrand vibrational coupling in DNA studied with heterodyned 2D-IR spectroscopy,” J. Phys. Chem. B 107, 9165–9169(2003).
[CrossRef]

S. Woutersen and P. Hamm, “Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy,” J. Phys. Chem. B 104, 11316–11320 (2000).
[CrossRef]

E. R. Andresen and P. Hamm, “Site-specific difference 2D-IR spectroscopy of Bacteriorhodopsin,” J. Phys. Chem. B 113, 6520–6527 (2009).
[CrossRef] [PubMed]

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

K. E. Amunson and J. Kubelka, “On the temperature dependence of amide I frequencies of peptides in solution,” J. Phys. Chem. B 111, 9993–9998 (2007).
[CrossRef] [PubMed]

Nature

T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, “Two-dimensional spectroscopy of electronic couplings in photosynthesis,” Nature 434, 625–628 (2005).
[CrossRef] [PubMed]

C. Kolano, J. Helbing, M. Kozinski, W. Sander, and P. Hamm, “Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy,” Nature 444, 469–472(2006).
[CrossRef] [PubMed]

Opt. Lett.

Phys. Chem. Chem. Phys.

R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, “Investigating the vibrational dynamics of a 17e- metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy,” Phys. Chem. Chem. Phys. 12, 1051–1063 (2010).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci, U.S.A.

H. S. Chung, Z. Ganim, K. C. Jones, and A. Tokmakoff, “Transient 2D IR spectroscopy of ubiquitin unfolding dynamics,” Proc. Natl. Acad. Sci, U.S.A. 104, 14237–14242 (2007).
[CrossRef] [PubMed]

J. N. Bandaria, S. Dutta, M. W. Nydegger, W. Rock, A. Kohen, and C. M. Cheatum, “Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase,” Proc. Natl. Acad. Sci, U.S.A. 107, 17974–17979 (2010).
[CrossRef] [PubMed]

C. Fang, J. D. Bauman, K. Das, A. Remorino, E. Arnold, and R. M. Hochstrasser, “Two-dimensional infrared spectra reveal relaxation of the nonnucleoside inhibitor TMC278 complexed with HIV-1 reverse transcriptase,” Proc. Natl. Acad. Sci, U.S.A. 105, 1472–1477 (2008).
[CrossRef]

H. Ishikawa, K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer, “Direct observation of fast protein conformational switching,” Proc. Natl. Acad. Sci, U.S.A. 105, 8619–8624 (2008).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. U.S.A.

R. M. Ballew, J. Sabelko, and M. Gruebele, “Direct observation of fast protein folding: the initial collapse of apomyoglobin,” Proc. Natl. Acad. Sci. U.S.A. 93, 5759–5764 (1996).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. USA

C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, “Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy,” Proc. Natl. Acad. Sci. USA 101, 4077–4082 (2004).
[CrossRef] [PubMed]

H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, “Conformational changes during the nanosecond to millisecond unfolding of ubiquitin,” Proc. Natl. Acad. Sci. USA 102, 612–617(2005).
[CrossRef] [PubMed]

Q. Rev. Biophys.

A. Barth and C. Zscherp, “What vibrations tell us about proteins,” Q. Rev. Biophys. 35, 369–430 (2002).
[CrossRef]

Rev. Sci. Instrum.

H. Ma, J. Ervin, and M. Gruebele, “Single-sweep detection of relaxation kinetics by submicrosecond midinfrared spectroscopy,” Rev. Sci. Instrum. 75, 486–491 (2004).
[CrossRef]

H. S. Chung, M. Khalil, A. W. Smith, and A. Tokmakoff, “Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics,” Rev. Sci. Instrum. 78, 063101 (2007).
[CrossRef] [PubMed]

Science

J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, “Determining transition-state geometries in liquids using 2D-IR,” Science 319, 1820–1823 (2008).
[CrossRef] [PubMed]

J. R. Zheng, K. Kwak, J. Asbury, X. Chen, I. R. Piletic, and M. D. Fayer, “Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time,” Science 309, 1338–1343 (2005).
[CrossRef] [PubMed]

A. Remorino, I. V. Korendovych, Y. Wu, W. F. DeGrado, and R. M. Hochstrasser, “Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer,” Science 332, 1206–1209 (2011).
[CrossRef] [PubMed]

C. J. Fecko, J. D. Eaves, J. J. Loparo, A. Tokmakoff, and P. L. Geissler, “Ultrafast hydrogen bond dynamics in the infrared spectroscopy of water,” Science 301, 1698–1702 (2003).
[CrossRef] [PubMed]

Other

Although the transient absorption signal is formally 3rd order, here we take a phenomenological approach in which the T-jump pulse is not considered in the nonlinear spectral response.

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Figures (10)

Fig. 1
Fig. 1

The output of a femtosecond Ti:sapphire regenerative amplifier is converted to the IR by difference frequency generation in an optical parametric amplifier and split into four IR beams in the 2D IR interferometer. Inlay: Three IR beams generate IR third-order signal at the sample. The T-jump laser is overlapped spatially with the IR beams at the sample and delayed in time electronically. The LO beam is overlapped spatially with the IR beams at the sample, but delayed from the other IR pulses. The signal and LO beams are overlapped spatially and temporally at the detector and detected using balanced detection. The LO beam’s delay can be stepped using the piezo-controlled stage for PMSI or FTSI measurements. L: lens, S: sample, B: beam-splitter, V: vertically displaced mirror, F: low pass λ = 3.4 μm filter.

Fig. 2
Fig. 2

IR beams (blue) 1,2 and 2,3 are delayed by τ 1 and τ 2 . The LO reaches the sample 60 ps after beam 3. The original IR pulse, from which beams 1,2,3 and LO are created, is generated at 1 kHz , which creates a 1 ms lag between sets of IR pulses. The 20 Hz T-jump pulse (green) is delayed electronically relative to the IR pulses. The first IR pulse set following the T-jump pulse arrives at a delay of τ = τ 0 . The next 49 IR pulse sets arrive at τ j = τ + j × ( 1 ms ) .

Fig. 3
Fig. 3

Absorptive (real) spectra of t-2D IR of diglycine are shown. Grid lines mark the three loss features shown in f. The first three columns (a-f) show data taken of 20 mg / mL diglycine ( OD = 0.9 ) following a T-jump from 20 to 30 ° C . The first row (a,c,e) shows equilibrium spectra at 20 ° C . The second row (b,d,f) shows the 1 ms difference spectra. Columns 1–3 are calculated from the same data but with different corrections for linear absorption of the IR beams. Column 1 (a,b) is uncorrected [ S 1 , 3 , Eq. (5)]. Column 2 (c,d) is ω 3 -corrected [ S 1 , Eq. (10)]. Column 3 (e,f) is ω 1 and ω 3 -corrected [S, Eq. (15)]. Column 4 (g,h) shows the real equilibrium 2D IR spectra of diglycine at 1 mg / mL (OD 0.05 ). g is the equilibrium 20 ° C spectrum. h shows the difference between the 30 and 20 ° C equilibrium spectra. The spectra are individually normalized and scaled such that 25 linearly-spaced contours span the entire magnitude range of sinh ( S Norm . × 0.1 ) .

Fig. 4
Fig. 4

5 ns , 1 μs , and 1 ms difference spectra for diglycine in D 2 O . (a) The transient difference absorption spectra of diglycine and solvent calculated from the transient LO spec tra ( log [ I ( ω ; τ j ) / I ( ω ; τ ref ) ] ). (b) The ω 3 -correction factor, exp [ 2 κ ( ω ; τ j ) ω l / c ] . c The ω 1 -correction factor, [ K ( ω ; τ j ) ] 1 .

Fig. 5
Fig. 5

For 20 mg / mL diglycine, HDVE-derived DPP slices are compared to projections of the real 2D IR spectrum onto ω 3 . Spectra are shown at equilibrium (first row) and at 1 ms delay time (second row). The three columns represent uncorrected (a,b), ω 3 ‐corrected (c,d), and ω 3 –and– ω 1 –corrected (e,f) data analogous to the data shown in Fig. 3. The vertical lines indicate the maximum of the amide I’ peak difference spectrum, whose traces are shown in Fig. 6.

Fig. 6
Fig. 6

Slices taken from the DPP spectra shown in Fig. 5 at 1677, 1672, and 1672 cm 1 , respectively. Traces are offset to allow comparison. The dashed line shows the solvent transmission.

Fig. 7
Fig. 7

TZ2 transient spectra from t-HDVE measurements. (a,b) DPP and DVE spectra are shown at selected delays. The DVE spectra are actually presented as the square-root of the DVE power spectrum (the square-root is taken before subtraction gives the difference spectra) to remove the apparent factor of two rate of population change between the absolute-value-squared measurement and the DPP, which is linear in concentration [25].

Fig. 8
Fig. 8

The TZ2 time-dependent trace and exponential fit. The top two traces are from the DPP [Fig. 7a], the middle two traces are from the square-root of the DVE [Fig. 7b], and the bottom two traces are from integrated boxes shown in Fig. 9a.

Fig. 9
Fig. 9

(a-e) The absorptive (real) correlation t-2D IR spectra at selected time delays for TZ2. (f-j) The t-2D IR square-root power spectra at selected time delays. The spectra are individually normalized and scaled such that 25 linearly-spaced contours span the entire magnitude range of sinh 1 ( S Norm . × 27.29 ) .

Fig. 10
Fig. 10

TZ2 uncorrected [ S 1 , 3 , Eq. (5)] difference DPP (a) and difference 2D IR (b,c) spectra, which can compared to the corrected data in Figs. 7a, 9a, 9d . The 2D contours are plotted as described in Fig. 9.

Equations (17)

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τ j = τ + j × ( 1 ms ) , for     j = 0 , 1 , 2 , , 49 .
n ˜ ( ω ; τ j ) = n ( ω ; τ j ) + i κ ( ω ; τ j ) .
E ˜ α ( ω ; τ j ) = e α ( ω ) exp [ i ϕ α ( ω ) ] exp [ i n ˜ ( ω ; τ j ) ω l / c ] , α = 1 , 2 , 3 , LO ,
K ( ω n ; τ j ) = 1 exp [ 2 κ ( ω n ; τ j ) ω n l / c ] 2 κ ( ω n ; τ j ) ω n l / c .
S ˜ 1 , 3 ( ω 1 , ω 3 ; τ 2 , τ j ) S ˜ ( ω 1 , ω 3 ; τ 2 , τ j ) × K ( ω 1 ; τ j ) × exp [ 2 κ ( ω 3 ; τ j ) ω 3 l / c ] .
E ˜ sig 1 , 3 ( ω 3 ; τ 1 , τ j ) = e sig 1 ( ω 3 ; τ 1 , τ j ) exp [ i ϕ sig ( ω 3 ; τ 1 , τ j ) ] exp [ i n ˜ ( ω 3 ; τ j ) ω 3 l / c ] .
I ± ( ω ; τ j ) = | E ˜ LO ( ω ; τ j ) | 2 = [ e LO ( ω ) ] 2 exp [ 2 κ ( ω ; τ j ) ω l / c ]
I ± 1 , 3 ( ω 3 ; τ 1 , τ j , τ LO ) = | E ˜ sig 1 , 3 ( ω 3 ; τ 1 , τ j ) + E ˜ LO ( ω 3 ; τ j ) exp [ i ω 3 τ LO ] | 2 = exp [ 2 κ ( ω 3 ; τ j ) ω 3 l / c ] × { [ e LO ( ω 3 ) ] 2 + [ e sig 1 ( ω 3 ; τ 1 , τ j ) ] 2 ± 2 e LO ( ω 3 ) e sig 1 ( ω 3 ; τ 1 , τ j ) cos [ Δ ϕ ( ω 3 ; τ 1 , τ j ) + τ LO ω 3 ] } .
Δ ϕ ( ω 3 ; τ 1 , τ j ) = ϕ sig ( ω 3 ; τ 1 , τ j ) ϕ LO ( ω 3 ) .
S 1 ( ω 3 ; τ 1 , τ j , τ LO ) = [ I + 1 , 3 I 1 , 3 I + 1 , 3 + I 1 , 3 I + I I + + I ] × [ e LO ( ω 3 ) ] 2 .
= 2 e LO ( ω 3 ) e sig 1 ( ω 3 ; τ 1 , τ j ) cos [ Δ ϕ ( ω 3 ; τ 1 , τ j ) + τ LO ω 3 ] .
S ( ω 3 ; τ 1 , τ j , τ LO ) × K ( ω 1 ; τ j ) .
κ ( ω ; τ j ) = Δ κ j , ref ( ω ; τ j ) + κ FTIR Eq ( ω ) ,
= c 2 ω l ln [ I + ( ω ; τ j ) + I ( ω ; τ j ) I + ( ω ; τ ref ) + I ( ω ; τ ref ) ] + κ FTIR Eq ( ω ) , { ref = 48 , for     j = 0 , 2 , , 48 ref = 49 , for     j = 1 , 3 , , 49 .
S ˜ ( ω 1 , ω 3 ; τ j , τ LO ) S ˜ 1 ( ω 1 , ω 3 ; τ j , τ LO ) × [ K ( ω 1 ; τ j ) ] 1 .
S ( ω 3 ; τ 1 , τ j , τ LO ) S 1 ( ω 3 ; τ 1 , τ j , τ LO ) × [ K ( ω 3 ; τ j ) ] 1 .
Δ S ( τ j ) = S ( τ j ) S ( τ ref ) , { ref = 48 , for     j = 0 , 2 , , 48 ref = 49 , for     j = 1 , 3 , , 49 .

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