This review presents an overview of the relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method for measuring structures and energy transport dynamics in molecules. The method strongly enhances the range of accessible distances compared to traditional 2DIR and offers new structural reporters, such as the energy transport time, cross-peak amplification factors, and connectivity patterns. The use of the method for assigning vibrational modes with various levels of delocalization is illustrated. RA 2DIR relies on vibrational energy transport in molecules; as such, the transport mechanism can be conveniently studied by the method. Applications to identify diffusive and ballistic energy transport are demonstrated.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Hamm P, Lim M, Hochstrasser RM. 1.  1998. Structure of the amide I band of peptides measured by femtosecond non-linear infrared spectroscopy. J. Phys. Chem. B 102:6123–38 [Google Scholar]
  2. Cho M, Scherer NF, Fleming GR, Mukamel S. 2.  1992. Photon echoes and related four-wave-mixing spectroscopies using phase-locked pulses. J. Chem. Phys. 96:5618–29 [Google Scholar]
  3. Hybl JD, Albrecht AW, Gallagher Faeder SM, Jonas DM. 3.  1998. Two-dimensional electronic spectroscopy. Chem. Phys. Lett. 297:307–13 [Google Scholar]
  4. Goodno GD, Dadusc G, Miller RJD. 4.  1998. Ultrafast heterodyne-detected transient-grating spectroscopy using diffractive optics. J. Opt. Soc. Am. 15:1791–94 [Google Scholar]
  5. Zimdars D, Tokmakoff A, Chen S, Greenfield SR, Fayer MD. 5.  1993. Picosecond, infrared, vibrational photon echoes in a liquid and glass using a free-electron laser. Phys. Rev. Lett. 70:2718–21 [Google Scholar]
  6. Mukamel S. 6.  1995. Principles of Nonlinear Spectroscopy New York: Oxford Univ. Press
  7. Zhao W, Wright JC. 7.  1999. Measurement of χ(3) for doubly vibrationally enhanced four wave mixing spectroscopy. Phys. Rev. Lett 83:1950–53 [Google Scholar]
  8. Bredenbeck J, Helbing J, Hamm P. 8.  2005. Solvation beyond the linear response regime. Phys. Rev. Lett. 95:083201 [Google Scholar]
  9. Rubtsov IV, Wang J, Hochstrasser RM. 9.  2003. Dual frequency 2D-IR heterodyned photon echo of the peptide bond. Proc. Natl. Acad. Sci. USA 100:5601–6 [Google Scholar]
  10. Asplund MC, Zanni MT, Hochstrasser RM. 10.  2000. Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes. Proc. Natl. Acad. Sci. USA 97:8219–24 [Google Scholar]
  11. Shim S-H, Strasfeld DB, Ling YL, Zanni MT. 11.  2007. Automated two-dimensional IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide. Proc. Natl. Acad. Sci. USA 104:14197–202 [Google Scholar]
  12. Hochstrasser RM. 12.  2006. Dynamical models for two-dimensional infrared spectroscopy of peptides. Adv. Chem. Phys. 132:1–56 [Google Scholar]
  13. Reddy AS, Wang L, Lin Y-S, Ling Y, Chopra M. 13.  et al. 2010. Solution structures of rat amylin peptide: simulation, theory, and experiment. Biophys. J. 98:443–51 [Google Scholar]
  14. Demirdöven N, Cheatum CM, Chung HS, Khalil M, Knoester J, Tokmakoff A. 14.  2004. Two-dimensional infrared spectroscopy of antiparallel β-sheet secondary structure. J. Am. Chem. Soc. 126:7981–90 [Google Scholar]
  15. Jeong KS, Pensack RD, Asbury JB. 15.  2013. Vibrational spectroscopy of electronic processes in emerging photovoltaic materials. Acc. Chem. Res. 46:1538–47 [Google Scholar]
  16. Jones BH, Massari AM. 16.  2013. Origins of spectral broadening in iodated Vaska's complex in binary solvent mixtures. J. Phys. Chem. B 117:15741–49 [Google Scholar]
  17. Müller-Werkmeister HM, Bredenbeck J. 17.  2014. A donor-acceptor pair for the real time study of vibrational energy transfer in proteins. Phys. Chem. Chem. Phys. 16:3261–66 [Google Scholar]
  18. Zheng J, Kwak K, Xie J, Fayer MD. 18.  2006. Ultrafast carbon-carbon single-bond rotational isomerization in room-temperature solution. Science 313:1951–55 [Google Scholar]
  19. Cahoon JF, Sawyer KR, Schlegel JP, Harris CB. 19.  2008. Determining transition-state geometries in liquids using 2D-IR. Science 319:1820–23 [Google Scholar]
  20. Strasfeld DB, Ling YL, Shim S-H, Zanni MT. 20.  2008. Tracking fiber formation in human islet amyloid polypeptide with automated 2D-IR spectroscopy. J. Am. Chem. Soc. 130:6698–99 [Google Scholar]
  21. Hamm P, Hochstrasser RM. 21.  2000. Structure and dynamics of proteins and peptides: femtosecond two-dimensional infrared spectroscopy. Ultrafast Infrared and Raman Spectroscopy MD Fayer 273–347 New York: Marcel Dekker [Google Scholar]
  22. Zhuang W, Hayashi T, Mukamel S. 22.  2009. Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges. Angew. Chem. Int. Ed. Engl. 48:3750–81 [Google Scholar]
  23. Arrivo SM, Heilweil EJ. 23.  1996. Conservation of vibrational excitation during hydrogen-bonding reactions. J. Phys. Chem. 100:11975–83 [Google Scholar]
  24. Zheng J, Fayer MD. 24.  2008. Solute-solvent complex kinetics and thermodynamics probed by 2D-IR vibrational echo chemical exchange spectroscopy. J. Phys. Chem. B 112:10221–27 [Google Scholar]
  25. Maekawa H, Ge N-H. 25.  2012. Picosecond rotational interconversion adjacent to a C=O bond studied by two-dimensional infrared spectroscopy. J. Phys. Chem. B 116:11292–301 [Google Scholar]
  26. Corcelli SA, Lawrence CP, Asbury JB, Steinel T, Fayer MD, Skinner JL. 26.  2004. Spectral diffusion in a fluctuating charge model of water. J. Chem. Phys. 121:8897–900 [Google Scholar]
  27. Ernst RR, Bodenhausen G, Wokaun A. 27.  1987. Principles of Nuclear Magnetic Resonance in One and Two Dimensions New York: Oxford Univ. Press
  28. Gruebele M, Wolynes PG. 28.  2004. Vibrational energy flow and chemical reactions. Acc. Chem. Res. 37:261–67 [Google Scholar]
  29. Stratt RM. 29.  2008. Chemistry: nonlinear thinking about molecular energy transfer. Science 321:1789–90 [Google Scholar]
  30. Nitzan A. 30.  2007. Molecules take the heat. Science 317:759–60 [Google Scholar]
  31. Leitner DM. 31.  2005. Heat transport in molecules and reaction kinetics: the role of quantum energy flow and localization. Adv. Chem. Phys. 130:205–56 [Google Scholar]
  32. Mukamel S. 32.  1979. Non-Markovian theory of molecular relaxation. I. Vibrational relaxation and dephasing in condensed phases. Chem. Phys. 37:33–47 [Google Scholar]
  33. Naraharisetty SG, Kasyanenko VM, Rubtsov IV. 33.  2008. Bond connectivity measured via relaxation-assisted two-dimensional infrared spectroscopy. J. Chem. Phys. 128:104502 [Google Scholar]
  34. Kasyanenko VM, Lin Z, Rubtsov GI, Donahue JP, Rubtsov IV. 34.  2009. Energy transport via coordination bonds. J. Chem. Phys. 131:154508 [Google Scholar]
  35. Lim M, Hamm P, Hochstrasser RM. 35.  1998. Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes. Proc. Natl. Acad. Sci. USA 95:15315–20 [Google Scholar]
  36. Woutersen S, Mu Y, Stock G, Hamm P. 36.  2001. Subpicosecond conformational dynamics of small peptides probed by two-dimensional vibrational spectroscopy. Proc. Natl. Acad. Sci. USA 98:11254–58 [Google Scholar]
  37. Rubtsov IV, Hochstrasser RM. 37.  2002. Vibrational dynamics, mode coupling and structure constraints for acetylproline-NH2. J. Phys. Chem. B 106:9165–71 [Google Scholar]
  38. Leger J, Nyby C, Varner C, Tang J, Rubtsova NI. 38.  et al. 2014. Fully automated dual-frequency three-pulse-echo 2DIR spectrometer accessing spectral range from 800 to 4000 wavenumbers. Rev. Sci. Instrum. 85:083109 [Google Scholar]
  39. Burin AL, Tesar SL, Kasyanenko VM, Rubtsov IV, Rubtsov GI. 39.  2010. Semiclassical model for vibrational dynamics of polyatomic molecules: investigation of internal vibrational relaxation. J. Phys. Chem. C 114:20510–17 [Google Scholar]
  40. Kurochkin DV, Naraharisetty SG, Rubtsov IV. 40.  2007. Relaxation-assisted 2DIR spectroscopy method. Proc. Natl. Acad. Sci. USA 104:14209–14 [Google Scholar]
  41. Kurochkin DV, Naraharisetty SG, Rubtsov IV. 41.  2007. Relaxation-assisted 2D IR using weak vibrational modes. Ultrafast Phenomena XV P Corkum, DM Jonas, RJD Miller, AM Weiner 344–46 New York: Springer [Google Scholar]
  42. Jiji LM. 42.  2009. Heat Conduction New York: Springer418
  43. Kasyanenko VM, Keiffer P, Rubtsov IV. 43.  2012. Intramolecular contribution to temperature dependence of vibrational modes frequencies. J. Chem. Phys. 136:144503 [Google Scholar]
  44. Lin Z, Rubtsov IV. 44.  2012. Constant-speed vibrational signaling along polyethyleneglycol chain up to 60-Å distance. Proc. Natl. Acad. Sci. USA 109:1413–18 [Google Scholar]
  45. Lin Z, Zhang N, Jayawickramarajah J, Rubtsov IV. 45.  2012. Ballistic energy transport along PEG chains: distance dependence of the transport efficiency. Phys. Chem. Chem. Phys. 30:10445–54 [Google Scholar]
  46. Barone V. 46.  2005. Anharmionic vibrational properties by a fully automated second-order pertubative approach. J. Chem. Phys. 122:014108 [Google Scholar]
  47. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA. 47.  et al. 2009. Gaussian 09, Revision A.02 Gaussian, Inc., Wallingford, CT
  48. Kasyanenko VM, Tesar SL, Rubtsov GI, Burin AL, Rubtsov IV. 48.  2011. Structure dependent energy transport: relaxation-assisted 2DIR and theoretical studies. J. Phys. Chem. B 115:11063–73 [Google Scholar]
  49. Keating CS, McClure BA, Rack JJ, Rubtsov IV. 49.  2010. Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy. J. Chem. Phys. 133:144513 [Google Scholar]
  50. Keating CS, McClure BA, Rack JJ, Rubtsov IV. 50.  2010. Mode coupling pattern changes drastically upon photoisomerization in Ru II complex. J. Phys. Chem. C 114:16740–45 [Google Scholar]
  51. Naraharisetty SRG, Kasyanenko VM, Zimmermann J, Thielges MC, Romesberg FE, Rubtsov IV. 51.  2009. C-D modes of deuterated side chain of leucine as structural reporters via dual-frequency two-dimensional infrared spectroscopy. J. Phys. Chem. B 113:4940–46 [Google Scholar]
  52. Lin Z, Keiffer P, Rubtsov IV. 52.  2011. A method for determining small anharmonicity values from 2DIR spectra using thermally induced shifts of frequencies of high-frequency modes. J. Phys. Chem. B 115:5347–53 [Google Scholar]
  53. Rubtsov IV. 53.  2009. Relaxation-assisted 2DIR: accessing distances over 10Å and measuring bond connectivity patterns. Acc. Chem. Res. 42:1385–94 [Google Scholar]
  54. Krimm S, Bandekar J. 54.  1986. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv. Protein Chem. 38:181–364 [Google Scholar]
  55. Torii H, Tasumi M. 55.  1992. Model calculations on the amide I infrared bands of globular proteins. J. Chem. Phys. 96:3379–87 [Google Scholar]
  56. Kim YS, Liu L, Axelsen PH, Hochstrasser RM. 56.  2008. Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Aβ40. Proc. Natl. Acad. Sci. USA 105:7720–25 [Google Scholar]
  57. Schade M, Moretto A, Donaldson PM, Toniolo C, Hamm P. 57.  2010. Vibrational energy transport through a capping layer of appropriately designed peptide helices over gold nanoparticles. Nano Lett. 10:3057–61 [Google Scholar]
  58. Botan V, Backus EHG, Pfister R, Moretto A, Crisma M. 58.  et al. 2007. Energy transport in peptide helices. Proc. Natl. Acad. Sci. USA 104:12749–54 [Google Scholar]
  59. Sengupta N, Maekawa H, Zhuang W, Toniolo C, Mukamel S. 59.  et al. 2009. Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide. J. Phys. Chem. B 113:12037–49 [Google Scholar]
  60. Tesar SL, Kasyanenko VM, Rubtsov IV, Rubtsov GI, Burin AL. 60.  2013. Theoretical study of internal vibrational relaxation and energy transport in polyatomic molecules. J. Phys. Chem. A 117:315–23 [Google Scholar]
  61. Müller-Werkmeister HM, Li Y-L, Lerch E-BW, Bigourd D, Bredenbeck J. 61.  2013. Ultrafast hopping from band to band: assigning infrared spectra based on vibrational energy transfer. Angew. Chem. Int. Ed. Engl. 52:6214–17 [Google Scholar]
  62. Backus EHG, Nguyen PH, Botan V, Pfister R, Moretto A. 62.  et al. 2008. Energy transport in peptide helices: a comparison between high- and low-energy excitation. J. Phys. Chem. 112:9091–99 [Google Scholar]
  63. Lin Z, Bendiak B, Rubtsov IV. 63.  2012. Discrimination between coupling networks of glucopyranosides varying at a single stereocenter using two-dimensional vibrational correlation spectroscopy. Phys. Chem. Chem. Phys. 14:6179–91 [Google Scholar]
  64. Golonzka O, Khalil M, Demirdöven N, Tokmakoff A. 64.  2001. Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibrational echo spectroscopy. J. Chem. Phys. 115:10814–28 [Google Scholar]
  65. Hochstrasser RM. 65.  2001. Two-dimensional IR-spectroscopy: polarization anisotropy effects. Chem. Phys. 266:273–84 [Google Scholar]
  66. Bredenbeck J, Helbing J, Hamm P. 66.  2004. Transient two-dimensional infrared spectroscopy: exploring the polarization dependence. J. Chem. Phys. 121:5943–57 [Google Scholar]
  67. Qian W, Jonas DM. 67.  2003. Role of cyclic sets of transition dipoles in the pump-probe polarization anisotropy: application to square symmetric molecules and perpendicular chromophore pairs. J. Chem. Phys. 119:1611–22 [Google Scholar]
  68. Rubtsov IV, Khudiakov DV, Nadtochenko VA, Lobach AS, Moravskii AP. 68.  1994. Rotational reorientation dynamics of C60 in various solvents: picosecond transient grating dynamics. Chem. Phys. Lett. 229:517–23 [Google Scholar]
  69. Yu X, Leitner DM. 69.  2003. Vibrational energy transfer and heat conduction in a protein. J. Phys. Chem. B 107:1698–707 [Google Scholar]
  70. Davydov AS. 70.  1985. Solitons in Molecular Systems Dordrecht: Kluwer Acad.
  71. Onsager L. 71.  1936. Electric moments of molecules in liquids. J. Am. Chem. Soc. 58:1486–93 [Google Scholar]
  72. Buckingham AD. 72.  1958. Solvent effects in infra-red spectroscopy. Proc. R. Soc. Lond. A 248:169–82 [Google Scholar]
  73. Amunson KE, Kubelka J. 73.  2007. On the temperature dependence of amide I frequencies of peptides in solution. J. Phys. Chem. 111:9993–98 [Google Scholar]
  74. Manas ES, Getahum Z, Wright WW, DeGrado WF, Vanderkooi JM. 74.  2000. Infrared spectra of amide groups in α-helical proteins: evidence for hydrogen bonding between helices and water. J. Am. Chem. Soc. 122:9883–90 [Google Scholar]
  75. Nucci NV, Scott JN, Vanderkooi JM. 75.  2008. Coupling of complex aromatic ring vibrations to solvent through hydrogen bonds: effect of varied on-ring and off-ring hydrogen-bonding substitution. J. Phys. Chem. B 112:4022–35 [Google Scholar]
  76. Fecko CJ, Eaves JD, Loparo JJ, Tokmakoff A, Geissler PL. 76.  2003. Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water. Science 301:1698–702 [Google Scholar]
  77. Tayama J, Ishihara A, Banno M, Ohta K, Saito S, Tominaga K. 77.  2010. Temperature dependence of vibrational frequency fluctuation of N3 in D2O. J. Chem. Phys. 133:014505 [Google Scholar]
  78. Maienschein-Cline MG, Londergan CH. 78.  2007. The CN stretching band of aliphatic thiocyanate is sensitive to solvent dynamics and specific solvation. J. Phys. Chem. Lett. 111:10020–25 [Google Scholar]
  79. Bian H, Wen X, Li J, Zheng J. 79.  2010. Mode-specific intermolecular vibrational energy transfer. II. Deuterated water and potassium selenocyanate mixture. J. Chem. Phys. 133:034505 [Google Scholar]
  80. Elsaesser T, Kaiser W. 80.  1991. Vibrational and vibronic relaxation of large polyatomic molecules in liquids. Annu. Rev. Phys. Chem. 42:83–107 [Google Scholar]
  81. Lian T, Locke B, Kholodenko Y, Hochstrasser RM. 81.  1994. Energy flow from solute to solvent probed by femtosecond IR spectroscopy: malachite green and heme protein solutions. J. Phys. Chem. 98:11648–56 [Google Scholar]
  82. Ashihara S, Huse N, Espagne A, Nibbering ETJ, Elsaesser T. 82.  2007. Ultrafast structural dynamics of water induced by dissipation of vibrational energy. J. Phys. Chem. A 111:743–46 [Google Scholar]
  83. Deàk JC, Iwaki LK, Rhea ST. 83.  2000. Ultrafast infrared–Raman studies of vibrational energy redistribution in polyatomic liquids. J. Raman Spectrosc. 31:263–74 [Google Scholar]
  84. Wang Z, Pakoulev A, Dlott DD. 84.  2002. Watching vibrational energy transfer in liquids with atomic spatial resolution. Science 296:2201–3 [Google Scholar]
  85. Pang Y, Deàk JC, Huang W, Lagutchev A, Pakoulev A. 85.  et al. 2007. Vibrational energy in molecules probed with high time and space resolution. Int. Rev. Phys. Chem. 26:223–48 [Google Scholar]
  86. Wang J-S, Wang J, Lu JT. 86.  2008. Quantum thermal transport in nanostructures. Eur. Phys. J. B 62:381–404 [Google Scholar]
  87. Maultzsch J, Reich S, Thomsen C, Dobardzic E, Milosevic I, Damnjanovic M. 87.  2002. Phonon dispersion of carbon nanotubes. Solid State Commun. 121:471–74 [Google Scholar]
  88. Segal D, Nitzan A, Hanggi P. 88.  2003. Thermal conductance through molecular wires. J. Chem. Phys. 119:6840–55 [Google Scholar]
  89. Schroder C, Vikhrenko V, Schwarzer D. 89.  2009. Molecular dynamics simulation of heat conduction through a molecular chain. J. Phys. Chem. A 113:14039–51 [Google Scholar]
  90. Benderskii VA, Kats EI. 90.  2011. Propagating vibrational excitations in molecular chains. JETP Lett. 94:459–64 [Google Scholar]
  91. Bloem R, Dijkstra AG, Jansen TL, Knoester J. 91.  2008. Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution. J. Chem. Phys. 129:055101 [Google Scholar]
  92. Schade M, Moretto A, Crisma M, Toniolo C, Hamm P. 92.  2009. Vibrational energy transport in peptide helices after excitation of C–D modes in Leu-d10. J. Phys. Chem. B 113:13393–97 [Google Scholar]
  93. Wang Z, Carter JA, Lagutchev A, Koh YK, Seong N-H. 93.  et al. 2007. Ultrafast flash thermal conductance of molecular chains. Science 317:787–90 [Google Scholar]
  94. Yu C, Shi L, Yao Z, Li D, Majumdar A. 94.  2005. Thermal conductance and thermopower of an individual single-wall carbon nanotube. Nano Lett. 5:1842–46 [Google Scholar]
  95. Schwarzer D, Hanisch C, Kutne P, Troe J. 95.  2002. Vibrational energy transfer in highly excited bridged azulene-aryl compounds: direct observation of energy flow through aliphatic chains and into the solvent. J. Phys. Chem. A 106:8019–28 [Google Scholar]
  96. Backus EHG, Bloem R, Pfister R, Moretto A, Crisma M. 96.  et al. 2009. Dynamical transition in a small helical peptide and its implication for vibrational energy transport. J. Phys. Chem. B 113:13405–9 [Google Scholar]
  97. Cahill DG, Ford WK, Goodson KE, Mahan GD, Majumdar A. 97.  et al. 2003. Nanoscale thermal transport. J. Appl. Phys. 93:793–818 [Google Scholar]
  98. Schwarzer D, Kutne P, Schroeder C, Troe J. 98.  2004. Intramolecular vibrational energy redistribution in bridged azulene-anthracene compounds: ballistic energy transport through molecular chains. J. Chem. Phys. 121:1754–64 [Google Scholar]
  99. Lin Z, Rubtsova NI, Kireev VV, Rubtsov IV. 99.  2013. Ballistic energy transport in PEG oligomers. EPJ Web Conf. 41:05039 [Google Scholar]
  100. Watkins EK, Jorgensen WL. 100.  2001. Perfluoroalkanes: conformational analysis and liquid-state properties from ab initio and Monte Carlo calculations. J. Phys. Chem. A 105:4118–25 [Google Scholar]
  101. Rubtsova NI, Rubtsov IV. 101.  2013. Ballistic energy transport via perfluoroalkane linker. Chem. Phys. 422:16–21 [Google Scholar]
  102. Rubtsova NI, Kurnosov AA, Burin AL, Rubtsov IV. 102.  2014. Temperature dependence of the ballistic energy transport in perfluoroalkanes. J. Phys. Chem. B 118:8381–87 [Google Scholar]
  103. Glowacki DR, Rose RA, Greaves SJ, Orr-Ewing AJ, Harvey JN. 103.  2011. Ultrafast energy flow in the wake of solution-phase bimolecular reactions. Nat. Chem. 3:850–55 [Google Scholar]
  104. Lin Z, Lawrence CM, Xiao D, Kireev VV, Skourtis SS. 104.  et al. 2009. Modulating unimolecular charge transfer by exciting bridge vibrations. J. Am. Chem. Soc. 131:18060–62 [Google Scholar]

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error