75. Rubtsova NI, Rubtsov IV (2015) Vibrational energy transport in molecules studied by relaxationassisted two-dimensional infrared spectroscopy. Annu Rev Phys Chem 66:717–738. doi:10.1146/
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76. Golonzka O, Khalil M, Demirdo ¨ven N, Tokmakoff A (2001) Coupling and orientation between
anharmonic vibrations characterized with two-dimensional infrared vibration echo spectroscopy.
J Chem Phys 115:10814–10828. doi:10.1063/1.1417504
77. Woutersen S, Mu Y, Stock G, Hamm P (2001) Subpicosecond conformational dynamics of small
peptides probed by two-dimensional vibrational spectroscopy. Proc Natl Acad Sci USA
98:11254–11258. doi:10.1073/pnas.201169498
78. Zanni MT, Ge NH, Kim YS, Hochstrasser RM (2001) Two-dimensional IR spectroscopy can be
designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure
determination. Proc Natl Acad Sci USA 98:11265–11270. doi:10.1073/pnas.201412998
79. Krummel AT, Mukherjee P, Zanni MT (2003) Inter and intrastrand vibrational coupling in DNA
studied with heterodyned 2D-IR spectroscopy. J Phys Chem B 107:9165–9169. doi:10.1021/
jp035473h
80. Buchanan LE, Dunkelberger EB, Zanni MT (2012) Examining amyloid structure and kinetics with
1D and 2D infrared spectroscopy and isotope labeling BT - protein folding and misfolding: shining
light by infrared spectroscopy. In: Fabian H, Naumann D (eds) Protein fold. Misfolding. Springer,
Berlin, pp 217–237
81. Buchanan LE, Carr JK, Fluitt AM et al (2014) Structural motif of polyglutamine amyloid fibrils
discerned with mixed-isotope infrared spectroscopy. Proc Natl Acad Sci 111:5796–5801. doi:10.
1073/pnas.1401587111
82. Moran A, Mukamel S (2004) The origin of vibrational mode couplings in various secondary
structural motifs of polypeptides. Proc Natl Acad Sci USA 101:506–510. doi:10.1073/pnas.
2533089100
83. Bereau T, Meuwly M (2014) Computational Two-Dimensional Infrared Spectroscopy without
Maps: N-Methylacetamide in Water. J Phys Chem B 118:8135-8147. doi: 10.1021/jp5011692
84. Woutersen S, Hamm P (2000) Structure determination of trialanine in water using polarization
sensitive two-dimensional vibrational spectroscopy. J Phys Chem B 104:11316–11320. doi:10.
1021/jp001546a
85. Krummel AT, Zanni MT (2006) DNA Vibrational Coupling Revealed with Two-Dimensional
Infrared Spectroscopy : Insight into Why Vibrational Spectroscopy Is Sensitive to DNA Structure.
J Phys Chem B 110:13991–14000. doi: 10.1021/jp062597w
86. Baiz CR, Reppert M, Tokmakoff A (2013) Introduction to protein 2D IR spectroscopy. In: Fayer
MD (ed) Ultrafast infrared Vib. Spectrosc. CRC Press/Taylor & Francis Group, Boca Raton/New
York, pp 361–405
87. Baiz CR, Peng CS, Reppert ME et al (2012) Coherent two-dimensional infrared spectroscopy:
quantitative analysis of protein secondary structure in solution. Analyst 137:1793–1799. doi:10.
1039/c2an16031e
88. Waegele MM, Culik RM, Gai F (2011) Site-specific spectroscopic reporters of the local electric
field, hydration, structure, and dynamics of biomolecules. J Phys Chem Lett 2:2598–2609. doi:10.
1021/jz201161b
89. Kim H, Cho M (2013) Infrared probes for studying the structure and dynamics of biomolecules.
Chem Rev 113:5817–5847. doi:10.1021/cr3005185
90. Buchanan LE, Dunkelberger EB, Tran HQ et al (2013) Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient beta-sheet. Proc Natl Acad Sci USA
110:19285–19290. doi:10.1073/pnas.1314481110
91. Strasfeld DB, Ling YL, Shim S-H, Zanni MT (2008) Tracking fiber formation in human islet
amyloid polypeptide with automated 2D-IR spectroscopy. J Am Chem Soc 130:6698–6699. doi:10.
1021/ja801483n
92. Shim S-H, Gupta R, Ling YL et al (2009) Two-dimensional IR spectroscopy and isotope labeling
defines the pathway of amyloid formation with residue-specific resolution. Proc Natl Acad Sci
106:6614–6619. doi:10.1073/pnas.0805957106
93. Middleton CT, Marek P, Cao P et al (2012) Two-dimensional infrared spectroscopy reveals the
complex behaviour of an amyloid fibril inhibitor. Nat Chem 4:355–360. doi:10.1038/nchem.1293
94. Moran SD, Woys AM, Buchanan LE et al (2012) Two-dimensional IR spectroscopy and segmental
13C labeling reveals the domain structure of human D-crystallin amyloid fibrils. Proc Natl Acad Sci
109:3329–3334. doi:10.1073/pnas.1117704109
Top Curr Chem (Z) (2017) 375:86
123
192
Reprinted from the journal
annurev-physchem-040214-121337
76. Golonzka O, Khalil M, Demirdo ¨ven N, Tokmakoff A (2001) Coupling and orientation between
anharmonic vibrations characterized with two-dimensional infrared vibration echo spectroscopy.
J Chem Phys 115:10814–10828. doi:10.1063/1.1417504
77. Woutersen S, Mu Y, Stock G, Hamm P (2001) Subpicosecond conformational dynamics of small
peptides probed by two-dimensional vibrational spectroscopy. Proc Natl Acad Sci USA
98:11254–11258. doi:10.1073/pnas.201169498
78. Zanni MT, Ge NH, Kim YS, Hochstrasser RM (2001) Two-dimensional IR spectroscopy can be
designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure
determination. Proc Natl Acad Sci USA 98:11265–11270. doi:10.1073/pnas.201412998
79. Krummel AT, Mukherjee P, Zanni MT (2003) Inter and intrastrand vibrational coupling in DNA
studied with heterodyned 2D-IR spectroscopy. J Phys Chem B 107:9165–9169. doi:10.1021/
jp035473h
80. Buchanan LE, Dunkelberger EB, Zanni MT (2012) Examining amyloid structure and kinetics with
1D and 2D infrared spectroscopy and isotope labeling BT - protein folding and misfolding: shining
light by infrared spectroscopy. In: Fabian H, Naumann D (eds) Protein fold. Misfolding. Springer,
Berlin, pp 217–237
81. Buchanan LE, Carr JK, Fluitt AM et al (2014) Structural motif of polyglutamine amyloid fibrils
discerned with mixed-isotope infrared spectroscopy. Proc Natl Acad Sci 111:5796–5801. doi:10.
1073/pnas.1401587111
82. Moran A, Mukamel S (2004) The origin of vibrational mode couplings in various secondary
structural motifs of polypeptides. Proc Natl Acad Sci USA 101:506–510. doi:10.1073/pnas.
2533089100
83. Bereau T, Meuwly M (2014) Computational Two-Dimensional Infrared Spectroscopy without
Maps: N-Methylacetamide in Water. J Phys Chem B 118:8135-8147. doi: 10.1021/jp5011692
84. Woutersen S, Hamm P (2000) Structure determination of trialanine in water using polarization
sensitive two-dimensional vibrational spectroscopy. J Phys Chem B 104:11316–11320. doi:10.
1021/jp001546a
85. Krummel AT, Zanni MT (2006) DNA Vibrational Coupling Revealed with Two-Dimensional
Infrared Spectroscopy : Insight into Why Vibrational Spectroscopy Is Sensitive to DNA Structure.
J Phys Chem B 110:13991–14000. doi: 10.1021/jp062597w
86. Baiz CR, Reppert M, Tokmakoff A (2013) Introduction to protein 2D IR spectroscopy. In: Fayer
MD (ed) Ultrafast infrared Vib. Spectrosc. CRC Press/Taylor & Francis Group, Boca Raton/New
York, pp 361–405
87. Baiz CR, Peng CS, Reppert ME et al (2012) Coherent two-dimensional infrared spectroscopy:
quantitative analysis of protein secondary structure in solution. Analyst 137:1793–1799. doi:10.
1039/c2an16031e
88. Waegele MM, Culik RM, Gai F (2011) Site-specific spectroscopic reporters of the local electric
field, hydration, structure, and dynamics of biomolecules. J Phys Chem Lett 2:2598–2609. doi:10.
1021/jz201161b
89. Kim H, Cho M (2013) Infrared probes for studying the structure and dynamics of biomolecules.
Chem Rev 113:5817–5847. doi:10.1021/cr3005185
90. Buchanan LE, Dunkelberger EB, Tran HQ et al (2013) Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient beta-sheet. Proc Natl Acad Sci USA
110:19285–19290. doi:10.1073/pnas.1314481110
91. Strasfeld DB, Ling YL, Shim S-H, Zanni MT (2008) Tracking fiber formation in human islet
amyloid polypeptide with automated 2D-IR spectroscopy. J Am Chem Soc 130:6698–6699. doi:10.
1021/ja801483n
92. Shim S-H, Gupta R, Ling YL et al (2009) Two-dimensional IR spectroscopy and isotope labeling
defines the pathway of amyloid formation with residue-specific resolution. Proc Natl Acad Sci
106:6614–6619. doi:10.1073/pnas.0805957106
93. Middleton CT, Marek P, Cao P et al (2012) Two-dimensional infrared spectroscopy reveals the
complex behaviour of an amyloid fibril inhibitor. Nat Chem 4:355–360. doi:10.1038/nchem.1293
94. Moran SD, Woys AM, Buchanan LE et al (2012) Two-dimensional IR spectroscopy and segmental
13C labeling reveals the domain structure of human D-crystallin amyloid fibrils. Proc Natl Acad Sci
109:3329–3334. doi:10.1073/pnas.1117704109
Top Curr Chem (Z) (2017) 375:86
123
192
Reprinted from the journal