Theoretical Sum Frequency Generation Spectroscopy of Peptides

Journal of Physical Chemistry B

Volumn 119, Issue 29, 2015, Pages 8969-8983

  Carr, Joshua K ^a   Wang, Lu ^a   Roy, Santanu ^a   Skinner, James L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOPHORES; INTERFEROMETRY; MOLECULAR DYNAMICS; PEPTIDES; POLARIZATION; STEREOCHEMISTRY;

ANTIMICROBIAL PEPTIDE; CHIRAL MOLECULE; COUPLING EFFECT; MOLECULAR DYNAMICS SIMULATIONS; PROTEIN SECONDARY STRUCTURE; SUM-FREQUENCY GENERATION SPECTROSCOPY; THEORETICAL SPECTRA; VIBRATIONAL SUM-FREQUENCY GENERATIONS;

PROTEINS;

ACETAMIDE DERIVATIVE; CARBON; GRAMICIDIN; HYDROGEN; N-METHYLACETAMIDE; NITROGEN; OXYGEN; PEPTIDE;

CHEMICAL MODEL; CHEMISTRY; MOLECULAR DYNAMICS; PROCEDURES; PROTEIN SECONDARY STRUCTURE; SPECTROSCOPY; VALIDATION STUDY; VIBRATION;

ACETAMIDES; CARBON; GRAMICIDIN; HYDROGEN; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; NITROGEN; OXYGEN; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SPECTRUM ANALYSIS; VIBRATION;

EID: 84937872392     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp507861t     Document Type: Article

References (132)

1. Brogden, K. A. Antimicrobial Peptides: Pore Formers or Metabolic Inhibitors in Bacteria? Nat. Rev. Microbiol. 2005, 3, 238-250
2. Mátyus, E.; Kandt, C.; Tieleman, D. P. Computer Simulation of Antimicrobial Peptides Curr. Med. Chem. 2007, 14, 2789-2798
3. Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry; W. H. Freeman and Co.: New York, 2005.
4. Clark, A.; Cooper, G. J. S.; Lewis, C. E.; Morris, J. F.; Willis, A. C.; Reid, K. B. M.; Turner, R. C. Islet amyloid formed from diabetes-associated peptide may be pathogenic in type-2 diabetes Lancet 1987, 2, 231-234
5. Lorenzo, A.; Razzaboni, B.; Weir, G. C.; Yankner, B. A. Pancreatic Islet Cell Toxicity of Amylin Associated with Type-2 Diabetes Mellitus Nature 1994, 368, 756-760
6. Chiti, F.; Dobson, C. M. Protein Misfolding, Functional Amyloid, and Human Disease Annu. Rev. Biochem. 2006, 75, 333-366
7. MacKenzie, K. R.; Pretegard, J. H.; Engelman, D. M. A Transmembrane Helix Dimer: Structure and Implications Science 1997, 276, 131-133
8. Cady, S. D.; Schmidt-Rohr, K.; Wang, J.; Soto, C. S.; DeGrado, W. F.; Hong, M. Structure of the Amantadine Binding Site of Influenza M2 Proton Channels in Lipid Bilayers Nature 2010, 463, 689-692
9. Hubbell, W. L.; Cafiso, D. S.; Altenbach, C. Identifying Conformational Changes with Site-Directed Spin Labeling Nat. Struct. Biol. 2000, 7, 735-739
10. Perozo, E.; Kloda, A.; Cortes, D. M.; Martinac, B. Physical Principles Underlying the Transduction of Bilayer Deformation Forces During Mechanosensitive Channel Gating Nat. Struct. Biol. 2002, 9, 696-703
11. Woys, A. M.; Lin, Y.-S.; Reddy, A. S.; Xiong, W.; de Pablo, J. J.; Skinner, J. L.; Zanni, M. T. 2D IR Line Shapes Probe Ovispirin Peptide Conformation and Depth in Lipid Bilayers J. Am. Chem. Soc. 2010, 132, 2832-2838
12. Ling, Y. L.; Strasfeld, D. B.; Shim, S.-H.; Raleigh, D. P.; Zanni, M. T. Two-Dimensional Infrared Spectroscopy Provides Evidence of an Intermediate in the Membrane-Catalyzed Assembly of Diabetic Amyloid J. Phys. Chem. B 2009, 113, 2498-2505
13. Middleton, C. T.; Buchanan, L. E.; Dunkelberger, E. B.; Zanni, M. T. Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides J. Phys. Chem. Lett. 2011, 2, 2357-2361
14. Axelsen, P. H.; Kaufman, B. K.; McElhaney, R. N.; Lewis, R. N. A. H. The Infrared Dichroism of Transmembrane Helical Polypeptides Biophys. J. 1995, 69, 2770-2781
15. Bechinger, B.; Ruysschaert, J.-M.; Goormaghtigh, E. Membrane Helix Orientation from Linear Dichroism of Infrared Attenuated Total Reflection Spectra Biophys. J. 1999, 76, 552-563
16. Marsh, D.; Müller, M.; Schmitt, F. Orientation of the Infrared Transition Moments for an α-Helix Biophys. J. 2000, 78, 2499-2510
17. Chen, X.; Wang, J.; Sniadecki, J. J.; Even, M. A.; Chen, Z. Probing α-Helical and β-Sheet Structures of Peptides at Solid/Liquid Interfaces with SFG Langmuir 2005, 21, 2662-2664
18. Nguyen, K. T.; King, J. T.; Chen, Z. Orientation Determination of Interfacial β-Sheet Structures in Situ J. Phys. Chem. B 2010, 114, 8291-8300
19. Ye, S.; Nguyen, K. T.; Chen, Z. Interactions of Alamethicin with Model Cell Membranes Investigated Using Sum Frequency Generation Vibrational Spectroscopy in Real Time in Situ J. Phys. Chem. B 2010, 114, 3334-3340
20. Shen, Y. R. Surface Properties Probed by Second-Harmonic and Sum-Frequency Generation Nature 1989, 337, 519-525
21. Du, Q.; Superfine, R.; Freysz, E.; Shen, Y. R. Vibrational Spectroscopy of Water at the Vapor/Water Interface Phys. Rev. Lett. 1993, 70, 2313-2316
22. Du, Q.; Freysz, E.; Shen, Y. R. Surface Vibrational Spectroscopic Studies of Hydrogen Bonding and Hydrophobicity Science 1994, 264, 826-828
23. Eisenthal, K. B. Liquid Interfaces Probed by Second-Harmonic and Sum-Frequency Spectroscopy Chem. Rev. 1996, 96, 1343-1360
24. Chen, X.; Chen, Z. SFG Studies on Interactions Between Antimicrobial Peptides and Supported Lipid Bilayers Biochim. Biophys. Acta 2006, 1758, 1257-1273
25. Sovago, M.; Campen, R. K.; Wurpel, G. W. H.; Müller, M.; Bakker, H. J.; Bonn, M. Vibrational Response of Hydrogen-Bonded Interfacial Water is Dominated by Intramolecular Coupling Phys. Rev. Lett. 2008, 100, 173901-1-173901-4
26. Jungwirth, P.; Winter, B. Ions at Aqueous Interfaces: From Water Surface to Hydrated Proteins Annu. Rev. Phys. Chem. 2008, 59, 343-366
27. Ye, S.; Nguyen, K. T.; Clair, S. V. L; Chen, Z. In Situ Molecular Level Studies on Membrane Related Peptides and Proteins in Real Time Using Sum Frequency Generation Vibrational Spectroscopy J. Struct. Biol. 2009, 168, 61-77
28. Bonn, M.; Campen, R. K. Optical Methods for the Study of Dynamics in Biological Membrane Models Surf. Sci. 2009, 603, 1945-1952
29. Weidner, T.; Apte, J. S.; Gamble, L. J.; Castner, D. G. Probing the Orientation and Conformation of α-Helix and β-Strand Model Peptides on Self-Assembled Monolayers Using Sum Frequency Generation and NEXAFS Spectroscopy Langmuir 2010, 26, 3433-3440
30. Boughton, A. P.; Andricioaei, I.; Chen, Z. Surface Orientation of Magainin 2: Molecular Dynamics Simulation and Sum Frequency Generation Vibrational Spectroscopic Studies Langmuir 2010, 26, 16031-16036
31. Fu, L.; Ma, G.; Yan, E. C. Y. In Situ Misfolding of Human Islet Amyloid Polypeptide at Interfaces Probed by Vibrational Sum Frequency Generation J. Am. Chem. Soc. 2010, 132, 5405-5412
32. Fu, L.; Liu, J.; Yan, E. C. Y. Chiral Sum Frequency Generation Spectroscopy for Characterizing Protein Secondary Structures at Interfaces J. Am. Chem. Soc. 2011, 133, 8094-8097
33. Fu, L.; Wang, Z.; Yan, E. C. Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy Int. J. Mol. Sci. 2011, 12, 9404-9425
34. Boughton, A. P.; Nguyen, K.; Andricioaei, I.; Chen, Z. Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies Langmuir 2011, 27, 14343-14351
35. Liu, Y.; Jasensky, J.; Chen, Z. Molecular Interactions of Proteins and Peptides at Interfaces Studied by Sum Frequency Generation Vibrational Spectroscopy Langmuir 2012, 28, 2113-2121
36. Yang, P.; Homan, A. B. K. T.; Tesmer, J. J. G.; Chen, Z. Membrane Orientation of Gαiβ1γ2 and Gβ1γ2 Determined Via Combined Vibrational Spectroscopic Studies J. Am. Chem. Soc. 2013, 135, 5044-5051
37. Liu, Y.; Ogorzalek, T. L.; Yang, P.; Schroeder, M. M.; Marsh, E. N. G.; Chen, Z. Molecular Orientation of Enzymes Attached to Surfaces Through Defined Chemical Linkages at the Solid-Liquid Interface J. Am. Chem. Soc. 2013, 135, 12660-12669
38. Lee, C. M.; Mohamed, N. M. A.; Watts, H. D.; Kubicki, J. D.; Kim, S. H. Sum-Frequency-Generation Vibration Spectroscopy and Density Functional Theory Calculations with Dispersion Corrections (DFT-D2) for Cellulose Iα and Iβ J. Phys. Chem. B 2013, 117, 6681-6692
39. Chen, X.; Wang, J.; Boughton, A. P.; Kristalyn, C. B.; Chen, Z. Multiple Orientation of Melittin Inside a Single Lipid Bilayer Determined by Combined Vibrational Spectroscopic Studies J. Am. Chem. Soc. 2007, 129, 1420-1427
40. Chen, X.; Boughton, A. P.; Tesmer, J. J. G.; Chen, Z. In Situ Investigation of Heterotrimeric G Protein βγ Subunit Binding and Orientation on Membrane Bilayers J. Am. Chem. Soc. 2007, 129, 12658-12659
41. Ye, S.; Li, H.; Wei, F.; Jasensky, J.; Boughton, A. P.; Yang, P.; Chen, Z. Observing a Model Ion Channel Gating Action in Model Cell Membranes in Real Time in Situ: Membrane Potential Change Induced Alamethicin Orientation Change J. Am. Chem. Soc. 2012, 134, 6237-6243
42. Wei, F.; Ye, S.; Li, H.; Luo, Y. Phosphate Ions Promoting Association Between Peptide and Modeling Cell Membrane Revealed by Sum Frequency Generation Vibrational Spectroscopy J. Phys. Chem. C 2013, 117, 11095-11103
43. Fu, L.; Xiao, D.; Wang, Z.; Batista, V. S.; Yan, E. C. Y. Chiral Sum Frequency Generation for in Situ Probing Proton Exchange in Antiparallel β-Sheets at Interfaces J. Am. Chem. Soc. 2013, 135, 3592-3598
44. Wang, Z.; Fu, L.; Yan, E. C. Y. C-H stretch for Probing Kinetics of Self-Assembly into Macromolecular Chiral Structures at Interfaces by Chiral Sum Frequency Generation Spectroscopy Langmuir 2013, 29, 4077-4083
45. Lin, Y.-S.; Shorb, J. M.; Mukherjee, P.; Zanni, M. T.; Skinner, J. L. Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles J. Phys. Chem. B 2009, 113, 592-602
46. Reddy, A. S.; Wang, L.; Lin, Y.-S.; Ling, Y.; Chopra, M.; Zanni, M. T.; Skinner, J. L.; de Pablo, J. J. Solution Structures of Rat Amylin Peptide: Simulation, Theory and Experiment Biophys. J. 2010, 98, 443-451
47. Reddy, A. S.; Wang, L.; Singh, S.; Ling, Y. L.; Buchanan, L.; Zanni, M. T.; Skinner, J. L.; de Pablo, J. J. Stable and Metastable States of Human Amylin in Solution Biophys. J. 2010, 99, 2208-2216
48. Wang, L.; Middleton, C. T.; Zanni, M. T.; Skinner, J. L. Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides J. Phys. Chem. B 2011, 115, 3713-3724
49. Wang, L.; Middleton, C. T.; Singh, S.; Reddy, A. S.; Woys, A. M.; Strasfeld, D. B.; Marek, P.; Raleigh, D. P.; de Pablo, J. J.; Zanni, M. T.; et al. 2DIR Spectroscopy of Human Amylin Fibrils Reflects Stable β-Sheet Structure J. Am. Chem. Soc. 2011, 133, 16062-16071
50. Middleton, C. T.; Marek, P.; Cao, P.; Chiu, C.; Singh, S.; Woys, A. M.; de Pablo, J. J.; Raleigh, D. P.; Zanni, M. T. Two-Dimensional Infrared Spectroscopy Reveals the Complex Behaviour of an Amyloid Fibril Inhibitor Nat. Chem. 2012, 4, 355-360
51. Wang, L.; Skinner, J. L. Thermally-Induced Protein Unfolding Probed by Isotope-Edited IR Spectroscopy J. Phys. Chem. B 2012, 116, 9627-9634
52. Clarke, M. L.; Wang, J.; Chen, Z. Conformational Changes of Fibrinogen After Adsorption J. Phys. Chem. B 2005, 109, 22027-22035
53. Shen, Y. R. The Principles of Nonlinear Optics; Wiley-Interscience: Hoboken, NJ, 2003.
54. Boyd, R. W. Nonlinear Optics, 2nd ed.; Academic Press: San Diego, 2003.
55. Hirose, C.; Akamatsu, N.; Domen, K. Formulas for the Analysis of the Surface SFG Spectrum and Transformation Coefficients of Cartesian SFG Tensor Components Appl. Spectrosc. 1992, 46, 1051-1072
56. Zhuang, X.; Miranda, P. B.; Kim, D.; Shen, Y. R. Mapping Molecular Orientation and Conformation at Interfaces by Surface Nonlinear Optics Phys. Rev. B 1999, 59, 12632-12640
57. Raymond, E. A.; Tarbuck, T. L.; Richmond, G. L. Isotopic Dilution Studies of the Vapor/Water Interface as Investigated by Vibrational Sum-Frequency Spectroscopy J. Phys. Chem. B 2002, 106, 2817-2820
58. Raymond, E. A.; Tarbuck, T. L.; Brown, M. G.; Richmond, G. L. Hydrogen Bonding Interactions at the Vapor/Water Interface Investigated by Vibrational Sum-Frequency Spectroscopy of HOD/H2O/D2O Mixtures and Molecular Dynamics Simulations J. Phys. Chem. B 2003, 107, 546-556
59. Wang, H.-F.; Gan, W.; Lu, R.; Rao, Y.; Wu, B.-H. Quantitative Spectral and Orientational Analysis in Surface Sum Frequency Generation Vibrational Spectroscopy (SFG-VS) Int. Rev. Phys. Chem. 2005, 24, 191-256
60. Nguyen, K. T.; Clair, S. V. L; Ye, S.; Chen, Z. Orientation Determination of Protein Helical Secondary Structures Using Linear and Nonlinear Vibrational Spectroscopy J. Phys. Chem. B 2009, 113, 12169-12180
61. Ye, S.; Li, H.; Yang, W.; Luo, Y. Accurate Determination of Interfacial Protein Secondary Structure by Combining Interfacial-Sensitive Amide I and Amide III Spectral Signals J. Am. Chem. Soc. 2014, 136, 1206-1209
62. Han, X.; Liu, Y.; Wu, F.-G.; Jansensky, J.; Kim, T.; Wang, Z.; C. L. Brooks, I.; Wu, J.; Xi, C.; Mello, C. M.; et al. Different Interfacial Behaviors of Peptides Chemically Immobilized on Surfaces with Different Linker Lengths and Via Different Termini J. Phys. Chem. B 2014, 118, 2904-2912
63. Giordmaine, J. A. Nonlinear Optical Properties of Liquids Phys. Rev. 1965, 138, A1599-A1606
64. Belkin, M. A.; Kulakov, T. A.; Ernst, J.-H.; Yan, L.; Shen, Y. R. Sum-Frequency Vibrational Spectroscopy on Chiral Liquids: A Novel Technique to Probe Molecular Chirality Phys. Rev. Lett. 2000, 85, 4474-4477
65. Wang, J.; Chen, X.; Clarke, M. L.; Chen, Z. Detection of Chiral Sum Frequency Generation Vibrational Spectra of Proteins and Peptides at Interfaces in Situ Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4978-4983
66. Xiao, D.; Fu, L.; Liu, J.; Batista, V. S.; Yan, E. C. Y. Amphiphilic Adsorption of Human Islet Amyloid Polypeptide Aggregates to Lipid/Aqueous Interfaces J. Mol. Biol. 2012, 421, 537-547
67. Perry, J. M.; Moad, A. J.; Begue, N. J.; Wampler, R. D.; Simpson, G. J. Electronic and Vibrational Second-Order Nonlinear Optical Properties of Protein Secondary Structural Motifs J. Phys. Chem. B 2005, 109, 20009-20026
68. Haupert, L. M.; Simpson, G. J. Chirality in Nonlinear Optics Annu. Rev. Phys. Chem. 2009, 60, 345-365
69. Weidner, T.; Breen, N. F.; Li, K.; Drobny, G. P.; Castner, D. G. Sum Frequency Generation and Solid-State NMR Study of the Structure, Orientation, and Dynamics of Polystyrene-Adsorbed Peptides Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 13288-13293
70. Ding, B.; Laaser, J. E.; Liu, Y.; Wang, P.; Zanni, M. T.; Chen, Z. Site-Specific Orientation of an α-Helical Peptide Ovispirin-1 from Isotope Labeled SFG Spectroscopy J. Phys. Chem. B 2013, 117, 14625-14634
71. Simpson, G. J. Molecular Origins of the Remarkable Chiral Sensitivity of Second-Order Nonlinear Optics ChemPhysChem 2004, 5, 1301-1310
72. Liang, C.; Louhivuori, M.; Marrink, S. J.; Jansen, T. L. C.; Knoester, J. Vibrational Spectra of a Mechanosensitive Channel J. Phys. Chem. Lett. 2013, 4, 448-452
73. Liang, C.; Jansen, T. L. C. Simulation of Two-Dimensional Sum-Frequency Generation Response Functions: Application to Amide I in Proteins J. Phys. Chem. B 2013, 117, 6937-6945
74. Roeters, S. J.; van Dijk, C. N.; Torres-Knoop, A.; Backus, E. H. G.; Campen, R. K.; Bonn, M.; Woutersen, S. Determining in Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment J. Phys. Chem. A 2013, 117, 6311-6322
75. Buchanan, L. E.; Carr, J. K.; Fluitt, A. M.; Hoganson, A. J.; Moran, S. D.; de Pablo, J. J.; Skinner, J. L.; Zanni, M. T. Structural Motif of Polyglutamine Amyloid Fibrils Discerned with Mixed-Isotope Infrared Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 5796-5801
76. Hull, S. E.; Karlsson, R.; Main, P.; Woolfson, M. M.; Dodson, E. J. The Crystal Structure of a Hydrated Gramicidin S-Urea Complex Nature 1978, 275, 206-207
77. Krauss, E. M.; Chan, S. I. Spectroscopic Studies of Intramolecular Hydrogen Bonding in Gramicidin S J. Am. Chem. Soc. 1982, 104, 1824-1830
78. Smith, A. W.; Tokmakoff, A.; Amide, I. Two-Dimensional Infrared Spectroscopy of β-Hairpin Peptides J. Chem. Phys. 2007, 126, 045109-1-045109-11
79. Kupser, P.; Pagel, K.; Oomens, J.; Polfer, N.; Koksch, B.; Meijer, G.; von Helden, G. Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase J. Am. Chem. Soc. 2010, 132, 2085-2093
80. Joshi, K.; Semrouni, D.; Ohanessian, G.; Clavaguéra, C. Structure and IR Spectra of the Gramicidin S Peptide: Pushing the Quest for Low-Energy Conformations J. Phys. Chem. B 2012, 116, 483-490
81. Auer, B. M.; Skinner, J. L. Vibrational Sum-Frequency Spectroscopy of the Liquid/Vapor Interface for Dilute HOD in D2O J. Chem. Phys. 2008, 129, 214705-1-214705-14
82. Auer, B. M.; Skinner, J. L. Water: Hydrogen Bonding and Vibrational Spectroscopy, in the Bulk Liquid and at the Liquid/Vapor Interface Chem. Phys. Lett. 2009, 470, 13-20
83. Auer, B. M.; Skinner, J. L. Vibrational Sum-Frequency Spectroscopy of the Water Liquid/Vapor Interface J. Phys. Chem. B 2009, 113, 4125-4130
84. Torii, H.; Tasumi, M. Model Calculations on the Amide-I Infrared Bands of Globular Proteins J. Chem. Phys. 1992, 96, 3379-3387
85. Torii, H.; Tatsumi, T.; Kanazawa, T.; Tasumi, M. Effects of Intermolecular Hydrogen-Bonding Interactions on the Amide I Mode of N-Methylacetamide: Matrix-Isolation Infrared Studies and ab Initio Molecular Orbital Calculations J. Phys. Chem. B 1998, 102, 309-314
86. Torii, H. In Atoms, Molecules and Clusters in Electric Fields. Theoretical Approaches to the Calculation of Electric Polarizability; Maroulis, G., Ed.; Imperial College Press: London, 2006; pp 179-214.
87. Torii, H. Nature of Vibrational Frequency Modulations and the Related One- and Two-Dimensional Vibrational Spectral Features Analysed for the Amide I Mode of Tetraalanine in Aqueous Solution Mol. Phys. 2009, 107, 1855-1866
88. Schmidt, J. R.; Corcelli, S. A.; Skinner, J. L. Ultrafast Vibrational Spectroscopy of Water and Aqueous N-Methylacetamide: Comparison of Different Electronic Structure/Molecular Dynamics Approaches J. Chem. Phys. 2004, 121, 8887-8896
89. Schmidt, J. R.; Corcelli, S. A.; Skinner, J. L. Pronounced Non-Condon Effects in the Ultrafast Infrared Spectroscopy of Water J. Chem. Phys. 2005, 123, 044513-1-044513-13
90. Auer, B. M.; Kumar, R.; Schmidt, J. R.; Skinner, J. L. Hydrogen Bonding and Raman, IR, and 2D-IR Spectroscopy of Dilute HOD in Liquid D2O Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14215-14220
91. Auer, B. M.; Skinner, J. L. Dynamical Effects in Line Shapes for Coupled Chromophores: Time-Averaging Approach J. Chem. Phys. 2007, 127, 104105-1-104105-10
92. Auer, B. M.; Skinner, J. L. IR and Raman Spectra of Liquid Water: Theory and Interpretation J. Chem. Phys. 2008, 128, 224511-1-224511-12
93. Skinner, J. L. Vibrational Line Shapes and Spectral Diffusion in Fluids Mol. Phys. 2010, 106, 2245-2253
94. Manor, J.; Mukherjee, P.; Lin, Y.-S.; Leonov, H.; Skinner, J. L.; Zanni, M. T.; Arkin, I. T. Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D Spectroscopies Structure 2009, 17, 247-254
95. Pieniazek, P. A.; Tainter, C. J.; Skinner, J. L. Surface of liquid water: Three-Body Interactions and Vibrational Sum-Frequency Spectroscopy J. Am. Chem. Soc. 2011, 133, 10360-10363
96. Pieniazek, P. A.; Tainter, C. J.; Skinner, J. L. Interpretation of the Water Surface Vibrational Sum-Frequency Spectrum J. Chem. Phys. 2011, 135, 044701-1-044701-12
97. Skinner, J. L.; Pieniazek, P. A.; Gruenbaum, S. M. Vibrational Spectroscopy of Water at Interfaces Acc. Chem. Res. 2012, 45, 93-100
98. Mukherjee, P.; Krummel, A. T.; Fulmer, E. C.; Kass, I.; Arkin, I. T.; Zanni, M. T. Site-Specific Vibrational Dynamics of the CD3ζ Membrane Peptide Using Heterodyned Two-Dimensional Infrared Photon Echo Spectroscopy J. Chem. Phys. 2004, 120, 10215-10224
99. Torii, H.; Tasumi, M. Ab Initio Molecular Orbital Study of the Amide I Vibrational Interactions Between the Peptide Groups in Di- and Tripeptides and Considerations on the Conformation of the Extended Helix J. Raman Spectrosc. 1998, 29, 81-86
100. Jansen, T. L. C.; Dijkstra, A. G.; Watson, T. M.; Hirst, J. D.; Knoester, J. Modeling the Amide I Bands of Small Peptides J. Chem. Phys. 2006, 125, 044312-1-044312-9
101. Roy, S.; Lessing, J.; Meisl, G.; Ganim, Z.; Tokmakoff, A.; Knoester, J.; Jansen, T. L. C. Solvent and Conformation Dependence of Amide I Vibrations in Peptides and Proteins Containing Proline J. Chem. Phys. 2011, 135, 234507-1-234507-11
102. Tsuboi, M.; Ikeda, T.; Ueda, T. Raman Microscopy of a Small Uniaxial Crystal: Tetragonal Aspartame J. Raman Spectrosc. 1991, 22, 619-626
103. Laaser, J. E.; Zanni, M. T. Extracting Structural Information from the Polarization Dependence of One- and Two-Dimensional Sum Frequency Generation Spectra J. Phys. Chem. A 2013, 117, 5875-5890
104. McQuarrie, D. A. Statistical Mechanics; Harper and Row: New York, 1976.
105. Schmidt, J. R.; Roberts, S. T.; Loparo, J. J.; Tokmakoff, A.; Fayer, M. D.; Skinner, J. L. Are Water Simulation Models Consistent with Steady-State and Ultrafast Vibrational Spectroscopy Experiments? Chem. Phys. 2007, 341, 143-157
106. Chen, X. G.; Schweitzer-Stenner, R.; Asher, S. A.; Mirkin, N. G.; Krimm, S. Vibrational Assignments of Trans-N-Methylacetamide and Some of Its Deuterated Isotopomers from Band Decomposition of IR, Visible, and Resonance Raman Spectra J. Phys. Chem. 1995, 99, 3074-3083
107. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theor. Comput. 2008, 4, 435-447
108. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
109. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981.
110. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
111. Nosé, S. A Unified Formulation of the Constant Temperature Molecular Dynamics Methods J. Chem. Phys. 1984, 81, 511-519
112. Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31, 1695-1697
113. Welch, W. R. W.; Kubelka, J.; Keiderling, T. A. Infrared, Vibrational Circular Dichroism, and Raman Spectral Simulations for β-sheet Structures with Various Isotopic Labels, Interstrand, and Stacking Arrangements Using Density Functional Theory J. Phys. Chem. B 2013, 117, 10343-10358
114. Wampler, R. D.; Zhou, M.; Thompson, D. H.; Simpson, G. J. Mechanism of the Chiral SHG Activity of Bacteriorhodopsin Films J. Am. Chem. Soc. 2006, 128, 10994-10995
115. Ji, N.; Ostroverkhov, V.; Chen, C.-Y.; Shen, Y.-R. Phase-Sensitive Sum-Frequency Vibrational Spectroscopy and Its Application to Studies of Interfacial Alkyl Chains J. Am. Chem. Soc. 2007, 129, 10056-10057
116. Stiopkin, I. V.; Jayathilake, H. D.; Bordenyuk, A. N.; Benderskii, A. V. Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy J. Am. Chem. Soc. 2008, 130, 2271-2275
117. Stiopkin, I. V.; Weeraman, C.; Pieniazek, P. A.; Shalhout, F. Y.; Skinner, J. L.; Benderskii, A. V. Hydrogen Bonding at the Water Surface Revealed by Isotopic Dilution Spectroscopy Nature 2011, 474, 192-195
118. Laaser, J. E.; Xiong, W.; Zanni, M. T. Time-Domain SFG Spectroscopy Using Mid-IR Pulse Shaping: Practical and Intrinsic Advantages J. Phys. Chem. B 2011, 115, 2536-2546
119. Laaser, J. E.; Sko, D. R.; Ho, J.-J.; Joo, Y.; Serrano, A. L.; Steinkruger, J. D.; Gopalan, P.; Gellman, S. H.; Zanni, M. T. Two-Dimensional Sum-Frequency Generation Reveals Structure and Dynamics of a Surface-Bound Peptide J. Am. Chem. Soc. 2014, 136, 956-962
120. Torres, J.; Adams, P. D.; Arkin, I. T. Use of a New Label, 13C=18O, in the Determination of a Structural Model of Phospholamban in a Lipid Bilayer. Spatial Restraints Resolve the Ambiguity Arising from Interpretations of Mutagenesis Data J. Mol. Biol. 2000, 300, 677-685
121. Torres, J.; Kukol, A.; Goodman, J. M.; Arkin, I. T. Site-Specific Examination of Secondary Structure and Orientation Determination in Membrane Proteins: The Peptidic 13C=18O Group as a Novel Infrared Probe Biopolymers 2001, 59, 396-401
122. Fang, C.; Wang, J.; Charnley, A. K.; Barber-Armstrong, W.; Smith, A. B.; Decatur, S. M.; Hochstrasser, R. M. Two-Dimensional Infrared Measurements of the Coupling Between Amide Modes of an α-Helix Chem. Phys. Lett. 2003, 382, 586-592
123. Fang, C.; Wang, J.; Kim, Y. S.; Charnley, A. K.; Barber-Armstrong, W.; Smith, A. B.; Decatur, S. M.; Hochstrasser, R. M. Two-Dimensional Infrared Spectroscopy of Isotopomers of an Alanine Rich α-Helix J. Phys. Chem. B 2004, 108, 10415-10427
124. Fang, C.; Hochstrasser, R. M. Two-Dimensional Infrared Spectra of the 13C=18O Isotopomers of Alanine Residues in an α-Helix J. Phys. Chem. B 2005, 109, 18652-18663
125. Arkin, I. T. Isotope-Edited IR Spectroscopy for the Study of Membrane Proteins Curr. Opin. Chem. Biol. 2006, 10, 394-401
126. Brewer, S. H.; Song, B.; Raleigh, D. P.; Dyer, R. B. Residue Specific Resolution of Protein Folding Dynamics Using Isotope-Edited Infrared Temperature Jump Spectroscopy Biochemistry 2007, 46, 3279-3285
127. Decatur, S. M. Elucidation of Residue-Level Structure and Dynamics of Polypeptides Via Isotope-Edited Infrared Spectroscopy Acc. Chem. Res. 2006, 39, 169-175
128. Mukherjee, P.; Kass, I.; Arkin, I.; Zanni, M. T. Picosecond Dynamics of a Membrane Protein Revealed by 2D IR Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3528-3533
129. Mukherjee, P.; Kass, I.; Arkin, I. T.; Zanni, M. T. Structural Disorder of the CD3ζ Transmembrane Domain Studied with 2D IR Spectroscopy and Molecular Dynamics Simulation J. Phys. Chem. B 2006, 110, 24740-24749
130. Shim, S.-H.; Gupta, R.; Ling, Y. L.; Strasfeld, D. B.; Raleigh, D. P.; Zanni, M. T. Two-Dimensional IR Spectroscopy and Isotope Labeling Defines the Pathway of Amyloid Formation with Residue Specific Resolution Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6614-6619
131. Nagarajan, S.; Taskent-Sezgin, H.; Parul, D.; Carrico, I.; Raleigh, D. P.; Dyer, R. B. Differential Ordering of the Protein Backbone and Side Chains During Protein Folding Revealed by Site-Specific Recombinant Infrared Probes J. Am. Chem. Soc. 2011, 133, 20335-20340
132. Goldstein, H. Classical Mechanics; Addison-Wesley: Reading, MA, 1980.