Amide i vibrational properties affected by hydrogen bonding out-of-plane of the peptide group

Journal of Physical Chemistry Letters

Volumn 6, Issue 4, 2015, Pages 727-733

  Torii, Hajime ^a  

^a SHIZUOKA UNIVERSITY   (Japan)

Author keywords

electrostatic interaction; hydrogen bond; peptide; vibrational mode

Indexed keywords

AMIDES; COULOMB INTERACTIONS; HYDRATION; MOLECULAR DYNAMICS; MOLECULES; PEPTIDES;

ANGULAR POSITIONS; FREQUENCY SHIFT; INFRARED INTENSITY; LOW-FREQUENCY SHIFT; MODEL PARAMETER SETS; MOLECULAR PROPERTIES; VIBRATIONAL MODES; VIBRATIONAL PROPERTIES;

HYDROGEN BONDS;

AMIDE; PEPTIDE;

CHEMISTRY; HYDROGEN BOND; THEORETICAL MODEL; VIBRATION;

AMIDES; HYDROGEN BONDING; MODELS, THEORETICAL; PEPTIDES; VIBRATION;

EID: 84923354346     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/acs.jpclett.5b00004     Document Type: Article

References (54)

1. Byler, D. M.; Susi, H. Examination of the Secondary Structure of Proteins by Deconvolved FTIR Spectra Biopolymers 1986, 25, 469-487
2. Miyazawa, T. Perturbation Treatment of the Characteristic Vibrations of Polypeptide Chains in Various Configurations J. Chem. Phys. 1960, 32, 1647-1652
3. Miyazawa, T.; Blout, E. R. The Infrared Spectra of Polypeptides in Various Conformations: Amide I and II Bands J. Am. Chem. Soc. 1961, 83, 712-719
4. Krimm, S.; Bandekar, J. Vibrational Spectroscopy and Conformation of Peptides, Polypeptides, and Proteins Adv. Protein Chem. 1986, 38, 181-364
5. Mantsch, H. H.; Casal, H. L.; Jones, R. N. Resolution Enhancement of Infrared Spectra of Biological Systems. In Spectroscopy of Biological Systems, Advances in Spectroscopy; Clark, R. J. H.; Hester, R. E., Eds.; Wiley: New York, 1986; Vol. 13, pp 1-46.
6. Surewicz, W. K.; Mantsch, H. H.; Chapman, D. Determination of Protein Secondary Structure by Fourier Transform Infrared Spectroscopy: A Critical Assessment Biochemistry 1993, 32, 389-394
7. Torii, H.; Tasumi, M. Theoretical Analyses of the Amide I Infrared Bands of Globular Proteins. In Infrared Spectroscopy of Biomolecules; Mantsch, H. H.; Chapman, D., Eds.; Wiley-Liss: New York, 1996; pp 1-18.
8. Barth, A. Infrared Spectroscopy of Proteins Biochim. Biophys. Acta 2007, 1767, 1073-1101
9. Schweitzer-Stenner, R. Visible and UV-Resonance Raman Spectroscopy of Model Peptides J. Raman Spectrosc. 2001, 32, 711-732
10. Brauner, J. W.; Flach, C. R.; Mendelsohn, R. A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Globular Proteins: From Structure to Spectrum J. Am. Chem. Soc. 2005, 127, 100-109
11. Chen, X. G.; Schweitzer-Stenner, R.; Krimm, S.; Mirkin, N. G.; Asher, S. A. N -Methylacetamide and Its Hydrogen-Bonded Water Molecules Are Vibrationally Coupled J. Am. Chem. Soc. 1994, 116, 11141-11142
12. Hamm, P.; Lim, M.; DeGrado, W. F.; Hochstrasser, R. M. The Two-Dimensional IR Nonlinear Spectroscopy of a Cyclic Penta-Peptide in Relation to Its Three-Dimensional Structure Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2036-2041
13. Chung, H. S.; Khalil, M.; Tokmakoff, A. Nonlinear Infrared Spectroscopy of Protein Conformational Change during Thermal Unfolding J. Phys. Chem. B 2004, 108, 15332-15342
14. Krimm, S.; Abe, Y. Intermolecular Interaction Effects in the Amide I Vibrations of ? Polypeptides Proc. Natl. Acad. Sci. U.S.A. 1972, 69, 2788-2792
15. Torii, H.; Tasumi, M. Model Calculations on the Amide-I Infrared Bands of Globular Proteins J. Chem. Phys. 1992, 96, 3379-3387
16. 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
17. Hamm, P.; Woutersen, S. Coupling of the Amide I Modes of the Glycine Dipeptide Bull. Chem. Soc. Jpn. 2002, 75, 985-988
18. Gorbunov, R. D.; Kosov, D. S.; Stock, G. Ab Initio -Based Exciton Model of Amide I Vibrations in Peptides: Definition, Conformational Dependence, and Transferability J. Chem. Phys. 2005, 122, 224904
19. Ham, S.; Cho, M. Amide I Modes in the N -Methylacetamide Dimer and Glycine Dipeptide Analog: Diagonal Force Constants J. Chem. Phys. 2003, 118, 6915-6922
20. Kwac, K.; Cho, M. Molecular Dynamics Simulation Study of N -Methylacetamide in Water. I. Amide I Mode Frequency Fluctuation J. Chem. Phys. 2003, 119, 2247-2255
21. Bouř, P.; Keiderling, T. A. Empirical Modeling of the Peptide Amide I Band IR Intensity in Water Solution J. Chem. Phys. 2003, 119, 11253-11262
22. Watson, T. M.; Hirst, J. D. Theoretical Studies of the Amide I Vibrational Frequencies of [Leu]-Enkephalin Mol. Phys. 2005, 103, 1531-1546
23. Torii, H. Electrostatic Origin of the Cooperative Effect on the C=O Bond Lengths and the Amide I Vibrational Frequencies of the N -Methylacetamide Oligomers J. Mol. Struct. 2005, 735/736, 21-26
24. 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
25. 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
26. Jansen, T. l. C.; Knoester, J. A Transferable Electrostatic Map for Solvation Effects on Amide I Vibrations and its Application to Linear and Two-Dimensional Spectroscopy J. Chem. Phys. 2006, 124, 044502
27. Reppert, M.; Tokmakoff, A. Electrostatic Frequency Shifts in Amide I Vibrational Spectra: Direct Parameterization against Experiment J. Chem. Phys. 2013, 138, 134116
28. Moran, A. M.; Park, S.-M.; Mukamel, S. Infrared Photon Echo Signatures of Hydrogen Bond Connectivity in the Cyclic Decapeptide Antamanide J. Chem. Phys. 2003, 118, 9971-9980
29. Maekawa, H.; Ballano, G.; Toniolo, C.; Ge, N.-H. Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains J. Phys. Chem. B 2011, 115, 5168-5182
30. Torii, H. Effects of Intermolecular Vibrational Coupling and Liquid Dynamics on the Polarized Raman and Two-Dimensional Infrared Spectral Profiles of Liquid N, N -Dimethylformamide Analyzed with a Time-Domain Computational Method J. Phys. Chem. A 2006, 110, 4822-4832
31. Jansen, T. l. C.; Knoester, J. Nonadiabatic Effects in the Two-Dimensional Infrared Spectra of Peptides: Application to Alanine Dipeptide J. Phys. Chem. B 2006, 110, 22910-22916
32. Ganim, Z.; Tokmakoff, A. Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra Biophys. J. 2006, 91, 2636-2646
33. Gilmanshin, R.; Williams, S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Fast Events in Protein Folding: Relaxation Dynamics and Structure of the I Form of Apomyoglobin Biochemistry 1997, 36, 15006-15012
34. Reisdorf, W. C., Jr.; Krimm, S. Infrared Amide I? Band of the Coiled Coil Biochemistry 1996, 35, 1383-1386
35. Manas, E. S.; Getahun, Z.; Wright, W. W.; DeGrado, W. F.; Vanderkooi, J. M. Infrared Spectra of Amide Groups in α-Helical Proteins: Evidence for Hydrogen Bonding between Helices and Water J. Am. Chem. Soc. 2000, 122, 9883-9890
36. Walsh, S. T. R.; Cheng, R. P.; Wright, W. W.; Alonso, D. O. V.; Daggett, V.; Vanderkooi, J. M.; DeGrado, W. F. The Hydration of Amides in Helices; A Comprehensive Picture from Molecular Dynamics, IR, and NMR Protein Sci. 2003, 12, 520-531
37. Cho, M. Vibrational Solvatochromism and Electrochromism: Coarse-Grained Models and Their Relationships J. Chem. Phys. 2009, 130, 094505
38. Torii, H.; Tatsumi, T.; Tasumi, M. Effects of Hydration on the Structure, Vibrational Wavenumbers, Vibrational Force Field, and Resonance Raman Intensities of N -Methylacetamide J. Raman Spectrosc. 1998, 29, 537-546
39. Torii, H. Intermolecular Charge Flux as the Origin of Infrared Intensity Enhancement upon Halogen-Bond Formation of the Peptide Group J. Chem. Phys. 2010, 133, 034504
40. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Gaussian 03, revision D.01; Gaussian, Inc.: Wallingford, CT, 2004.
41. Torii, H. Vibrational Interactions in the Amide I Subspace of the Oligomers and Hydration Clusters of N -Methylacetamide J. Phys. Chem. A 2004, 108, 7272-7280
42. Torii, H. Mechanism of the Secondary Structure Dependence of the Infrared Intensity of the Amide II Mode of Peptide Chains J. Phys. Chem. Lett. 2012, 3, 112-116
43. 2O from 10 to 90 °C J. Phys. Chem. A 2005, 109, 6154-6165
44. 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
45. Torii, H. Time-Domain Calculations of the Polarized Raman Spectra, the Transient Infrared Absorption Anisotropy, and the Extent of Delocalization of the OH Stretching Mode of Liquid Water J. Phys. Chem. A 2006, 110, 9469-9477
46. Torii, H. Intra- and Intermolecular Charge Fluxes Induced by the OH Stretching Mode of Water and Their Effects on the Infrared Intensities and Intermolecular Vibrational Coupling J. Phys. Chem. B 2010, 114, 13403-13409
47. Torii, H. The Role of Electrical Property Derivatives in Intermolecular Vibrational Interactions and Their Effects on Vibrational Spectra Vib. Spectrosc. 2002, 29, 205-209
48. Torii, H. Responses of Molecular Vibrations to Intermolecular Electrostatic Interactions and Their Effects on Vibrational Spectroscopic Features. 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.
49. Decius, J. C. An Effective Atomic Charge Model for Infrared Intensities J. Mol. Spectrosc. 1975, 57, 348-362
50. van Straten, A. J.; Smit, W. M. A. Bond Charge Parameters from Integrated Infrared Intensities J. Mol. Spectrosc. 1976, 62, 297-312
51. Gussoni, M.; Castiglioni, C.; Zerbi, G. Physical Meaning of Electrooptical Parameters Derived from Infrared Intensities J. Phys. Chem. 1984, 88, 600-604
52. Torii, H.; Tasumi, M. Infrared Intensities of Vibrational Modes of an α-Helical Polypeptide: Calculations Based on the Equilibrium Charge/Charge Flux (ECCF) Model J. Mol. Struct. 1993, 300, 171-179
53. Palmo, K.; Mannfors, B.; Mirkin, N. G.; Krimm, S. Potential Energy Functions: From Consistent Force Fields to Spectroscopically Determined Polarizable Force Fields Biopolymers 2003, 68, 383-394
54. Torii, H. Delocalized Electrons in Infrared Intensities J. Mol. Struct. 2014, 1056/1057, 84-96