UV transition moments of tyrosine

Journal of Physical Chemistry B

Volumn 118, Issue 31, 2014, Pages 9247-9257

  Fornander, Louise H ^a   Feng, Bobo ^a   Beke Somfai, Tamás ^a   Nordén, Bengt ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHROMOPHORES; CYCLOHEXANE; HYDROGEN BONDS; METHANOL; POLARIZATION; POLYVINYL ALCOHOLS; PROTEINS; QUANTUM THEORY; SOLVENTS; ULTRAVIOLET SPECTROSCOPY;

NONPOLAR ENVIRONMENT; ORIENTATION DISTRIBUTIONS; ORTHOGONAL POLARIZATIONS; POLAR ENVIRONMENTS; QUANTUM MECHANICAL; SOLVENT ENVIRONMENTS; TRANSITION MOMENTS; VIBRATIONAL STRUCTURES;

ORGANIC SOLVENTS;

4-CRESOL; CRESOL; CYCLOHEXANE; CYCLOHEXANE DERIVATIVE; HYDROGEN; METHANOL; POLYETHYLENE; POLYVINYL ALCOHOL; SOLVENT; TYROSINE; WATER;

CHEMICAL MODEL; CHEMISTRY; HYDROGEN BOND; PHOTOCHEMISTRY; PROCEDURES; QUANTUM THEORY; SPECTROSCOPY; ULTRAVIOLET RADIATION; VIBRATION;

CRESOLS; CYCLOHEXANES; HYDROGEN; HYDROGEN BONDING; METHANOL; MODELS, CHEMICAL; PHOTOCHEMICAL PROCESSES; POLYETHYLENE; POLYVINYL ALCOHOL; QUANTUM THEORY; SOLVENTS; SPECTRUM ANALYSIS; TYROSINE; ULTRAVIOLET RAYS; VIBRATION; WATER;

EID: 84905728439     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp5065352     Document Type: Article

References (65)

1. Ilari, A.; Savino, C. Protein Structure Determination by X-Ray Crystallography Methods Mol. Biol. (Totowa, NJ, U.S.) 2008, 452, 63-87
2. Clore, G. M.; Gronenborn, A. M. Determining the Structures of Large Proteins and Protein Complexes by NMR Trends Biotechnol. 1998, 16, 22-34
3. Schneider, R.; Huang, J.; Yao, M.; Communie, G.; Ozenne, V.; Mollica, L.; Salmon, L.; Jensen, M. R.; Blackledge, M. Towards a Robust Description of Intrinsic Protein Disorder Using Nuclear Magnetic Resonance Spectroscopy Mol. Biosyst. 2012, 8, 58-68
4. Wider, G. NMR Techniques Used with Very Large Biological Macromolecules in Solution Methods Enzymol. 2005, 394, 382-398
5. Acharya, K. R.; Lloyd, M. D. The Advantages and Limitations of Protein Crystal Structures Trends Pharmacol. Sci. 2005, 26, 10-14
6. Lakowicz, J. R. Principles of Fluorescence; Academic, K., Ed., 2 nd ed.; Plenum Publishers: New York, 1999.
7. Förster, T. Energiewanderung Und Fluoreszenz Naturwissenschaften 1946, 33, 166-175
8. Förster, T. Zwischenmolekulare Energiewanderung Und Fluoreszenz Ann. Phys. (Berlin, Ger.) 1948, 2, 55-75
9. Nordén, B.; Kubista, M.; Kuruscev, T. Linear Dichroism Spectroscopy of Nucleic Acids Q. Rev. Biophys. 1992, 25, 51-170
10. Nordén, B.; Rodger, A.; Dafforn, T. Linear Dichroism and Circular Dichroism: A Textbook on Polarized-Light Spectroscopy; Royal Society of Chemistry: London, 2010.
11. Bulheller, B. M.; Rodger, A.; Hicks, M. R.; Dafforn, T. R.; Serpell, L. C.; Marshall, K. E.; Bromley, E. H. C.; King, P. J. S.; Channon, K. J.; Woolfson, D. N. Flow Linear Dichroism of Some Prototypical Proteins J. Am. Chem. Soc. 2009, 131, 13305-13314
12. Kitts, C. C.; Beke-Somfai, T.; Nordén, B. Michler's Hydrol Blue: A Sensitive Probe for Amyloid Fibril Detection Biochemistry 2011, 50, 3451-3461
13. Reymer, A.; Frykholm, K.; Morimatsu, K.; Takahashi, M.; Nordén, B. Structure of Human Rad51 Protein Filament from Molecular Modeling and Site-Specific Linear Dichroism Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 13248-13253
14. 2+ Improves Organization of Single-Stranded DNA Bases in Human Rad51 Filament, Explaining Stimulatory Effect on Gene Recombination Nucleic Acids Res. 2012, 40, 4904-4913
15. Scheiner, S.; Kar, T.; Pattanayak, J. Comparison of Various Types of Hydrogen Bonds Involving Aromatic Amino Acids J. Am. Chem. Soc. 2002, 124, 13257-13264
16. Pedone, A.; Barone, V. Unraveling Solvent Effects on the Electronic Absorption Spectra of TRITC Fluorophore in Solution: A Theoretical TD-DFT/PCM Study Phys. Chem. Chem. Phys. 2010, 12, 2722-2729
17. Bertolino, C. a.; Ferrari, A. M.; Barolo, C.; Viscardi, G.; Caputo, G.; Coluccia, S. Solvent Effect on Indocyanine Dyes: A Computational Approach Chem. Phys. 2006, 330, 52-59
18. d'Ischia, M.; Crescenzi, O.; Pezzella, A.; Arzillo, M.; Panzella, L.; Napolitano, A.; Barone, V. Structural Effects on the Electronic Absorption Properties of 5,6-Dihydroxyindole Oligomers: The Potential of an Integrated Experimental and DFT Approach to Model Eumelanin Optical Properties Photochem. Photobiol. 2008, 84, 600-607
19. Karthika, M.; Kanakaraju, R.; Senthilkumar, L. Spectroscopic Investigations and Hydrogen Bond Interactions of 8-Aza Analogues of Xanthine, Theophylline and Caffeine: A Theoretical Study J. Mol. Model. 2013, 19, 1835-1851
20. Champagne, B.; Guillaume, M.; Zutterman, F. TDDFT Investigation of the Optical Properties of Cyanine Dyes Chem. Phys. Lett. 2006, 425, 105-109
21. Rogers, D. M.; Hirst, J. D. Ab Initio Study of Aromatic Side Chains of Amino Acids in Gas Phase and Solution J. Phys. Chem. A 2003, 107, 11191-11200
22. Jacquemin, D.; Perpète, E. a; Ciofini, I.; Adamo, C. Accurate Simulation of Optical Properties in Dyes Acc. Chem. Res. 2009, 42, 326-334
23. Fabian, J. TDDFT-Calculations of Vis/NIR Absorbing Compounds Dyes Pigm. 2010, 84, 36-53
24. Fabian, J. Electronic Excitation of Sulfur-Organic Compounds: Performance of Time-Dependent Density Functional Theory Theor. Chem. Acc. 2001, 106, 199-217
25. Matson, M.; Carlsson, N.; Beke-Somfai, T.; Nordén, B. Spectral Properties and Orientation of Voltage-Sensitive Dyes in Lipid Membranes Langmuir 2012, 28, 10808-10817
26. Kelly, S. M.; Price, N. C. The Use of Circular Dichroism in the Investigation of Protein Structure and Function Curr. Protein Pept. Sci. 2000, 1, 349-384
27. Woody, R. W. Circular Dichroism of Protein-Folding Intermediates Methods Enzymol. 2004, 380, 242-285
28. Kelly, S. M.; Price, N. C. The Application of Circular Dichroism to Studies of Protein Folding and Unfolding Biochim. Biophys. Acta 1997, 1338, 161-185
29. Mach, H.; Middaugh, C. R. Simultaneous Monitoring of the Environment of Tryptophan, Tyrosine, and Phenylalanine Residues in Proteins by Near-Ultraviolet Second-Derivative Spectroscopy Anal. Biochem. 1994, 222, 323-331
30. Jakobsen, J. The Vibrational Spectra of P-Cresol * Spectrochim. Acta 1965, 21, 433-442
31. Laane, J.; Haller, K.; Sakurai, S.; Morris, K.; Autrey, D.; Arp, Z.; Chiang, W.-Y.; Combs, A. Raman Spectroscopy of Vapors at Elevated Temperatures J. Mol. Struct. 2003, 650, 57-68
32. Takeuchi, H.; Watanabe, N.; Harada, I. Vibrational Spectra and Normal Coordinate Analysis of P-Cresol and Its Deuterated Analogs Spectrochim. Acta, Part A 1988, 44, 749-761
33. Pohl, M.; Schmitt, M.; Kleinermanns, K. Vibrational Spectroscopy of Size-Assigned P-cresol/H2O-Clusters in the S0 and S1 State Chem. Phys. Lett. 1991, 177, 252-260
34. Song, K.; Hayes, J. M. Supersonic Jet Spectra of P-Alkylphenols J. Mol. Spectrosc. 1989, 134, 82-97
35. Richardson, P. R.; Chapman, M. a.; Wilson, D. C.; Bates, S. P.; Jones, A. C. The Nature of Conformational Preference in a Number of P-Alkyl Phenols and P-Alkyl Benzenes Phys. Chem. Chem. Phys. 2002, 4, 4910-4915
36. Smolyar, A.; Wong, C. F. Theoretical Studies of the Spectroscopic Properties of Tryptamine, Tryptophan and Tyrosine J. Mol. Struct.: THEOCHEM 1999, 488, 51-67
37. Platt, J. R. Classification of Spectra of Cata-Condensed Hydrocarbons J. Chem. Phys. 1949, 17, 484-495
38. Arp, Z.; Autrey, D.; Laane, J.; Overman, S. a; Thomas, G. J. Tyrosine Raman Signatures of the Filamentous Virus Ff Are Diagnostic of Non-Hydrogen-Bonded Phenoxyls: Demonstration by Raman and Infrared Spectroscopy of P-Cresol Vapor Biochemistry 2001, 40, 2522-2529
39. Chignell, D. A.; Gratzer, W. B. Solvent Effects on Aromatic Chromophores and Their Relation to Ultraviolet Difference Spectra of Proteins J. Phys. Chem. 1968, 283, 2934-2941
40. Guthmuller, J.; Simon, D. Linear and Nonlinear Optical Response of Aromatic Amino Acids: A Time-Dependent Density Functional Investigation J. Phys. Chem. A 2006, 110, 9967-9973
41. Lorentzon, J.; Malmqvist, P.-A.; Fuelscher, M.; Roos, B. O. A CASPT2 Study of the Valence and Lowest Rydberg Electronic States of Benzene and Phenol Theor. Chim. Acta 1995, 91, 91-108
42. Fang, W.-H. Theoretical Characterization of the Excited-State Structures and Properties of Phenol and Its One-Water Complex J. Chem. Phys. 2000, 112, 1204-1211
43. Granucci, G.; Hynes, J. T.; Millie, P.; Tran-Thi, T.-H. A Theoretical Investigation of Excited-State Acidity of Phenol and Cyanophenols J. Am. Chem. Soc. 2000, 122, 12243-12253
44. Schumm, S.; Gerhards, M.; Roth, W.; Gier, H.; Kleinermanns, K. A CASSCF Study of the S0 andS S1 States of Phenol Chem. Phys. Lett. 1996, 263, 126-132
45. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision B.01; 2010.
46. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
47. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density Phys. Rev. B 1988, 37, 785-789
48. Chai, J.-D.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
49. Cancès, E.; Mennucci, B.; Tomasi, J. A New Integral Equation Formalism for the Polarizable Continuum Model: Theoretical Background and Applications to Isotropic and Anisotropic Dielectrics J. Chem. Phys. 1997, 107, 3032-3041
50. Gerrard, D. L.; Maddams, W. F. Solvent Effects in U. V. Absorption Spectra. I. Phenol in Cyclohexane Ethanol Mixtures Spectrochim. Acta 1978, 34, 1205-1211
51. Thulstrup, E. W.; Vala, M.; Eggers, J. H. Moment Directions of the Electronic Transitions of Para-Dimethoxybenzene Chem. Phys. Lett. 1970, 7, 31-36
52. Michl, J.; Eggers, J. H.; Thulstrup, E. W. Polarization Spectra in Stretched Polymer Sheets. II. Separation of Pi-Pi* Absorption of Symmetrical Molecules into Components J. Phys. Chem. 1969, 74, 3868-3878
53. Michl, J.; Thulstrup, E. W.; Eggers, J. H. Polarization Spectra in Stretched Polymer Sheets. III. Physical Significance of the Orientation Factors and Determination of Transition Moment Directions in Molecules of Low Symmetry J. Phys. Chem. 1970, 74, 3878-3884
54. Matsuoka, Y.; Nordén, B. Linear Dichroism Study of 9-Substituted Acridines in Streched Poly(vinyl Alcohol) Film Chem. Phys. Lett. 1982, 85, 302-306
55. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry of Macromolecules, Pt. 3: The Behavior of Biological Macromolecules; W. H. Freeman & Co: New York, 1980.
56. Pohl, M.; Schmitt, M.; Kleinermanns, K. Microscopic Shifts of Size-Assigned P-cresol/H2O-Cluster Spectra J. Chem. Phys. 1991, 94, 1717-1723
57. Bayliss, N. S.; Hulme, L. Solvent Effects in the Spectra of Benzene, Toluene, and Chlorobenzene at 2600 and 2000 Å Aust. J. Chem. 1953, 6, 257-277
58. Arunan, E.; Desiraju, G. R.; Klein, R. a.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, P. Definition of the Hydrogen Bond (IUPAC Recommendations 2011) Pure Appl. Chem. 2011, 83, 1637-1641
59. Shirhatti, P. R.; Maity, D. K.; Wategaonkar, S. C-H⋯Y Hydrogen Bonds in the Complexes of P-Cresol and P-Cyanophenol with Fluoroform and Chloroform J. Phys. Chem. A 2013, 117, 2307-2316
60. Chiti, F.; Dobscon, C. Protein Misfolding, Functional Amyloid, and Human Disease Annu. Rev. Biochem. 2006, 75, 333-366
61. Frykholm, K.; Morimatsu, K.; Nordén, B. Conserved Conformation of RecA Protein after Executing the DNA Strand-Exchange Reaction. A Site-Specific Linear Dichroism Structure Study Biochemistry 2006, 45, 11172-11178
62. Pellegrini, L.; Yu, D. S.; Lo, T.; Anand, S.; Lee, M.; Blundell, T. L.; Venkitaraman, A. R. Insights into DNA Recombination from the Structure of a RAD51-BRCA2 Complex Nature 2002, 420, 287-293
63. Conway, A. B.; Lynch, T. W.; Zhang, Y.; Fortin, G. S.; Fung, C. W.; Symington, L. S.; Rice, P. a. Crystal Structure of a Rad51 Filament Nat. Struct. Mol. Biol. 2004, 11, 791-796
64. Aihara, H.; Ito, Y.; Kurumizaka, H.; Yokoyama, S.; Shibata, T. The N-Terminal Domain of the Human Rad51 Protein Binds DNA: Structure and a DNA Binding Surface as Revealed by NMR J. Mol. Biol. 1999, 290, 495-504
65. Selmane, T.; Camadro, J.-M.; Conilleau, S.; Fleury, F.; Tran, V.; Prévost, C.; Takahashi, M. Identification of the Subunit-Subunit Interface of Xenopus Rad51.1 Protein: Similarity to RecA J. Mol. Biol. 2004, 335, 895-904