Near-infrared laser induced conformational change of alanine in low-temperature matrixes and the tunneling lifetime of its conformer VI

Journal of Physical Chemistry A

Volumn 117, Issue 9, 2013, Pages 1952-1962

  Bazsó, Gábor ^a   Najbauer, Eszter E ^a   Magyarfalvi, Gábor ^a   Tarczay, György ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

BARRIER HEIGHTS; CONFORMATIONAL CHANGE; IRRADIATION EXPERIMENTS; LOW TEMPERATURES; NEAR-INFRARED LASERS; OVERTONE BANDS; PRODUCTION OF; VIBRATIONAL ASSIGNMENT;

ARGON LASERS; ATOM LASERS; EXPERIMENTS; INFRARED DEVICES; IRRADIATION; TEMPERATURE;

AMINO ACIDS;

ALANINE;

ARTICLE; CHEMISTRY; COLD; LASER; NEAR INFRARED SPECTROSCOPY; PROTEIN CONFORMATION;

ALANINE; COLD TEMPERATURE; LASERS; PROTEIN CONFORMATION; SPECTROSCOPY, NEAR-INFRARED;

EID: 84874868630     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp400196b     Document Type: Article

References (89)

1. Grenie, Y.; Lassegues, J. C.; Garrigou-Lagrange, C. Infrared Spectrum of Matrix-Isolated Glycine J. Chem. Phys. 1970, 53, 2980-2982
2. Grenie, Y.; Garrigou-Lagrange, C. Infrared Spectra of Glycine Isotopic Species Isolated in an Argon or Nitrogen Matrix J. Mol. Spectrosc. 1972, 41, 240-248
3. Reva, I. D.; Plokhotnichenko, A. M.; Stepanian, S. G.; Ivanov, A. Yu.; Radchenko, E. D.; Sheina, G. G.; Blagoi, Yu. P. The Rotamerization of Conformers of Glycine Isolated in Inert Gas Matrices. An Infrared Spectroscopic Study Chem. Phys. Lett. 1995, 232, 141-148
4. Erratum. Chem. Phys. Lett. 1995, 235, 617.
5. Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Rosado, M. T. S.; Duarte, M. L. T. S.; Fausto, R.; Adamowicz, L. Matrix-Isolation Infrared and Theoretical Studies of the Glycine Conformers J. Phys. Chem. A 1998, 102, 1041-1054
6. Ivanov, A. Yu.; Plokhotnichenko, A. M.; Izvekov, V.; Sheina, G. G.; Blagoi, Yu. P. FTIR Investigation of the Effect of Matrices (Kr, Ar, Ne) on the UV-Induced Isomerization of the Monomeric Links of Biopolymers J. Mol. Struct. 1997, 408-409, 459-462
7. Ivanov, A. Yu.; Sheina, G.; Blagoi, Yu. P. FTIR Spectroscopic Study of the UV-Induced Rotamerization of Glycine in the Low Temperature Matrices (Kr, Ar, Ne) Spectrochim. Acta, Part A 1999, 55, 219-228
8. Espinoza, C.; Szczepanski, J.; Vala, M.; Polfer, N. C. Glycine and Its Hydrated Complexes: A Matrix Isolation Infrared Study J. Phys. Chem. A 2010, 114, 5919-5927
9. Bazsó, G.; Magyarfalvi, G.; Tarczay, G. Near-Infrared Laser Induced Conformational Change and UV Laser Photolysis of Glycine in Low-Temperature Matrices: Observation of a Short-Lived Conformer J. Mol. Struct. 2012, 1025, 33-42
10. Bazsó, G.; Magyarfalvi, G.; Tarczay, G. Tunneling Lifetime of the ttc /VIp Conformer of Glycine in Low-Temperature Matrices J. Phys. Chem. A 2012, 116, 10539-10547
11. Rosado, M. T. S.; Duarte, M. L. R. S.; Fausto, R. Vibrational Spectra (FT-IR, Raman and MI-IR) of α- and β-Alanine J. Mol. Struct. 1997, 410-411, 343-348
12. Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Adamowicz, L. Conformational Behavior of α-Alanine. Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study J. Phys. Chem. A 1998, 102, 4623-4629
13. Lambie, B.; Ramaekers, R.; Maes, G. On the Contribution of Intramolecular H-Bonding Entropy to the Conformational Stability of Alanine Conformations Spectrochim. Acta, Part A 2003, 59, 1387-1397
14. Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Adamowicz, L. Combined Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study of the Nonionized Valine Conformers J. Phys. Chem. A 1999, 103, 4404-4412
15. Sheina, G. G.; Radchenko, E. D.; Ivanov, A. Yu.; Stepanian, S. G.; Blagoi, Yu. P. Oscillating Spectra of Leucine Zh. Fiz. Khim. 1988, 62, 985-990
16. Boeckx, B.; Maes, G. Potential Energy Surface and Matrix Isolation FT-IR Study of Isoleucine J. Phys. Chem. A 2012, 116, 3247-3258
17. Reva, I. D.; Stepanian, S. G.; Plokhotnichenko, A.; Radchenko, E. D.; Sheina, G.; Blagoi, Yu. P. Infrared Matrix Isolation Studies of Amino Acids. Molecular Structure of Proline J. Mol. Struct. 1994, 318, 1-13
18. Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Adamowicz, L. Conformers of Nonionized Proline. Matrix-Isolation Infrared and Post-Hartree-Fock ab Initio Study J. Phys. Chem. A 2001, 105, 10664-10672
19. Lambie, B.; Ramaekers, R.; Maes, G. Conformational Behavior of Serine: An Experimental Matrix-Isolation FT-IR and Theoretical DFT(B3LYP)/6-31++G* Study J. Phys. Chem. A 2004, 108, 10426-10433
20. Jarmelo, S.; Lapinski, L.; Nowak, M. J.; Carey, P. R.; Fausto, R. Preferred Conformers and Photochemical (λ > 200 nm) Reactivity of Serine and 3,3-Dideutero-Serine In the Neutral Form J. Phys. Chem. A 2005, 109, 5689-5707
21. Jarmelo, S.; Reva, I. D.; Rozenberg, M.; Carey, P. R.; Fausto, R. Low-Temperature Infrared Spectra and Hydrogen Bonding in Polycrystalline DL-Serine and Deuterated Derivatives Vib. Spectrosc. 2006, 41, 73-82
22. Kaczor, A.; Reva, I. D.; Proniewicz, L. M.; Fausto, R. Importance of Entropy in the Conformational Equilibrium of Phenylalanine: A Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Study J. Phys. Chem. A 2006, 110, 2360-2370
23. Ramaekers, R.; Pajak, J.; Rospenk, M.; Maes, G. Matrix-Isolation FT-IR Spectroscopic Study and Theoretical DFT(B3LYP)/6-31++G* Calculations of the Vibrational and Conformational Properties of Tyrosine Spectrochim. Acta Part A 2005, 61, 1347-1356
24. Kaczor, A.; Reva, I. D.; Proniewicz, L. M.; Fausto, R. Matrix-Isolated Monomeric Tryptophan: Electrostatic Interactions as Nontrivial Factors Stabilizing Conformers J. Phys. Chem. A 2007, 111, 2957-2965
25. Dobrowolski, J. C.; Jamróz, M. H.; Kołos, R.; Rode, J. E.; Sadlej, J. Theoretical Prediction and the First IR Matrix Observation of Several L-Cysteine Molecule Conformers ChemPhysChem 2007, 8, 1085-1094
26. Boeckx, B.; Maes, G. The Conformational Behavior and H-Bond Structure of Asparagine: A Theoretical and Experimental Matrix-Isolation FT-IR Study Biophys. Chem. 2012, 165, 62-73
27. Boeckx, B.; Maes, G. Experimental and Theoretical Observation of Different Intramolecular H-bonds in Lysine Conformations J. Phys. Chem. B 2012, 116, 12441-12449
28. Borba, A.; Gómez-Zavaglia, A.; Lapinski, L.; Fausto, R. Rotational Isomers of Lactic Acid: First Experimental Observation of Higher Energy Forms Phys. Chem. Chem. Phys. 2004, 6, 2101-2108
29. Felder, P.; Günthard, Hs. H. Freezing of Internal Rotation Temperature in a Supersonic Jet Detected by Matrix IR Spectroscopy Chem. Phys. Lett. 1979, 66, 283-286
30. Felder, P.; Günthard, Hs. H. Conformational Interconversions in Supersonic Jets: Matrix IR Spectroscopy and Model Calculations Chem. Phys. 1982, 71, 9-25
31. Vidya, V.; Sankaran, K.; Viswanathan, K. S. Matrix Isolation-Supersonic Jet Infrared Spectroscopy: Conformational Cooling in Trimethyl Phosphate Chem. Phys. Lett. 1996, 258, 113-117
32. Kudoh, S.; Takayanagi, M.; Nakata, M. Conformational Cooling in a Supersonic Jet of 1,2-Dichloroethane Studied by Matrix Isolation Infrared Spectroscopy Chem. Phys. Lett. 1998, 296, 329-335
33. Vidya, V.; Sankaran, K.; Sundararajan, K.; Viswanathan, K. S. Conformations of Triethyl Phosphate: A Supersonic Jet-Matrix Isolation and Semi-Empirical (AM1) Study J. Mol. Struct. 1999, 476, 97-104
34. Venkatesan, V.; Sundararajan, K.; Viswanathan, K. S. Conformations of 1,1-Dimethoxyethane: Matrix Isolation Infrared and ab Initio Studies J. Phys. Chem. A 2002, 106, 7707-7712
35. Futami, Y.; Kudoh, S.; Ito, F.; Nakanaga, T.; Nakata, M. Structures of Methyl Halide Dimers in Supersonic Jets by Matrix-Isolation Infrared Spectroscopy and Quantum Chemical Calculations J. Mol. Struct. 2004, 690, 9-16
36. Mátyus, E.; Magyarfalvi, G.; Tarczay, G. Conformers and Photochemistry of Propyl Nitrites: A Matrix Isolation Study J. Phys. Chem. A 2007, 111, 450-459
37. Wassermann, T. N.; Suhm, M. A.; Roubin, P.; Coussan, S. Isomerization around C-C and C-O Bonds in 1-Propanol: Collisional Relaxation in Supersonic Jets and Selective IR Photo-Isomerization in Cryogenic Matrices J. Mol. Struct. 2012, 1025, 20-32
38. Barnes, A. J. Matrix Isolation Vibrational Spectroscopy as a Tool for Studying Conformational Isomerism J. Mol. Struct. 1984, 113, 161-174
39. Klaeboe, P.; Nielsen, C. J. Recent Advances in Infrared Matrix Isolation Spectroscopy. Invited Lecture Analyst 1992, 117, 335-341
40. Reva, I. D.; Jesus, A. J. L.; Rosado, M. T. S.; Fausto, R.; Eusébio, M. E.; Redinha, J. S. Stepwise Conformational Cooling Towards a Single Isomeric State in the Four Internal Rotors System 1,2-Butanediol Phys. Chem. Chem. Phys. 2006, 8, 5339-5349
41. Maier, G.; Endres, J.; Reisenauer, H. P. Interconversions between Oxalic Acid Monoamide Rotamers: Photochemical Process versus Tunneling J. Mol. Struct. 2012, 1025, 2-5
42. Stepanian, S. G.; Ivanov, A. Yu.; Smyrnova, D. A.; Adamowicz, L. UV-Induced Isomerization of β-Alanine Isolated in Argon Matrices J. Mol. Struct. 2012, 1025, 6-19
43. Nagaya, M.; Iizumi, S.; Sekine, M.; Nakata, M. UV-Induced Intramolecular Hydrogen-Atom Migration of 4-Chlororesorcinol and 4,6-Dichlororesorcinol in Low-Temperature Argon Matrices J. Mol. Struct. 2012, 1025, 53-60
44. Reva, I.; Almeida, B. J. A. N.; Lapinski, L.; Fausto, R. UV-Induced Photoisomerization of Maleic Hydrazide J. Mol. Struct. 2012, 1025, 74-83
45. Ivanov, A. Yu.; Stepanian, S. G.; Adamowicz, L. Tautomeric Transitions of Isocytosine Isolated in Argon and Neon Matrices Induced by UV Irradiation J. Mol. Struct. 2012, 1025, 92-104
46. Pettersson, M.; Lundell, J.; Khriachtchev, L.; Räsänen, M. IR Spectrum of the Other Rotamer of Formic Acid, cis -HCOOH J. Am. Chem. Soc. 1997, 119, 11715-11716
47. Reva, I. D.; Jarmelo, S.; Lapinski, L.; Fausto, R. IR-Induced Photoisomerization of Glycolic Acid Isolated in Low-Temperature Inert Matrices J. Phys. Chem. A 2004, 108, 6982-6989
48. Maçoîas, E. M. S.; Khriachtchev, L.; Pettersson, M.; Fausto, R.; Räsänen, M. Rotational Isomerization of Small Carboxylic Acids Isolated in Argon Matrices: Tunnelling and Quantum Yields for the Photoinduced Processes Phys. Chem. Chem. Phys. 2005, 7, 743-749
49. Maçoîas, E. M. S.; Khriachtchev, L.; Pettersson, M.; Fausto, R.; Räsänen, M. Internal Rotation in Propionic Acid: Near-Infrared-Induced Isomerization in Solid Argon J. Phys. Chem. A 2005, 109, 3617-3625
50. Marushkevich, K.; Siltanen, M.; Räsänen, M.; Halonen, L.; Khriachtchev, L. Identification of New Dimers of Formic Acid: The Use of a Continuous-Wave Optical Parametric Oscillator in Matrix Isolation Experiments J. Phys. Chem. Lett. 2011, 2, 695-699
51. Bazsó, G.; Góbi, S.; Tarczay, G. Near-Infrared Radiation Induced Conformational Change and Hydrogen Atom Tunneling of 2-Chloropropionic Acid in Low-Temperature Ar Matrix J. Phys. Chem. A 2012, 116, 4823-4832
52. Aspiala, A.; Lotta, T.; Murto, J.; Räsänen, M. IR-induced Photorotamerization of Allyl Alcohol in Low-temperature Matrices and Ab Initio Calculations J. Chem. Phys. 1983, 79, 4183-4192
53. Lapinski, L.; Nowak, M. J.; Reva, I. D.; Rostkowska, H.; Fausto, R. NIR-Laser-Induced Selective Rotamerization of Hydroxy Conformers of Cytosine Phys. Chem. Chem. Phys. 2010, 12, 9615-9618
54. Reva, I. D.; Nowak, M. J.; Lapinski, L.; Fausto, R. Spontaneous Tunneling and Near-infrared-induced Interconversion between the Amino-hydroxy Conformers of Cytosine J. Chem. Phys. 2012, 136, 064511-1-8
55. Sharma, A.; Reva, I. D.; Fausto, R. Conformational Switching Induced by Near-Infrared Laser Irradiation J. Am. Chem. Soc. 2009, 131, 8752-8753
56. Cao, M.; Newton, S. Q.; Pranata, J.; Schäfer, L. Ab Initio Conformational Analysis of Alanine J. Mol. Struct. (THEOCHEM) 1995, 332, 251-267
57. Császár, A. G. On the Structures of Free Glycine and α-Alanine J. Mol. Struct. 1995, 346, 141-152
58. Császár, A. G. Conformers of Gaseous α-Alanine J. Phys. Chem. 1996, 100, 3541-3551
59. e Structures J. Chem. Theory Comput. 2010, 6, 3066-3078
60. Balabin, R. M. Conformational Equilibrium in Alanine: Focal-Point Analysis and Ab Initio Limit Comput. Theor. Chem. 2011, 965, 15-21
61. Cormanich, R. A.; Ducati, L. C.; Rittner, R. The Lack of Intramolecular Hydrogen Bonding and the Side Chain Effect in Alanine Conformers J. Mol. Struct. 2012, 1014, 12-16
62. 2H J. Mol. Struct. 1991, 248, 133-142
63. Iijima, K.; Nakano, M. Reinvestigation of Molecular Structure and Conformation of Gaseous l-Alanine by Joint Analysis using Electron Diffraction Data and Rotational Constants J. Mol. Struct. 1999, 485-486, 255-260
64. Godfrey, P. D.; Firth, S.; Hatherley, L. D.; Brown, R. D.; Pierlot, A. P. Millimeter-Wave Spectroscopy of Biomolecules: Alanine J. Am. Chem. Soc. 1993, 115, 9687-9691
65. Godfrey, P. D.; Brown, R. D.; Rodgers, F. M. The Missing Conformers of Glycine and Alanine: Relaxation in Seeded Supersonic Jets J. Mol. Struct. 1996, 376, 65-81
66. Blanco, S.; Lesarri, A.; Lopez, J. C.; Alonso, J. L. The Gas-Phase Structure of Alanine J. Am. Chem. Soc. 2004, 126, 11675-11683
67. Hirata, Y.; Kubota, S.; Watanabe, S.; Momose, T.; Kawaguchi, K. Millimeter-Wave Spectroscopy of α-Alanine J. Mol. Spectrosc. 2008, 251, 314-318
68. Linder, R.; Seefeld, K.; Vavra, A.; Kleinermans, K. Gas Phase Infrared Spectra of Nonaromatic Amino Acids Chem. Phys. Lett. 2008, 453, 1-6
69. Farrokhpour, H.; Fathi, F.; Naves De Brito, A. Theoretical and Experimental Study of Valence Photoelectron Spectrum of d,l-Alanine Amino Acid J. Phys. Chem. A 2012, 116, 7004-7015
70. Balabin, R. M. The Identification of the Two Missing Conformers of Gas-Phase Alanine: a Jet-Cooled Raman Spectroscopy Study Phys. Chem. Chem. Phys. 2010, 12, 5980-5982
71. Marushkevich, K.; Räsänen, M.; Khriachtchev, L. Interaction of Formic Acid with Nitrogen: Stabilization of the Higher-Energy Conformer J. Phys. Chem. A 2010, 114, 10584-10589
72. Lopes, S.; Domanskaya, A. V.; Fausto, R.; Räsänen, M.; Khriachtchev, L. Formic and Acetic Acids in a Nitrogen Matrix: Enhanced Stability of the Higher-Energy Conformer J. Chem. Phys. 2010, 133, 144507-1-7
73. PQS Version 3.2; Parallel Quantum Solutions, 2013 Green Acres Road, Fayetteville, Arkansas 72703, 2006.
74. Baker, J.; Wolinski, K.; Malagoli, M.; Kinghorn, D.; Wolinski, P.; Magyarfalvi, G.; Saebo, S.; Janowski, T.; Pulay, P. Quantum Chemistry in Parallel with PQS J. Comput. Chem. 2009, 30, 317-335
75. 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 A.1; Gaussian, Inc., Wallingford CT, 2009.
76. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
77. 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 1998, 37, 785-789
78. Hehre, W. J.; Ditchfield, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules J. Chem. Phys. 1972, 56, 2257-2261
79. Francl, M. M.; Petro, W. J.; Hehre, W. J.; Binkley, J. S.; Gordon, M. S.; DeFrees, D. J.; Pople, J. A. Self-Consistent Molecular Orbital Methods. XXIII. A Polarization-Type Basis Set for Second-Row Elements J. Chem. Phys. 1982, 77, 3654-3665
80. Krishnam, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. XX. A Basis Set for Correlated Wave Functions J. Chem. Phys. 1980, 72, 650-654
81. Gill, P. M. W.; Johnson, B. G.; Pople, J. A.; Frisch, M. J. The Performance of the Becke-Lee-Yang-Parr (B-LYP) Density Functional Theory with Various Basis Sets Chem. Phys. Lett. 1992, 197, 499-505
82. Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems Phys. Rev. 1934, 46, 618-622
83. Pulay, P.; Fogarasi, G.; Pongor, G.; Boggs, J. E.; Vargha, A. Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene J. Am. Chem. Soc. 1983, 105, 7037-7047
84. Baker, J.; Jarzecki, A. A.; Pulay, P. Direct Scaling of Primitive Valence Force Constants: An Alternative Approach to Scaled Quantum Mechanical Force Fields J. Phys. Chem. A 1998, 102, 1412-1424
85. Fábri, C.; Szidarovszky, T.; Magyarfalvi, G.; Tarczay, G. Gas-Phase and Ar-Matrix SQM Scaling Factors for Various DFT Functionals with Basis Sets Including Polarization and Diffuse Functions J. Phys. Chem. A 2011, 115, 4640-4649
86. Maçoîas, E. M. S.; Khriachtchev, L.; Pettersson, M.; Fausto, R.; Räsänen, M. Rotational Isomerism of Acetic Acid Isolated in Rare-gas Matrices: Effect of Medium and Isotopic Substitution on IR-Induced Isomerization Quantum Yield and Cis → Trans Tunneling Rate J. Chem. Phys. 2004, 121, 1331-1338
87. Skrdla, P. J. Comparison of Two Types of Dispersive Kinetic Approaches in Relation to Time-Dependent Marcus Theory J. Phys. Chem. A 2007, 111, 11809-11813
88. Plonka, A. Dispersive Kinetics Annu. Rep. Prog. Chem., Sect. C 2001, 97, 91-147
89. Balabin, R. M. Conformational Equilibrium in Glycine: Experimental Jet-Cooled Raman Spectrum J. Phys. Chem. Lett. 2010, 1, 20-23