Vibrational energy relaxation of the amide i mode of N-methylacetamide in D2O studied through born-oppenheimer molecular dynamics

Journal of Physical Chemistry B

Volumn 118, Issue 23, 2014, Pages 6186-6197

  Farag, Marwa H ^a   Bastida, Adolfo ^a   Ruiz López, Manuel F ^b,c   Monard, Gérald ^b,c   Ingrosso, Francesca ^b,c  

^a UNIVERSITY OF MURCIA   (Spain)

^b UNIVERSITÉ DE LORRAINE   (France)

^c NANCY UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; MOLECULAR VIBRATIONS;

BORN-OPPENHEIMER MOLECULAR DYNAMICS; INSTANTANEOUS NORMAL MODES; INTERMOLECULAR ENERGY; INTRAMOLECULAR VIBRATIONAL ENERGY REDISTRIBUTIONS; NON-EQUILIBRIUM SIMULATIONS; RELAXATION MECHANISM; VIBRATIONAL ENERGY RELAXATION; VIBRATIONAL RELAXATION;

AMIDES;

ACETAMIDE DERIVATIVE; DEUTERIUM OXIDE; N-METHYLACETAMIDE; SOLUTION AND SOLUBILITY; SOLVENT;

CHEMISTRY; MOLECULAR DYNAMICS; SOLUTION AND SOLUBILITY; TEMPERATURE; VIBRATION;

ACETAMIDES; DEUTERIUM OXIDE; MOLECULAR DYNAMICS SIMULATION; SOLUTIONS; SOLVENTS; TEMPERATURE; VIBRATION;

EID: 84902521059     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp500304z     Document Type: Article

References (80)

1. Hamm, P.; Lim, M. H.; Hochstrasser, R. M. Structure of the Amide I Band of Peptides Measured by Femtosecond Nonlinear-Infrared Spectroscopy J. Phys. Chem. B 1998, 102, 6123-6138
2. Zanni, M. T.; Asplund, M. C.; Hochstrasser, R. M. Two-dimensional Heterodyned and Stimulated Infrared Photon Echoes of N-Methylacetamide-D J. Chem. Phys. 2001, 114, 4579-4590
3. DeFlores, L. P.; Ganim, Z.; Ackley, S. F.; Chung, H. S.; Tokmakoff, A. The Anharmonic Vibrational Potential and Relaxation Pathways of the Amide I and II Modes of N -Methylacetamide J. Phys. Chem. B 2006, 110, 18973-18980
4. Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P. Subpicosecond Conformational Dynamics of Small Peptides probed by Two-dimensional Vibrational Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11254
5. Woutersen, S.; Pfister, R.; Hamm, P.; Mu, Y. G.; Kosov, D. S.; Stock, G. Peptide Conformational Heterogeneity Revealed from Nonlinear Vibrational Spectroscopy and Molecular-Dynamics Simulations J. Chem. Phys. 2002, 117, 6833-6840
6. Rubtsov, I. V.; Wang, J.; Hochstrasser, R. M. Dual-Frequency 2D-IR Spectroscopy Heterodyned Photo Echo of the Peptide Bond Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 5601
7. DeCamp, M. F.; DeFlores, L.; McCracken, J. M.; Tokmakoff, A.; Kwac, K.; Cho, M. Amide I Vibrational Dynamics of N -Methylacetamide in Polar Solvents: The Role of Electrostatic Interactions J. Phys. Chem. B 2005, 109, 11016-11026
8. 2O) Solution J. Phys. Chem. A 2009, 113, 75-84
9. Piatkowski, L.; Bakker, H. J. Vibrational Relaxation Pathways of AI and AII Modes in N -Methylacetamide Clusters J. Phys. Chem. A 2010, 114, 11462-11470
10. Gregurick, S. K.; Chaban, G. M.; Gerber, R. B. Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N -Methylacetamide J. Phys. Chem. A 2002, 106, 8696-8707
11. Nguyen, P. H.; Stock, G. Nonequilibrium Molecular Dynamics Study of the Vibrational Energy Relaxation of Peptides in Water J. Chem. Phys. 2003, 119, 11350-11358
12. Kwac, K.; Cho, M. H. Molecular Dynamics Simulation Study of N -Methylacetamide in Water. I. Amide I Mode Frequency Fluctuation J. Chem. Phys. 2003, 119, 2247-2255
13. Schmidt, J. R.; Corcelli, S. A.; Skinner, J. L. Ultrafast Vibrational Spectroscopy of Water and Aqueous N -Methylacetamide: Comparison of Different Electronic Structure J. Chem. Phys. 2004, 121, 8887-8896
14. Hayashi, T.; Zhuang, W.; Mukamel, S. Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA J. Phys. Chem. A 2005, 109, 9747-9759
15. Fujisaki, H.; Zhang, Y.; Straub, J. E. Time-Dependent Perturbation Theory for Vibrational Energy Relaxation and Dephasing in Peptides and Proteins J. Chem. Phys. 2006, 124, 144910
16. Dijkstra, A. G.; Jansen, T. C.; Bloem, R.; Knoester, J. Vibrational Relaxation in Simulated Two-Dimensional Infrared Spectra of Two Amide Modes in Solution J. Chem. Phys. 2007, 127, 194505
17. Fujisaki, H.; Yagi, K.; Hirao, K.; Straub, J. E. Quantum Dynamics of N -Methylacetamide Studied by the Vibrational Configuration Interaction Method Chem. Phys. Lett. 2007, 443, 6-11
18. Fujisaki, H.; Stock, G. Dynamic Treatment of Vibrational Energy Relaxation in a Heterogeneous and Fluctuating Environment J. Chem. Phys. 2008, 129, 134110
19. Park, S.; Nguyen, P. H.; Stock, G. Molecular Dynamics Simulation of Cooling: Heat Transfer from a Photoexcited Peptide to the Solvent J. Chem. Phys. 2010, 131, 184503
20. Fujisaki, H.; Yagi, K.; Straub, J. E.; Stock, G. Quantum and Classical Vibrational Relaxation Dynamics of N -Methylacetamide on Ab-Initio Potential Energy Surfaces Int. J. Quantum Chem. 2009, 109, 2047-2057
21. Bastida, A.; Soler, M. A.; Zuñiga, J.; Requena, A.; Kalstein, A.; Fernandez-Alberti, S. Instantaneous Normal Modes, Resonances, and Decay Channels in the Vibrational Relaxation of the Amide I Mode of N -Methylacetamide-D in Liquid Deutrated Water J. Chem. Phys. 2010, 132, 224501
22. 2O Solution J. Phys. Chem. B 2012, 116, 2969
23. Moran, A.; 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
24. Moran, A.; Mukamel, S. The origin of Vibrational Mode Couplings in Various Secondary Structural Motifs of Polypeptides Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 506-510
25. Peterson, K. A.; Rella, C. W.; Engholm, J. R.; Schwettman, H. A. Ultrafast Vibrational Dynamics of the Myoglobin Amide I Band J. Phys. Chem. B 1999, 103, 557-561
26. Xie, A.; van der Meer, L.; Hoff, W.; Austin, R. Long-Lived Amide I. Vibrational Modes in Myoglobin Phys. Rev. Lett. 2000, 84, 5435
27. Austin, R.; Xie, A.; van der Meer, L.; Redlich, B.; Lindgard, P.; Frauenfelder, H.; Fu, D. Picosecond Thermometer in the Amide I Band of Myoglobin Phys. Rev. Lett. 2005, 94, 128101
28. Zhang, Y.; Fujisaki, H.; Straub, J. E. Mode-Specific Vibrational Energy Relaxation of the Amide I' and II' Modes in N -Methylacetamide/Water Clusters: Intra- and Intermolecular Energy Transfer Mechanism J. Phys. Chem. A 2009, 113, 3051-3060
29. Fujisaki, H.; Zhang, Y.; Straub, J. Non-Markovian Theory of Vibrational Energy Relaxation and its Applications to Biomolecular Systems. In Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems: Clusters and Proteins; Komatsuzaki, T.; Berry, R. S.; Leitner, D. M., Eds.; Advances in Chemical Physics; John Wiley & Sons, Inc.: Hoboken, NJ, 2011; Vol. 145.
30. 2Cluster: A Molecular Dynamics with Quantum Transitions Study J. Chem. Phys. 1998, 109, 6320
31. Cieplak, P.; Dupradeau, F.-Y.; Duan, Y.; Wang, J. Polarization Effects in Molecular Mechanical Force Fields J. Phys.: Condens. Matter 2009, 21, 333102
32. Ponder, J. W. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114, 2549-2564
33. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: Cambridge, U.K., 2009.
34. Jeon, J.; Cho, M. Redistribution of Carbonyl Stretch Mode Energy in Isolated and Solvated N-Methylacetamide: Kinetic Energy Spectral Density Analyses J. Chem. Phys. 2011, 135, 214504
35. Monard, G.; Bernal-Uruchurtu, M. I.; van der Vaart, A.; Merz, K. M., Jr.; Ruiz-López, M. F. Simulation of Liquid Water Using Semiempirical Hamiltonians and the Divide and Conquer Approach J. Phys. Chem. A 2005, 109, 3425
36. Ingrosso, F.; Monard, G.; Farag, M. H.; Bastida, A.; Ruiz-López, M. F. Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution J. Chem. Theory Comput. 2011, 7, 1840-1849
37. Yang, W.; Lee, T.-S. A Density Matrix Divide and Conquer Approach for Electronic Structure Calculations of Large Molecules J. Chem. Phys. 1995, 103, 5674-5678
38. Dixon, S. L.; Merz, K. M., Jr. Semiempirical Molecular Orbital Calculations with Linear System Size Scaling J. Chem. Phys. 1996, 104, 6643-6649
39. Bastida, A.; Soler, M. A.; Zuñiga, J.; Requena, A.; Kalstein, A.; Fernandez-Alberti, S. Molecular Dynamics Simulations and Instantaneous Normal-Mode Analysis of the Vibrational Relaxation of the C-H Stretching Modes of N -methylacetamide- d in Liquid Deutrated Water J. Phys. Chem. A 2010, 114, 11450-11461
40. Kalstein, A.; Fernández-Alberti, S.; Bastida, A.; Soler, M. A.; Farag, M. H.; Zuñiga, J.; Requena, A. Vibrational Dynamics of Polyatomic Molecules in Solution: Assignment, Time Evolution and Mixing of Instantaneous Normal Modes Theor. Chem. Acc. 2011, 128, 769-782
41. Farag, M. H.; Zuñiga, J.; Requena, A.; Bastida, A. Instantaneous Normal Mode Analysis of the Vibrational Relaxation of the Amide I Mode of Alanine Dipeptide in Water J. Chem. Phys. 2013, 138, 205102
42. Pople, J. A.; Santry, D. P.; Segal, G. A. Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures J. Chem. Phys. 1965, 43, S129-S135
43. Dewar, M. J. S.; Thiel, W. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters J. Am. Chem. Soc. 1977, 99, 4899-4907
44. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and Use of Quantum Mechanical Molecular Models. 76. AM1: A New General Purpose Quantum Mechanical Molecular Model J. Am. Chem. Soc. 1985, 107, 3902-3909
45. Stewart, J. J. Optimization of Parameters for Semiempirical Methods. I. Method J. Comput. Chem. 1989, 10, 209
46. Csonka, G. I.; Angyan, J. G. The Origin of the Problems with the PM3 Core Repulsion Function J. Mol. Struct.: THEOCHEM 1997, 393, 31
47. Bernal-Uruchurtu, M. I.; Martins-Costa, M. T. C.; Millot, C.; Ruiz-López, M. F. Improving Description of Hydrogen Bonds at the Semiempirical Level: Water-Water Interactions as Test Case J. Comput. Chem. 2000, 21, 572
48. Harb, W.; Bernal-Uruchurtu, M. I.; Ruiz-López, M. F. An Improved Semiempirical Method for Hydrated Systems Theor. Chem. Acc. 2004, 112, 204
49. Stewart, J. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Modeling 2007, 13, 1173-1213
50. Stewart, J. Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximations and Re-optimization of Parameters J. Mol. Modeling 2013, 19, 1-32
51. Chang, D. T.; Schenter, G. K.; Garrett, B. C. Self-Consistent Polarization Neglect of Diatomic Differential Overlap: Application to Water Clusters J. Chem. Phys. 2008, 128, 164111
52. Murdachaew, G.; Mundy, C. J.; Schenter, G. K.; Laino, T.; Hutter, J. Semiempirical Self-Consistent Polarization Description of Bulk Water, the Liquid-Vapor Interface, and Cubic Ice J. Phys. Chem. A 2011, 115, 6046-6053
53. Thiel, W. Semiempirical Quantum-Chemical Methods Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2013, 4, 145-157
54. Wu, X.; Thiel, W.; Pezeshki, S.; Lin, H. Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models J. Chem. Theory Comput. 2013, 9, 2672-2686
55. Bernal-Uruchurtu, M. I.; Ruiz-López, M. F. Basic Ideas for the Correction of Semiempirical Methods Describing H-Bonded Systems Chem. Phys. Lett. 2000, 330, 118-124
56. Carpaneto, G.; Martello, S.; Toth, P. Algorithms and codes for the assigment problem Annals of Operations Research 1988, 13, 193-223
57. Farag, M. H. Study of the IR spectrum and the vibrational relaxation of peptides in water solution, Thesis, Universidad de Murcia, Murcia, Spain, 2012.
58. Case, D. A. AMBER 9, University of California, San Francisco, 2006.
59. Herbert, J. M.; Head-Gordon, M. Accelerated, Energy-Conserving Born-Oppenheimer Molecular Dynamics via Fock Matrix Extrapolation Phys. Chem. Chem. Phys. 2005, 7, 3269
60. Niklasson, A. M. N.; Tymczak, C. J.; Challacombe, M. Time-Reversible Born-Oppenheimer Molecular Dynamics Phys. Rev. Lett. 2006, 97, 123000
61. Nam, K.; Gao, J.; York, D. M. An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations J. Chem. Theory Comput. 2005, 1, 2
62. Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. Class-IV Charge Models: A New Semiempirical Approach in Quantum-Chemistry J. Comput. Aided Mol. Des. 1995, 9, 87
63. Andersen, H. C. Molecular Dynamics Simulations at Constant Pressure and/or Temperature J. Chem. Phys. 1980, 72, 2384
64. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Path J. Chem. Phys. 1984, 81, 3684
65. Pulay, P.; Fogarasi, G. Fock Matrix Dynamics Chem. Phys. Lett. 2004, 386, 272-278
66. Hayashi, T.; Zhuang, W.; Mukamel, S. Electrostatic DFT Map for Complete Vibrational Amide Band of NMA J. Phys. Chem. A 2005, 109, 9747
67. Bloem, R.; Dijkstra, A. G.; Jansen, T. C.; Knoester, J. Simulation of Vibrational Energy Transfer in Two-Dimensional Infrared Spectroscopy of Amide I and Amide II Modes in Solution J. Chem. Phys. 2008, 129, 055101
68. Bowman, J. M.; Gazdy, B.; Sun, Q. A Method to Constrain Vibrational Energy in Quasiclassical Trajectory Calculations J. Chem. Phys. 1989, 91, 2859-2862
69. Guo, Y.; Thompson, D. L.; Sewell, T. D. Analysis of the Zero-Point Energy Problem in Classical Trajectory Simulations J. Chem. Phys. 1996, 104, 576-582
70. Habershon, S.; Manolopoulos, D. E. Zero Point Energy Leakage in Condensed Phase Dynamics: An Assessment of Quantum Simulation Methods for Liquid Water J. Chem. Phys. 2009, 131, 244518
71. Soler, M.; Bastida, A.; Farag, M. H.; Zuñiga, J.; Requena, A. A Method for Analyzing the Vibrational Energy Flow in Biomolecules J. Chem. Phys. 2011, 135, 204106
72. Piatkowski, L.; Bakker, H. J. Vibrational Relaxation Pathways of Amide I and Amide II Modes in N -Methylacetamide J. Chem. Phys. 2012, 136, 164504
73. Dijkstra, A. G.; Jansen, T. C.; Bloem, R.; Knoester, J. Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution J. Chem. Phys. 2007, 127, 194505
74. Dijkstra, A. G.; la Cour Jansen, T.; Knoester, J. Modeling the Vibrational Dynamics and Nonlinear Infrared Spectra of Coupled Amide I and II Modes in Peptides J. Phys. Chem. B 2011, 115, 5392-5401
75. Ohmine, I.; Tanaka, H. Potential Energy Surfaces for Water Dynamics. II. Vibrational Mode Excitations, Mixing, and Relaxations J. Chem. Phys. 1990, 93, 8138-8147
76. Moritsugu, K.; Miyashita, O.; Kidera, A. Vibrational Energy Transfer in a Protein Molecule Phys. Rev. Lett. 2000, 85, 3970
77. Moritsugu, K.; Miyashita, O.; Kidera, A. Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule J. Phys. Chem. B 2003, 107, 3309
78. Mayne, L.; Hudson, B. Resonance Raman-Spectroscopy of N -Methylacetamide-Overtones and Combinations of the C-N Stretch (Amide II') and Effect of Solvation on the C - O Stretch (Amide I) Intensity J. Phys. Chem. 1991, 95, 2962
79. Chen, X.; Schweitzer-Stenner, R.; Asher, S.; Mirkin, N.; 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
80. Rey-Lafon, M.; Forel, M. T.; Garrigou-Lagrange, C. Discussion des Modes Normaux des Groupements Amides cis et trans aè Partir des Champs de Force du δ-Valérolactame et du N-Methylacetamide Spectrochim. Acta, Part A 1973, 29A, 471-486