Simplified sum-over-states approach for predicting resonance raman spectra. Application to nucleic acid bases

Journal of Physical Chemistry Letters

Volumn 2, Issue 11, 2011, Pages 1254-1260

  Rappoport, Dmitrij ^a   Shim, Sangwoo ^a   Aspuru Guzik, Alán ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONIC EXCITATION ENERGY; LIMITING CASE; NONRESONANT; NUCLEIC ACID BASIS; RAMAN EXCITATION PROFILE; RESONANCE ENHANCEMENT; RESONANCE RAMAN SPECTRA; SUM-OVER-STATES; SUM-OVER-STATES APPROACHES; SURFACE ENHANCED RAMAN SCATTERING; TIME DEPENDENT DENSITY FUNCTIONAL THEORY; TRANSITION DIPOLE MOMENTS;

DENSITY FUNCTIONAL THEORY; EXCITED STATES; NUCLEIC ACIDS; RAMAN SCATTERING; RAMAN SPECTROSCOPY; RESONANCE;

ELECTRON ENERGY LOSS SPECTROSCOPY;

EID: 79958197718     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz200413g     Document Type: Article

References (58)

1. Shorygin, P. P. Intensity of Combination Scattering Lines and Structure of Organic Compounds Zh. Fiz. Khim. 1947, 21, 1125-1134
2. Shorygin, P. P.; Krushinskij, L. L. Early Days and Later Development of Resonance Raman Spectroscopy J. Raman Spectrosc. 1997, 28, 383-388 (Pubitemid 127690492)
3. Parker, F. S. Applications of Infrared, Raman, and Resonance Raman Spectroscopy in Biochemistry; Springer: New York, 1983.
4. Spiro, T. G., Ed. Biological Applications of Raman Spectroscopy; Wiley: New York, 1987; Vol. 1-3.
5. Benevides, J. M.; Overman, S. A.; Thomas, G. J. Raman, Polarized Raman and Ultraviolet Resonance Raman Spectroscopy of Nucleic Acids and Their Complexes J. Raman Spectrosc. 2005, 36, 279-299 (Pubitemid 40653526)
6. Moskovits, M. Surface-Enhanced Spectroscopy Rev. Mod. Phys. 1985, 57, 783-826
7. Kneipp, K.; Moskovits, M.; Kneipp, H., Eds. Surface-Enhanced Raman Scattering: Physics and Applications; Springer: Berlin, Germany, 2006.
8. Jensen, L.; Aikens, C. M.; Schatz, G. C. Electronic Structure Methods for Studying Surface-Enhanced Raman Scattering Chem. Soc. Rev. 2008, 37, 1061-1073
9. Schatz, G.; Young, M.; Van Duyne, R. In Surface-Enhanced Raman Scattering; Kneipp, K.; Moskovits, M.; Kneipp, H., Eds.; Springer: Berlin, Germany, 2006; Vol. 103, pp 19-45.
10. Saikin, S. K.; Olivares-Amaya, R.; Rappoport, D.; Stopa, M.; Aspuru-Guzik, A. On the Chemical Bonding Effects in the Raman Response: Benzenethiol Adsorbed on Silver Clusters Phys. Chem. Chem. Phys. 2009, 11, 9401-9411
11. Saikin, S. K.; Chu, Y.; Rappoport, D.; Crozier, K. B.; Aspuru-Guzik, A. Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates J. Phys. Chem. Lett. 2010, 1, 2740-2746
12. Nie, S.; Emory, S. R. Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering Science 1997, 275, 1102-1106 (Pubitemid 27097304)
13. Kneipp, K.; Wang, Y.; Kneipp, H.; Perelman, L. T.; Itzkan, I.; Dasari, R. R.; Feld, M. S. Single Molecule Detection Using Surface-Enhanced Raman Scattering (SERS) Phys. Rev. Lett. 1997, 78, 1667-1670 (Pubitemid 127648192)
14. Dieringer, J. A.; Wustholz, K. L.; Masiello, D. J.; Camden, J. P.; Kleinman, S. L.; Schatz, G. C.; Van Duyne, R. P. Surface-Enhanced Raman Excitation Spectroscopy of a Single Rhodamine 6G Molecule J. Am. Chem. Soc. 2009, 131, 849-854
15. Schorygin, P.; Kuzina, L.; Ositjanskaja, L. Untersuchungen Über die Intensität der Ramanlinien Microchim. Acta 1955, 43, 630-636
16. Albrecht, A. C. On the Theory of Raman Intensities J. Chem. Phys. 1961, 34, 1476-1484
17. Long, D. A. The Raman Effect, 2 nd ed.; Wiley: Chichester, U.K., 2002.
18. Kramers, H. A.; Heisenberg, W. Über die Streuung von Strahlung durch Atome Z. Phys. 1925, 31, 681-708
19. Dirac, P. A. M. The Quantum Theory of Dispersion Proc. R. Soc. London, Ser. A 1927, 114, 710-728
20. van Vleck, J. H. On the Vibrational Selection Principles in the Raman Effect Proc. Natl. Acad. Sci. U.S.A. 1929, 15, 754-764
21. Placzek, G. In Handbuch der Radiologie; Marx, E., Ed.; Akademische Verlagsgesellschaft: Leipzig, Germany, 1934; Vol. VI/2, pp 209-374.
22. Behringer, J.; BrandmÜller, J. Der Resonanz-Raman-Effekt Z. Elektrochem. 1956, 60, 643-679
23. Albrecht, A. C. "Forbidden" Character in Allowed Electronic Transitions J. Chem. Phys. 1960, 33, 156-169
24. Fischer, G. Vibronic Coupling: The Interaction between the Electronic and Nuclear Motions; Academic Press: London, 1984.
25. Kane, K. A.; Jensen, L. Calculation of Absolute Resonance Raman Intensities: Vibronic Theory vs Short-Time Approximation J. Phys. Chem. C 2010, 114, 5540-5546
26. Lee, S.-Y.; Heller, E. J. Time-Dependent Theory of Raman Scattering J. Chem. Phys. 1979, 71, 4777-4788
27. Heller, E. J.; Sundberg, R. L.; Tannor, D. Simple Aspects of Raman Scattering J. Phys. Chem. 1982, 86, 1822-1833
28. Neugebauer, J.; Hess, B. A. Resonance Raman Spectra of Uracil Based on Kramers-Kronig Relations Using Time-Dependent Density Functional Calculations and Multireference Perturbation Theory J. Chem. Phys. 2004, 120, 11564-11577
29. Neese, F.; Petrenko, T.; Ganyushin, D.; Olbrich, G. Advanced Aspects of Ab Initio Theoretical Optical Spectroscopy of Transition Metal Complexes: Multiplets, Spin-Orbit Coupling and Resonance Raman Intensities Coord. Chem. Rev. 2007, 251, 288-327
30. Jensen, L.; Autschbach, J.; Schatz, G. C. Finite Lifetime Effects on the Polarizability Within Time-Dependent Density-Functional Theory J. Chem. Phys. 2005, 122, 224115
31. Jensen, L.; Zhao, L. L.; Autschbach, J.; Schatz, G. C. Theory and Method for Calculating Resonance Raman Scattering from Resonance Polarizability Derivatives J. Chem. Phys. 2005, 123, 174110
32. Furche, F.; Rappoport, D. Theoretical and Computational Chemistry. In Computational Photochemistry; Olivucci, M., Ed.; Elsevier: Amsterdam, The Netherlands, 2005; pp 93-128.
33. Yuen-Zhou, J.; Tempel, D. G.; Rodriguez-Rosario, C. A.; Aspuru-Guzik, A. Time-Dependent Density Functional Theory for Open Quantum Systems with Unitary Propagation Phys. Rev. Lett. 2010, 104, 043001
34. Yuen-Zhou, J.; Rodriguez-Rosario, C. A.; Aspuru-Guzik, A. Time-Dependent Current-Density Functional Theory for Generalized Open Quantum Systems Phys. Chem. Chem. Phys. 2009, 11, 4509-4522
35. Tempel, D. G.; Watson, M. A.; Olivares-Amaya, R.; Aspuru-Guzik, A. Time-Dependent Density Functional Theory of Open Quantum Systems in the Linear-Response Regime J. Chem. Phys. 2011, 134, 074116
36. Rappoport, D.; Furche, F. Lagrangian Approach to Molecular Vibrational Raman Intensities Using Time-Dependent Hybrid Density Functional Theory J. Chem. Phys. 2007, 126, 201104
37. Coriani, S.; Kjrgaard, T.; Jørgensen, P.; Ruud, K.; Huh, J.; Berger, R. An Atomic-Orbital-Based Lagrangian Approach for Calculating Geometric Gradients of Linear Response Properties J. Chem. Theory Comput. 2010, 6, 1028-1047
38. Furche, F.; Ahlrichs, R. Adiabatic Time-Dependent Density Functional Methods for Excited State Properties J. Chem. Phys. 2002, 117, 7433-7447 (Pubitemid 35354307)
39. Rappoport, D.; Furche, F. In Time-Dependent Density Functional Theory; Marques, M. A. L.; Ullrich, C. A.; Nogueira, F.; Rubio, A.; Burke, K.; Gross, E. K. U., Eds.; Springer: Berlin, Germany, 2006; Chapter 23, pp 337-354.
40. Perdew, J. P.; Ernzerhof, M.; Burke, K. Rationale for Mixing Exact Exchange With Density Functional Approximations J. Chem. Phys. 1996, 105, 9982-9985 (Pubitemid 126747886)
41. Schäfer, A.; Huber, C.; Ahlrichs, R. Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr J. Chem. Phys. 1994, 100, 5829-5835
42. Adamo, C.; Cossi, M.; Scalmani, G.; Barone, V. Accurate Static Polarizabilities by Density Functional Theory: Assessment of the PBE0 Model Chem. Phys. Lett. 1999, 307, 265-271 (Pubitemid 129556398)
43. Van Caillie, C.; Amos, R. D. Static and Dynamic Polarisabilities, Cauchy Coefficients and Their Anisotropies: An Evaluation of DFT Functionals Chem. Phys. Lett. 2000, 328, 446-452
44. Van Caillie, C.; Amos, R. D. Raman Intensities Using Time Dependent Density Functional Theory Phys. Chem. Chem. Phys. 2000, 2, 2123-2129
45. Merrick, J. P.; Moran, D.; Radom, L. An Evaluation of Harmonic Vibrational Frequency Scale Factors J. Phys. Chem. A 2007, 111, 11683-11700 (Pubitemid 350197612)
46. Adamo, C.; Scuseria, G. E.; Barone, V. Accurate Excitation Energies from Time-Dependent Density Functional Theory: Assessing the PBE0 Model J. Chem. Phys. 1999, 111, 2889-2899
47. TURBOMOLE V6.2 2010, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com.
48. Fodor, S. P. A.; Rava, R. P.; Hays, T. R.; Spiro, T. G. Ultraviolet Resonance Raman Spectroscopy of the Nucleotides With 266-, 240-, 218-, and 200-nm Pulsed Laser Excitation J. Am. Chem. Soc. 1985, 107, 1520-1529
49. Nishimura, Y.; Tsuboi, M.; Kubasek, W. L.; Bajdor, K.; Peticolas, W. L. Ultraviolet Resonance Raman Bands of Guanosine and Adenosine Residues Useful for the Determination of Nucleic Acid Conformation J. Raman Spectrosc. 1987, 18, 221-227
50. Clark, L. B. Electronic Spectra of Crystalline Guanosine: Transition Moment Directions of the Guanine Chromophore J. Am. Chem. Soc. 1994, 116, 5265-5270 (Pubitemid 24241764)
51. Shukla, M. K.; Leszczynski, J. TDDFT Investigation on Nucleic Acid Bases: Comparison With Experiments and Standard Approach J. Comput. Chem. 2004, 25, 768-778
52. Shukla, M.; Leszczynski, J. Electronic Spectra, Excited State Structures and Interactions of Nucleic Acid Bases and Base Assemblies: A Review J. Biomol. Struct. Dyn. 2007, 25, 93-118 (Pubitemid 47124370)
53. 18O Substitution Effects J. Raman Spectrosc. 1999, 30, 623-630
54. Voelter, W.; Records, R.; Bunnenberg, E.; Djerassi, C. Magnetic Circular Dichroism Studies. VI. Investigation of Some Purines, Pyrimidines, and Nucleosides J. Am. Chem. Soc. 1968, 90, 6163-6170
55. Mathlouthi, M.; Seuvre, A. M.; Koenig, J. L. F.T.-I.R. and Laser-Raman Spectra of Guanine and Guanosine Carbohydr. Res. 1986, 146, 15-27
56. Florián, J. Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid-State Nucleic Acid Constituents. 6. Guanine and Guanine Residue J. Phys. Chem. 1993, 97, 10649-10658
57. Giese, B.; McNaughton, D. Density Functional Theoretical (DFT) and Surface-Enhanced Raman Spectroscopic Study of Guanine and Its Alkylated Derivatives. Part 1. DFT Calculations on Neutral, Protonated and Deprotonated Guanine Phys. Chem. Chem. Phys. 2002, 4, 5161-5170
58. Tsuboi, M.; Nishimura, Y.; Hirakawa, A. Y. In Biological Applications of Raman Spectroscopy; Spiro, T. G., Ed.; Wiley: New York, 1987; Vol. 2, pp 109-179.