Suppressing sampling noise in linear and two-dimensional spectral simulations

Journal of Chemical Physics

Volumn 142, Issue 5, 2015, Pages

  Kruiger, Johannes F ^a   Van Der Vegte, Cornelis P ^a   Jansen, Thomas L C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES;

CROSS-POLARISATION; GAUSSIAN APODIZATION; INFRARED SPECTRUM; PROTEIN LYSOZYME; SPECTRAL CONTRIBUTION; SPECTRAL DYNAMICS; SPECTRAL SIMULATIONS; TIME-DOMAIN SIMULATIONS;

TIME DOMAIN ANALYSIS;

EID: 84923814755     PISSN: 00219606     EISSN: 10897690     Source Type: Journal    
DOI: 10.1063/1.4907277     Document Type: Article

References (60)

1. P. Hamm, M. H. Lim, and R. M. Hochstrasser, J. Phys. Chem. B 102, 6123 (1998). 10.1021/jp9813286
2. W. Xiong, J. E. Laaser, R. D. Mehlenbacher, and M. T. Zanni, Proc. Natl. Acad. Sci. U. S. A. 108, 20902 (2011). 10.1073/pnas.1115055108
3. J. Bredenbeck, A. Ghosh, M. Smits, and M. Bonn, J. Am. Chem. Soc. 130, 2152 (2008). 10.1021/ja710099c
4. J. D. Hybl, A. W. Albrecht, S. M. G. Faeder, and D. M. Jonas, Chem. Phys. Lett. 297, 307 (1998). 10.1016/S0009-2614(98)01140-3
5. T. Brixner, J. Stenger, H. M. Vaswani, M. Cho, R. E. Blankenship, and G. R. Fleming, Nature 434, 625 (2005). 10.1038/nature03429
6. Y. Tanimura and S. Mukamel, J. Chem. Phys. 99, 9496 (1993). 10.1063/1.465484
7. L. J. G. W. van Wilderen, A. T. Messmer, and J. Bredenbeck, Angew. Chem., Int. Ed. 53, 2667 (2014). 10.1002/anie.201305950
8. J. R. Widom, W. Lee, A. Perdomo-Ortiz, D. Rappoport, T. F. Molinski, A. Aspuru-Guzik, and A. H. Marcus, J. Phys. Chem. A 117, 6171 (2013). 10.1021/jp400394z
9. E. L. Hahn, Phys. Rev. 80, 580 (1950). 10.1103/PhysRev.80.580
10. C. L. Perrin and T. J. Dwyer, Chem. Rev. 90, 935 (1990). 10.1021/cr00104a002
11. S. Woutersen, Y. Mu, G. Stock, and P. Hamm, Chem. Phys. 266, 137 (2001). 10.1016/S0301-0104(01)00224-5
12. T. L. C. Jansen and J. Knoester, J. Chem. Phys. 127, 234502 (2007). 10.1063/1.2806179
13. J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, and C. B. Harris, Science 319, 1820 (2008). 10.1126/science.1154041
14. P. Hamm and M. T. Zanni, Concepts and Methods of 2D Infrared Spectroscopy (Cambridge University Press, Cambridge, 2011).
15. C. Liang and T. L. C. Jansen, J. Chem. Theory Comput. 8, 1706 (2012). 10.1021/ct300045c
16. J. Manor, P. Mukherjee, Y.-S. Lin, H. Leonov, J. L. Skinner, M. T. Zanni, and I. T. Arkin, Structure 17, 247 (2009). 10.1016/j.str.2008.12.015
17. A. Paarmann, T. Hayashi, S. Mukamel, and R. J. D. Miller, J. Chem. Phys. 128, 191103 (2008). 10.1063/1.2919050
18. T. L. C. Jansen, D. Cringus, and M. S. Pshenichnikov, J. Phys. Chem. A 113, 6260 (2009). 10.1021/jp900480r
19. J. R. Schmidt, S. A. Corcelli, and J. L. Skinner, J. Chem. Phys. 123, 044513 (2005). 10.1063/1.1961472
20. T. L. C. Jansen and W. M. Ruszel, J. Chem. Phys. 128, 214501 (2008). 10.1063/1.2931941
21. J. Krcmar, M. F. Gelin, and W. Domcke, Chem. Phys. 422, 53 (2013). 10.1016/j.chemphys.2013.01.002
22. T. Yagasaki and S. Saito, J. Chem. Phys. 128, 154521 (2008). 10.1063/1.2903470
23. L. Chen, R. Zheng, Q. Shi, and Y. J. Yan, J. Chem. Phys. 131, 094502 (2009). 10.1063/1.3213013
24. C. Liang, M. Louhivuori, S. J. Marrink, T. L. C. Jansen, and J. Knoester, J. Phys. Chem. Lett. 4, 448 (2013). 10.1021/jz3019258
25. C. Liang and T. L. C. Jansen, J. Phys. Chem. B 117, 6937 (2013). 10.1021/jp403111j
26. S. T. Roberts, J. J. Loparo, and A. Tokmakoff, J. Chem. Phys. 125, 084502 (2006). 10.1063/1.2232271
27. S. Roy, M. S. Pshenichnikov, and T. L. C. Jansen, J. Phys. Chem. B 115, 5431 (2011). 10.1021/jp109742p
28. A. A. Bakulin, P. A. Pieniazek, J. L. Skinner, T. L. C. Jansen, and M. S. Pshenichnikov, J. Phys. Chem. B 117, 15545 (2013). 10.1021/jp405853j
29. M. T. Zanni, N.-H. Ge, Y. S. Kim, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U. S. A. 98, 11265 (2001). 10.1073/pnas.201412998
30. H. Maekawa, C. Toniolo, Q. B. Broxterman, and N. H. Ge, J. Phys. Chem. B 111, 3222 (2007). 10.1021/jp0674874
31. H. Maekawa, F. Formaggio, C. Toniolo, and N. H. Ge, J. Am. Chem. Soc. 130, 6556 (2008). 10.1021/ja8007165
32. M. Yang and J. L. Skinner, J. Chem. Phys. 135, 154114 (2011). 10.1063/1.3654005
33. T. L. C. Jansen, B. M. Auer, M. Yang, and J. L. Skinner, J. Chem. Phys. 132, 224503 (2010). 10.1063/1.3454733
34. C. Falvo, B. Palmieri, and S. Mukamel, J. Chem. Phys. 130, 184501 (2009). 10.1063/1.3120771
35. C. Kreisbeck, T. Kramer, M. Rodriguez, and B. Hein, J. Chem. Theory Comput. 7, 2166 (2011). 10.1021/ct200126d
36. A. Ishizaki and Y. Tanimura, J. Phys. Soc. Jpn. 74, 3131 (2005). 10.1143/JPSJ.74.3131
37. T. L. C. Jansen, J. G. Snijders, and K. Duppen, J. Chem. Phys. 113, 307 (2000). 10.1063/1.481795
38. T. Hasegawa and Y. Tanimura, J. Chem. Phys. 128, 065411 (2008). 10.1063/1.2828189
39. P. Kjellberg, B. Brüggeman, and T. Pullerits, Phys. Rev. B 74, 024303 (2006). 10.1103/PhysRevB.74.024303
40. B. Brüggeman, P. Kjellberg, and T. Pullerits, Chem. Phys. Lett. 444, 192 (2007). 10.1016/j.cplett.2007.07.002
41. K. Kwac, H. Lee, and M. Cho, J. Chem. Phys. 120, 1477 (2004). 10.1063/1.1633549
42. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (Oxford University Press, New York, 1995).
43. T. L. C. Jansen and J. Knoester, Acc. Chem. Res. 42, 1405 (2009). 10.1021/ar900025a
44. K. Kwac and M. H. Cho, J. Chem. Phys. 119, 2256 (2003). 10.1063/1.1580808
45. T. L. C. Jansen and J. Knoester, J. Phys. Chem. B 110, 22910 (2006). 10.1021/jp064795t
46. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, Comput. Phys. Commun. 91, 43 (1995). 10.1016/0010-4655(95)00042-E
47. K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, R. Dror, and D. Shaw, Proteins 78, 1950 (2010). 10.1002/prot.22711
48. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987). 10.1021/j100308a038
49. P. Artymuik, C. Blake, D. Rice, and K. Wilson, Acta. Chrystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 38, 778 (1982). 10.1107/S0567740882004075
50. T. L. C. Jansen and J. Knoester, J. Chem. Phys. 124, 044502 (2006). 10.1063/1.2148409
51. S. Roy, J. Lessing, G. Meisl, Z. Ganim, A. Tokmakoff, J. Knoester, and T. L. C. Jansen, J. Chem. Phys. 135, 234507 (2011). 10.1063/1.3665417
52. T. L. C. Jansen, A. G. Dijkstra, T. M. Watson, J. D. Hirst, and J. Knoester, J. Chem. Phys. 125, 044312 (2006). 10.1063/1.2218516
53. T. L. C. Jansen, A. G. Dijkstra, T. M. Watson, J. D. Hirst, and J. Knoester, J. Chem. Phys. 136, 209901 (2012). 10.1063/1.4722584
54. H. Torii, J. Phys. Chem. A 110, 4822 (2006). 10.1021/jp060014c
55. R. M. Hochstrasser, Chem. Phys. 266, 273 (2001). 10.1016/S0301-0104(01)00232-4
56. T. L. C. Jansen and J. Knoester, Biophys. J. 94, 1818 (2008). 10.1529/biophysj.107.118851
57. K. Kwac and M. H. Cho, J. Chem. Phys. 119, 2247 (2003). 10.1063/1.1580807
58. J. Bredenbeck, A. Ghosh, H.-K. Nienhuys, and M. Bonn, Acc. Chem. Res. 42, 1332 (2009). 10.1021/ar900016c
59. S. Weiss, Science 283, 1676 (1999). 10.1126/science.283.5408.1676
60. M. Aeschlimann, T. Brixner, A. Fischer, C. Kramer, P. Melchior, W. Pfeiffer, C. Schneider, C. Strüber, P. Tuchscherer, and D. V. Voronine, Science 333, 1723 (2011). 10.1126/science.1209206