Ultrafast memory loss and relaxation processes in hydrogen-bonded systems

Biological Chemistry

Volumn 390, Issue 11, 2009, Pages 1125-1132

  Elsaesser, Thomas ^a  

^a MAX BORN INSTITUT   (Germany)

Author keywords

Femtosecond infrared spectroscopy; Hydrated DNA; Hydrogen bond; Structural memory; Water

Indexed keywords

DNA; PHOSPHATE; WATER;

DNA STRUCTURE; ENERGY; EXCITATION; HEAT; HYDRATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULE; PRIORITY JOURNAL; REVIEW; TERAHERTZ SPECTROSCOPY; TIME;

DNA; HYDROGEN BONDING; SPECTRUM ANALYSIS; TIME FACTORS; VIBRATION; WATER;

EID: 70349829517     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2009.126     Document Type: Review

References (41)

1. Asbury, J.B., Steinel, T., Stromberg, C., Corcelli, S.A., Lawrence, C.P., Skinner, J.L., and Fayer, M.D. (2004). Water dynamics: Vibrational echo correlation spectroscopy and comparison to molecular dynamics simulations. J. Phys. Chem. A 108, 1107-1119.
2. Ashihara, S., Huse, N., Espagne, A., Nibbering, E.T.J., and Elsaesser, T. (2007). Ultrafast structural dynamics of water induced by dissipation of vibrational energy. J. Phys. Chem. A 111, 743-746.
3. Asplund, M.C., Zanni, M.T., and Hochstrasser, R.M. (2000). Twodimensional infrared spectroscopy of peptides by phasecontrolled femtosecond vibrational photon echoes. Proc. Natl. Acad. Sci. USA 97, 8219-8224.
4. Brown, E.B. and Peticolas, W.L. (1975). Conformational and vibrational frequencies of nucleic acid chains. Biopolymers 14, 1259-1271.
5. Cowan, M.L., Bruner, B.D., Huse, N., Dwyer, J.R., Chugh, B., Nibbering, E.T.J., Elsaesser, T., and Miller, R.J.D. (2005). Ultrafast memory loss and energy redistribution in the hydrogen bond network of liquid H2O. Nature 434, 199-202.
6. Creighton, T.E. (1993). Proteins, 2nd edn (New York, USA: Freeman).
7. Dwyer, J.R., Szyc, L., Nibbering, E.T.J., and Elsaesser, T. (2008). Ultrafast vibrational dynamics of adenine-thymine base pairs in DNA oligomers. J. Phys. Chem. B 112, 11194-11197.
8. Eisenberg, D. and Kauzmann, W. (1969). The Structure and Properties of Water (New York, USA: Oxford University Press).
9. Elsaesser, T. and Kaiser, W. (1991). Vibrational and vibronic relaxation of large polyatomic molecules in liquids. Annu. Rev. Phys. Chem. 42, 83-108.
10. Falk, M., Hartman, K.A., and Lord, R.C. (1962). Hydration of deoxyribonucleic acid. I. A gravimetric study. J. Am. Chem. Soc. 84, 3843-3846.
11. Falk, M., Hartman, K.A., and Lord, R.C. (1963). Hydration of DNA. II. An infrared study. J. Am. Chem. Soc. 85, 387-391.
12. Fayer, M.D. (2001). Ultrafast Infrared and Raman Spectroscopy (New York, USA: Marcel Dekker).
13. Fecko, C.J., Eaves, J.D., Loparo, J.J., Tokmakoff, A., and Geissler, P.L. (2003). Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water. Science 301, 1698-1702.
14. Gale, G.M., Gallot, G., Hache, F., Lascoux, N., Bratos, S., and Leicknam, J.C. (1999). Femtosecond dynamics of hydrogen bonds in liquid water: A real time study. Phys. Rev. Lett. 82, 1068-1071.
15. Hamm, P., Lim, M., and Hochstrasser, R.M. (1998). Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy. J. Phys. Chem. B 102, 6123-6138.
16. Huse, N., Ashihara, S., Nibbering, E.T.J., and Elsaesser, T. (2005). Ultrafast vibrational relaxation of OH bending and librational excitations in liquid H2O. Chem. Phys. Lett. 404, 389-393.
17. Jonas, D.M. (2003). Two-dimensional femtosecond spectroscopy. Annu. Rev. Phys. Chem. 54, 425-463.
18. Korolev, N., Lyubartsev, A.P., Laaksonen, A., and Nordenskiold, L. (2002). On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study. Biophys. J. 82, 2860-2875.
19. Kraemer, D., Cowan, M.L., Paarmann, A., Huse, N., Nibbering, E.T.J., Elsaesser, T., and Miller, R.J.D. (2008). Temperature dependence of the two-dimensional infrared spectrum of liquid H2O. Proc. Natl. Acad. Sci. USA 105, 437-442.
20. Laage, D. and Hynes, J.T. (2006). A molecular jump mechanism of water reorientation. Science 311, 832-835.
21. Lock, A.J. and Bakker, H.J. (2002). Temperature dependence of vibrational relaxation in liquid H2O. J. Chem. Phys. 117, 1708-1713.
22. Luzar, A. and Chandler, D. (1996). Hydrogen-bond kinetics in liquid water. Nature 379, 55-57.
23. Maré chal, Y. and Witkowski, A. (1968). Infrared spectra of Hbonded systems. J. Chem. Phys. 48, 3697-3705.
24. Mukamel, S. (2000). Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. Annu. Rev. Phys. Chem. 51, 691-729.
25. Nibbering, E.T.J. and Elsaesser, T. (2004). Ultrafast vibrational dynamics of hydrogen bonds in the condensed phase. Chem. Rev. 104, 1887-1914.
26. Oxtoby, D.W. (1979). Dephasing of molecular vibrations in liquids. Adv. Chem. Phys. 40, 1-48.
27. Paarmann, A., Hayashi, S., Mukamel, S., and Miller, R.J.D. (2008). Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy. J. Chem. Phys. 128, 191103/1-5.
28. Pal, S., Maiti, P.K., and Bagchi, B. (2006). Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation. J. Chem. Phys. 125, 234903.
29. Piryatinski, A., Lawrence, C.P., and Skinner, J.L. (2003). Vibrational spectroscopy of HOD in liquid D2O. V. Infrared threepulse photon echoes. J. Chem. Phys. 118, 9672-9679.
30. Prescott, B., Steinmetz, W., and Thomas, G.J., Jr. (1984). Characterization of DNA structures by laser Raman spectroscopy. Biopolymers 23, 235-256.
31. Rey, R., Moller, K.B., and Hynes, J.T. (2002). Hydrogen bond dynamics in water and ultrafast infrared spectroscopy. J. Phys. Chem. A 106, 11993-11996.
32. Saenger, W. (1984). Principles of Nucleic Acid Structure (New York, USA: Springer).
33. Saenger, W., Hunter, W.N., and Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385-388.
34. Schneider, B., Patel, K., and Berman, H.M. (1998). Hydration of the phosphate group in double-helical DNA. Biophys. J. 75, 2422-2434.
35. Schuster, P., Zundel, G., and Sandorfy, C. (1976). The Hydrogen Bond: Recent Developments in Theory and Experiments (Amsterdam, The Netherlands: North Holland).
36. Stenger, J., Madsen, D., Hamm, P., Nibbering, E.T.J., and Elsaesser, T. (2002). A photon echo peak shift study of liquid water. J. Phys. Chem. A 106, 2341-2350.
37. Szyc, L., Dwyer, J.R., Nibbering, E.T.J., and Elsaesser, T. (2009). Ultrafast dynamics of NH and OH stretching excitations in hydrated DNA oligomers. Chem. Phys. 357, 36-44.
38. Walrafen, G.E. and Blatz, L.A. (1973). Weak Raman bands from water. J. Chem. Phys. 59, 2646-2650.
39. Watson, J.D. and Crick, F.H.C. (1953). Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171, 737-738.
40. Woutersen, S. and Bakker, H.J. (1999a). Hydrogen bond in liquid water as a Brownian oscillator. Phys. Rev. Lett. 83, 2077-2080.
41. Woutersen, S. and Bakker, H.J. (1999b). Resonant intermolecular transfer of vibrational energy in liquid water. Nature 402, 507-509.