Testing for memory-free spectroscopic coordinates by 3D IR exchange spectroscopy

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 29, 2014, Pages 10462-10467

  Borek, Joanna A ^a   Perakis, Fivos ^a   Hamm, Peter ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

3D IR spectroscopy; Solvent dynamics; Ultrafast dynamics

Indexed keywords

BENZENE; PHENOL;

ABSORPTION SPECTROSCOPY; ARTICLE; COMPLEX FORMATION; CORRELATION FUNCTION; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIGNAL NOISE RATIO; THREE DIMENSIONAL INFRARED EXCHANGE SPECTROSCOPY;

EID: 84904618647     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1406967111     Document Type: Article

References (41)

1. English BP, et al. (2006) Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nat Chem Biol 2(2):87-94.
2. Schmidt-Rohr K, Spiess HW (1991) Nature of nonexponential loss of correlation above the glass transition investigated by multidimensional NMR. Phys Rev Lett 66(23):3020-3023.
3. Geissler PL, Dellago C, Chandler D (1999) Kinetic pathways of ion pair dissociation in water. J Phys Chem B 103(18):3706-3710. (Pubitemid 129702423)
4. Best RB, Hummer G (2005) Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 102(19):6732-6737. (Pubitemid 40675384)
5. Krivov SV, Karplus M (2008) Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci USA 105(37):13841-13846.
6. Pande VS, Beauchamp K, Bowman GR (2010) Everything you wanted to know about Markov State Models but were afraid to ask. Methods 52(1):99-105.
7. Van Kampen NG (1992) Stochastic Processes in Physics and Chemistry (Elsevier, Amsterdam).
8. Woutersen S, Mu Y, Stock G, Hamm P (2001) Hydrogen-bond lifetime measured by time-resolved 2D-IR spectroscopy: N-methylacetamide in methanol. Chem Phys 266(2):137-147. (Pubitemid 32416834)
9. Kwac K, Lee H, Cho M (2004) Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: Linear and nonlinear vibrational spectra. J Chem Phys 120(3):1477-1490.
10. Kim YS, Hochstrasser RM (2005) Chemical exchange 2D IR of hydrogen-bond making and breaking. Proc Natl Acad Sci USA 102(32):11185-11190. (Pubitemid 41153795)
11. Zheng J, et al. (2005) Ultrafast dynamics of solute-solvent complexation observed at thermal equilibrium in real time. Science 309(5739):1338-1343. (Pubitemid 41209356)
12. Kwak K, Zheng J, Cang H, Fayer MD (2006) Ultrafast two-dimensional infrared vibrational echo chemical exchange experiments and theory. J Phys Chem B 110(40):19998-20013. (Pubitemid 44626363)
13. Kwac K, et al. (2006) Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy. J Chem Phys 125(24):244508.
14. Zheng J, Kwak K, Xie J, Fayer MD (2006) Ultrafast carbon-carbon single-bond rotational isomerization in room-temperature solution. Science 313(5795):1951-1955. (Pubitemid 44498000)
15. Sanda F, Mukamel S (2006) Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy. J Chem Phys 125(1):014507.
16. Cahoon JF, Sawyer KR, Schlegel JP, Harris CB (2008) Determining transition-state geometries in liquids using 2D-IR. Science 319(5871):1820-1823. (Pubitemid 351451588)
17. Jansen TL, Knoester J (2009) Waiting time dynamics in two-dimensional infrared spectroscopy. Acc Chem Res 42(9):1405-1411.
18. Anna JM, Ross MR, Kubarych KJ (2009) Dissecting enthalpic and entropic barriers to ultrafast equilibrium isomerization of a flexible molecule using 2DIR chemical exchange spectroscopy. J Phys Chem A 113(24):6544-6547.
19. Ji M, Odelius M, Gaffney KJ (2010) Large angular jump mechanism observed for hydrogen bond exchange in aqueous perchlorate solution. Science 328(5981):1003-1005.
20. Olschewski M, Knop S, Seehusen J, Lindner J, Vöhringer P (2011) Ultrafast internal dynamics of flexible hydrogen-bonded supramolecular complexes. J Phys Chem A 115(7):1210-1221.
21. Ding F, Zanni MT (2007) Heterodyned 3D-IR spectroscopy. Chem Phys 341:95-105.
22. Garrett-Roe S, Hamm P (2009) Purely absorptive three-dimensional infrared spectroscopy. J Chem Phys 130(16):164510.
23. Garrett-Roe S, Hamm P (2008) Three-point frequency fluctuation correlation functions of the OH stretch in liquid water. J Chem Phys 128(10):104507.
24. Garrett-Roe S, Perakis F, Rao F, Hamm P (2011) Three-dimensional infrared spectroscopy of isotope-substituted liquid water reveals heterogeneous dynamics. J Phys Chem B 115(21):6976-6984.
25. Mukherjee SS, Skoff DR, Middleton CT, Zanni MT (2013) Fully absorptive 3D IR spectroscopy using a dual mid-infrared pulse shaper. J Chem Phys 139(14):144205.
26. Perakis F, Borek JA, Hamm P (2013) Three-dimensional infrared spectroscopy of isotope-diluted ice Ih. J Chem Phys 139(1):014501.
27. Turner DB, Stone KW, Gundogdu K, Nelson KA (2009) Three-dimensional electronic spectroscopy of excitons in GaAs quantum wells. J Chem Phys 131(14):144510.
28. Fidler AF, Harel E, Engel GS (2010) Dissecting hidden couplings using fifth-order three-dimensional electronic spectroscopy. J. Phys. Chem. Lett 1(19):2876-2880.
29. Davis JA, et al. (2011) Three-dimensional electronic spectroscopy of excitons in asymmetric double quantum wells. J Chem Phys 135(4):044510.
30. Zhang Z, Wells KL, Tan H-S (2012) Purely absorptive fifth-order three-dimensional electronic spectroscopy. Opt Lett 37(24):5058-5060.
31. Li H, Bristow AD, Siemens ME, Moody G, Cundiff ST (2013) Unraveling quantum pathways using optical 3D Fourier-transform spectroscopy. Nat Commun 4:1390.
32. 2. J Phys Chem A 117(29):5981-5986.
33. Garrett-Roe S, Hamm P (2009) What can we learn from three-dimensional infrared spectroscopy? Acc Chem Res 42(9):1412-1422.
34. Cundiff ST (2014) Optical three dimensional coherent spectroscopy. Phys Chem Chem Phys 16(18):8193-8200.
35. Schmidt-Rohr K, Spiess HW (1994) Multidimensional Solid-State NMR and Polymers (Academic, London).
36. Volkov V, Schanz R, Hamm P (2005) Active phase stabilization in Fourier-transform two-dimensional infrared spectroscopy. Opt Lett 30(15):2010-2012. (Pubitemid 41145898)
37. Middleton CT, Strasfeld DB, Zanni MT (2009) Polarization shaping in the mid-IR and polarization-based balanced heterodyne detection with application to 2D IR spectroscopy. Opt Express 17(17):14526-14533.
38. Bloem R, Garrett-Roe S, Strzalka H, Hamm P, Donaldson P (2010) Enhancing signal detection and completely eliminating scattering using quasi-phase-cycling in 2D IR experiments. Opt Express 18(26):27067-27078.
39. Backus EHG, Garrett-Roe S, Hamm P (2008) Phasing problem of heterodyne-detected two-dimensional infrared spectroscopy. Opt Lett 33(22):2665-2667.
40. Jorgensen WL, Severance DL (1990) Aromatic-aromatic interactions: Free energy profiles for the benzene dimer in water, chloroform and liquid benzene. J Am Chem Soc 112(12):4768-4774.
41. Van Der Spoel D, et al. (2005) GROMACS: Fast, flexible, and free. J Comput Chem 26(16):1701-1718. (Pubitemid 43076182)