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51
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Mukamel S, Abramavicius D. Many-Body Approaches for Simulating Coherent Nonlinear Spectroscopies of Electronic and Vibrational Excitons. Chem Rev 2004; 104:2073-98. [PMID: 15080721 DOI: 10.1021/cr020681b] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697, USA.
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52
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Asbury JB, Steinel T, Fayer MD. Hydrogen Bond Networks: Structure and Evolution after Hydrogen Bond Breaking. J Phys Chem B 2004. [DOI: 10.1021/jp036600c] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John B. Asbury
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Tobias Steinel
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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53
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Nibbering ETJ, Elsaesser T. Ultrafast Vibrational Dynamics of Hydrogen Bonds in the Condensed Phase. Chem Rev 2004; 104:1887-914. [PMID: 15080715 DOI: 10.1021/cr020694p] [Citation(s) in RCA: 422] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Erik T J Nibbering
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
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54
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Glasbeek M, Zhang H. Femtosecond Studies of Solvation and Intramolecular Configurational Dynamics of Fluorophores in Liquid Solution. Chem Rev 2004; 104:1929-54. [PMID: 15080717 DOI: 10.1021/cr0206723] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Max Glasbeek
- Laboratory for Physical Chemistry, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands.
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55
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Gulmen TS, Sibert EL. Vibrational Energy Relaxation of the OH Stretch in Liquid Methanol. J Phys Chem A 2004. [DOI: 10.1021/jp037417m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tolga S. Gulmen
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706
| | - Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706
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56
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Asbury JB, Steinel T, Stromberg C, Corcelli SA, Lawrence CP, Skinner JL, Fayer MD. Water Dynamics: Vibrational Echo Correlation Spectroscopy and Comparison to Molecular Dynamics Simulations. J Phys Chem A 2004. [DOI: 10.1021/jp036266k] [Citation(s) in RCA: 406] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John B. Asbury
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Tobias Steinel
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - C. Stromberg
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - S. A. Corcelli
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - C. P. Lawrence
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - J. L. Skinner
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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57
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Asbury JB, Steinel T, Stromberg C, Gaffney KJ, Piletic IR, Fayer MD. Hydrogen bond breaking probed with multidimensional stimulated vibrational echo correlation spectroscopy. J Chem Phys 2003. [DOI: 10.1063/1.1627762] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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58
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Sheu SY, Yang DY, Selzle HL, Schlag EW. Energetics of hydrogen bonds in peptides. Proc Natl Acad Sci U S A 2003; 100:12683-7. [PMID: 14559970 PMCID: PMC240678 DOI: 10.1073/pnas.2133366100] [Citation(s) in RCA: 250] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from approximately 5-6 kcal/mol for the isolated bond to approximately 0.5-1.5 kcal/mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a beta-sheet under isolated conditions is 4.76 kcal/mol, and the activation energy is 1.58 kcal/mol for the same beta-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Science, National Yang-Ming University, Taipei 112, Taiwan; Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan; and Institut für Physikalische und Theoretische Chemie, Technische Universität Muenchen, Lichtenbergstrasse 4, 85748 Garching, Germany
- To whom correspondence may be addressed. E-mail: , , or
| | - Dah-Yen Yang
- Department of Life Science, National Yang-Ming University, Taipei 112, Taiwan; Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan; and Institut für Physikalische und Theoretische Chemie, Technische Universität Muenchen, Lichtenbergstrasse 4, 85748 Garching, Germany
- To whom correspondence may be addressed. E-mail: , , or
| | - H. L. Selzle
- Department of Life Science, National Yang-Ming University, Taipei 112, Taiwan; Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan; and Institut für Physikalische und Theoretische Chemie, Technische Universität Muenchen, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - E. W. Schlag
- Department of Life Science, National Yang-Ming University, Taipei 112, Taiwan; Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan; and Institut für Physikalische und Theoretische Chemie, Technische Universität Muenchen, Lichtenbergstrasse 4, 85748 Garching, Germany
- To whom correspondence may be addressed. E-mail: , , or
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59
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Piletic IR, Gaffney KJ, Fayer MD. Structural dynamics of hydrogen bonded methanol oligomers: Vibrational transient hole burning studies of spectral diffusion. J Chem Phys 2003. [DOI: 10.1063/1.1578058] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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60
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Ultrafast heterodyne detected infrared multidimensional vibrational stimulated echo studies of hydrogen bond dynamics. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00643-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Pakoulev A, Wang Z, Dlott DD. Vibrational relaxation and spectral evolution following ultrafast OH stretch excitation of water. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00314-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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62
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Gaffney KJ, Davis PH, Piletic IR, Levinger NE, Fayer MD. Hydrogen Bond Dissociation and Reformation in Methanol Oligomers Following Hydroxyl Stretch Relaxation. J Phys Chem A 2002. [DOI: 10.1021/jp021696g] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. J. Gaffney
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Paul H. Davis
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - I. R. Piletic
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Nancy E. Levinger
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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