Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
Keywords
Last Name
Institution

Contact Us
If you have any questions or feedback please contact us.

James T Hynes

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemistry & Biochemistry
Phone303/492-6926

    Collapse Research 
    Collapse research activities and funding
    R01GM101160     (HYNES, JAMES THOMAS)Apr 5, 2012 - Mar 31, 2015
    NIH/NIGMS
    The Physiological Role of Carbonic Acid and Lactic Acid as Protonating Agents of
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Wilkins DM, Manolopoulos DE, Pipolo S, Laage D, Hynes JT. Nuclear Quantum Effects in Water Reorientation and Hydrogen-Bond Dynamics. J Phys Chem Lett. 2017 Jun 15; 8(12):2602-2607. PMID: 28530836.
      View in: PubMed
    2. Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. Struct Dyn. 2017 Jul; 4(4):044018. PMID: 28470026.
      View in: PubMed
    3. Laage D, Elsaesser T, Hynes JT. Water Dynamics in the Hydration Shells of Biomolecules. Chem Rev. 2017 Aug 23; 117(16):10694-10725. PMID: 28248491.
      View in: PubMed
    4. Rey R, Hynes JT. Solvation Dynamics in Liquid Water. III. Energy Fluxes and Structural Changes. J Phys Chem B. 2017 Feb 16; 121(6):1377-1385. PMID: 28095693.
      View in: PubMed
    5. Malhado JP, Hynes JT. Non-adiabatic transition probability dependence on conical intersection topography. J Chem Phys. 2016 Nov 21; 145(19):194104. PMID: 27875884.
      View in: PubMed
    6. Rey R, Hynes JT. Solvation Dynamics in Water: 2. Energy Fluxes on Excited- and Ground-State Surfaces. J Phys Chem B. 2016 Nov 03; 120(43):11287-11297. PMID: 27740771.
      View in: PubMed
    7. Duboué-Dijon E, Fogarty AC, Hynes JT, Laage D. Dynamical Disorder in the DNA Hydration Shell. J Am Chem Soc. 2016 Jun 22; 138(24):7610-20. PMID: 27240107.
      View in: PubMed
    8. Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path. J Phys Chem B. 2016 Mar 10; 120(9):2281-90. PMID: 26876428.
      View in: PubMed
    9. Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics. J Phys Chem B. 2016 Mar 10; 120(9):2271-80. PMID: 26879554.
      View in: PubMed
    10. Pines D, Ditkovich J, Mukra T, Miller Y, Kiefer PM, Daschakraborty S, Hynes JT, Pines E. How Acidic Is Carbonic Acid? J Phys Chem B. 2016 Mar 10; 120(9):2440-51. PMID: 26862781.
      View in: PubMed
    11. Lim CH, Holder AM, Hynes JT, Musgrave CB. Catalytic Reduction of CO2 by Renewable Organohydrides. J Phys Chem Lett. 2015 Dec 17; 6(24):5078-92. PMID: 26722706.
      View in: PubMed
    12. Tuñón I, Laage D, Hynes JT. Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step. Arch Biochem Biophys. 2015 Sep 15; 582:42-55. PMID: 26087289; PMCID: PMC4560206.
    13. Rey R, Hynes JT. Solvation Dynamics in Liquid Water. 1. Ultrafast Energy Fluxes. J Phys Chem B. 2015 Jun 18; 119(24):7558-70. PMID: 25635521.
      View in: PubMed
    14. Pines D, Keinan S, Kiefer PM, Hynes JT, Pines E. Effect of Solvent Dielectric Constant and Acidity on the OH Vibration Frequency in Hydrogen-Bonded Complexes of Fluorinated Ethanols. J Phys Chem B. 2015 Jul 23; 119(29):9278-86. PMID: 25420059.
      View in: PubMed
    15. Malhado JP, Bearpark MJ, Hynes JT. Non-adiabatic dynamics close to conical intersections and the surface hopping perspective. Front Chem. 2014; 2:97. PMID: 25485263; PMCID: PMC4240175.
    16. Lim CH, Holder AM, Hynes JT, Musgrave CB. Reduction of CO2 to methanol catalyzed by a biomimetic organo-hydride produced from pyridine. J Am Chem Soc. 2014 Nov 12; 136(45):16081-95. PMID: 25323134.
      View in: PubMed
    17. Hynes JT. Molecules in motion: chemical reaction and allied dynamics in solution and elsewhere. Annu Rev Phys Chem. 2015 Apr; 66:1-20. PMID: 25293391.
      View in: PubMed
    18. Keinan S, Pines D, Kiefer PM, Hynes JT, Pines E. Solvent-induced O-H vibration red-shifts of oxygen-acids in hydrogen-bonded O-H···base complexes. J Phys Chem B. 2015 Jan 22; 119(3):679-92. PMID: 24975617.
      View in: PubMed
    19. Kiefer PM, Pines E, Pines D, Hynes JT. Solvent-induced red-shifts for the proton stretch vibrational frequency in a hydrogen-bonded complex. 1. A valence bond-based theoretical approach. J Phys Chem B. 2014 Jul 17; 118(28):8330-51. PMID: 24807301.
      View in: PubMed
    20. Bianco R, Hay PJ, Hynes JT. Theoretical study of water oxidation by the ruthenium blue dimer. II. Proton relay chain mechanism for the step [bpy2(HOO)Ru(IV)ORu(IV)(OH)bpy2]4+ ? [bpy2(O2(–))Ru(IV)ORu(III)(OH2)bpy2]4+. J Phys Chem B. 2013 Dec 12; 117(49):15761-73. PMID: 23952641.
      View in: PubMed
    21. Lim CH, Holder AM, Hynes JT, Musgrave CB. Roles of the Lewis acid and base in the chemical reduction of CO2 catalyzed by frustrated Lewis pairs. Inorg Chem. 2013 Sep 03; 52(17):10062-6. PMID: 23941178.
      View in: PubMed
    22. Xu X, Ge H, Gu C, Gao YQ, Wang SS, Thio BJ, Hynes JT, Xie XS, Cao J. Modeling spatial correlation of DNA deformation: DNA allostery in protein binding. J Phys Chem B. 2013 Oct 24; 117(42):13378-87. PMID: 23795567; PMCID: PMC3808477.
    23. Fogarty AC, Duboué-Dijon E, Sterpone F, Hynes JT, Laage D. Biomolecular hydration dynamics: a jump model perspective. Chem Soc Rev. 2013 Jul 07; 42(13):5672-83. PMID: 23612685.
      View in: PubMed
    24. Malhado JP, Hynes JT. Photoisomerization for a model protonated Schiff base in solution: sloped/peaked conical intersection perspective. J Chem Phys. 2012 Dec 14; 137(22):22A543. PMID: 23249080.
      View in: PubMed
    25. Petersen J, Møller KB, Rey R, Hynes JT. Ultrafast librational relaxation of H2O in liquid water. J Phys Chem B. 2013 Apr 25; 117(16):4541-52. PMID: 23131075.
      View in: PubMed
    26. Wilhelm M, Mukherjee A, Bouvier B, Zakrzewska K, Hynes JT, Lavery R. Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA. J Am Chem Soc. 2012 May 23; 134(20):8588-96. PMID: 22548344.
      View in: PubMed
    27. Rey R, Hynes JT. Tracking energy transfer from excited to accepting modes: application to water bend vibrational relaxation. Phys Chem Chem Phys. 2012 May 14; 14(18):6332-42. PMID: 22402668.
      View in: PubMed
    28. Boisson J, Stirnemann G, Laage D, Hynes JT. Water reorientation dynamics in the first hydration shells of F- and I-. Phys Chem Chem Phys. 2011 Nov 28; 13(44):19895-901. PMID: 21915404.
      View in: PubMed
    29. Stirnemann G, Castrillón SR, Hynes JT, Rossky PJ, Debenedetti PG, Laage D. Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity: competing effects of the hydration structure and hydrogen-bond strength. Phys Chem Chem Phys. 2011 Nov 28; 13(44):19911-7. PMID: 21897944.
      View in: PubMed
    30. Laage D, Stirnemann G, Sterpone F, Hynes JT. Water jump reorientation: from theoretical prediction to experimental observation. Acc Chem Res. 2012 Jan 17; 45(1):53-62. PMID: 21749157.
      View in: PubMed
    31. Bianco R, Hay PJ, Hynes JT. Theoretical study of O--O single bond formation in the oxidation of water by the ruthenium blue dimer. J Phys Chem A. 2011 Jul 14; 115(27):8003-16. PMID: 21615127.
      View in: PubMed
    32. Laage D, Stirnemann G, Sterpone F, Rey R, Hynes JT. Reorientation and allied dynamics in water and aqueous solutions. Annu Rev Phys Chem. 2011; 62:395-416. PMID: 21219140.
      View in: PubMed
    33. Tuñón I, Hynes JT. A simple model for barrier frequencies for enzymatic reactions. Chemphyschem. 2011 Jan 17; 12(1):184-90. PMID: 21226200.
      View in: PubMed
    34. Malhado JP, Spezia R, Hynes JT. Dynamical friction effects on the photoisomerization of a model protonated Schiff base in solution. J Phys Chem A. 2011 Apr 28; 115(16):3720-35. PMID: 20932049.
      View in: PubMed
    35. Wang S, Bianco R, Hynes JT. Dissociation of nitric acid at an aqueous surface: Large amplitude motions in the contact ion pair to solvent-separated ion pair conversion. Phys Chem Chem Phys. 2010 Aug 01; 12(29):8241-9. PMID: 20498901.
      View in: PubMed
    36. Stirnemann G, Hynes JT, Laage D. Water hydrogen bond dynamics in aqueous solutions of amphiphiles. J Phys Chem B. 2010 Mar 04; 114(8):3052-9. PMID: 20141150.
      View in: PubMed
    37. Sterpone F, Stirnemann G, Hynes JT, Laage D. Water hydrogen-bond dynamics around amino acids: the key role of hydrophilic hydrogen-bond acceptor groups. J Phys Chem B. 2010 Feb 11; 114(5):2083-9. PMID: 20085364.
      View in: PubMed
    38. Ramesh SG, Re S, Boisson J, Hynes JT. Vibrational symmetry breaking of NO3- in aqueous solution: NO asymmetric stretch frequency distribution and mean splitting. J Phys Chem A. 2010 Jan 28; 114(3):1255-69. PMID: 19689153.
      View in: PubMed
    39. Stirnemann G, Rossky PJ, Hynes JT, Laage D. Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface. Faraday Discuss. 2010; 146:263-81; discussion 283-98, 395-401. PMID: 21043427.
      View in: PubMed
    40. Rey R, Ingrosso F, Elsaesser T, Hynes JT. Pathways for H2O bend vibrational relaxation in liquid water. J Phys Chem A. 2009 Aug 06; 113(31):8949-62. PMID: 19719303.
      View in: PubMed
    41. Ingrosso F, Rey R, Elsaesser T, Hynes JT. Ultrafast energy transfer from the intramolecular bending vibration to librations in liquid water. J Phys Chem A. 2009 Jun 18; 113(24):6657-65. PMID: 19469516.
      View in: PubMed
    42. Laage D, Stirnemann G, Hynes JT. Why water reorientation slows without iceberg formation around hydrophobic solutes. J Phys Chem B. 2009 Feb 26; 113(8):2428-35. PMID: 19193030.
      View in: PubMed
    43. Wang S, Bianco R, Hynes JT. Depth-dependent dissociation of nitric acid at an aqueous surface: Car-Parrinello molecular dynamics. J Phys Chem A. 2009 Feb 19; 113(7):1295-307. PMID: 19173580.
      View in: PubMed
    44. Laage D, Hynes JT. Echoes of a salty exchange. Proc Natl Acad Sci U S A. 2009 Jan 27; 106(4):967-8. PMID: 19164540; PMCID: PMC2633541.
    45. De Schryver FC, Hynes JT. Editorial: Pushing through interdisciplinary boundaries. Chemphyschem. 2009 Jan 12; 10(1):4. PMID: 19130543.
      View in: PubMed
    46. Laage D, Hynes JT. On the molecular mechanism of water reorientation. J Phys Chem B. 2008 Nov 13; 112(45):14230-42. PMID: 18942871.
      View in: PubMed
    47. Bianco R, Wang S, Hynes JT. Infrared signatures of HNO3 and NO3(-) at a model aqueous surface. A theoretical study. J Phys Chem A. 2008 Oct 02; 112(39):9467-76. PMID: 18714961.
      View in: PubMed
    48. Mukherjee A, Lavery R, Bagchi B, Hynes JT. On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes. J Am Chem Soc. 2008 Jul 30; 130(30):9747-55. PMID: 18611009.
      View in: PubMed
    49. Laage D, Hynes JT. On the residence time for water in a solute hydration shell: application to aqueous halide solutions. J Phys Chem B. 2008 Jul 03; 112(26):7697-701. PMID: 18510295.
      View in: PubMed
    50. Ruiz-Pernía JJ, Tuñón I, Moliner V, Hynes JT, Roca M. Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach. J Am Chem Soc. 2008 Jun 11; 130(23):7477-88. PMID: 18479090.
      View in: PubMed
    51. Ramesh SG, Re S, Hynes JT. Charge transfer and OH vibrational frequency red shifts in nitrate-water clusters. J Phys Chem A. 2008 Apr 17; 112(15):3391-8. PMID: 18351755.
      View in: PubMed
    52. Bianco R, Wang S, Hynes JT. Theoretical study of the dissociation of nitric acid at a model aqueous surface. J Phys Chem A. 2007 Nov 01; 111(43):11033-42. PMID: 17918815.
      View in: PubMed
    53. Laage D, Hynes JT. Reorientional dynamics of water molecules in anionic hydration shells. Proc Natl Acad Sci U S A. 2007 Jul 03; 104(27):11167-72. PMID: 17581877; PMCID: PMC2040870.
    54. Hynes JT. Physical chemistry: the peripatetic proton. Nature. 2007 Mar 15; 446(7133):270-3. PMID: 17361168.
      View in: PubMed
    55. Pal S, Maiti PK, Bagchi B, Hynes JT. Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations. J Phys Chem B. 2006 Dec 28; 110(51):26396-402. PMID: 17181299.
      View in: PubMed
    56. Burghardt I, Hynes JT. Excited-state charge transfer at a conical intersection: effects of an environment. J Phys Chem A. 2006 Oct 12; 110(40):11411-23. PMID: 17020251.
      View in: PubMed
    57. Jana B, Pal S, Maiti PK, Lin ST, Hynes JT, Bagchi B. Entropy of water in the hydration layer of major and minor grooves of DNA. J Phys Chem B. 2006 Oct 05; 110(39):19611-8. PMID: 17004828.
      View in: PubMed
    58. Nigro B, Re S, Laage D, Rey R, Hynes JT. On the ultrafast infrared spectroscopy of anion hydration shell hydrogen bond dynamics. J Phys Chem A. 2006 Oct 05; 110(39):11237-43. PMID: 17004732.
      View in: PubMed
    59. Roca M, Moliner V, Tuñón I, Hynes JT. Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase. J Am Chem Soc. 2006 May 10; 128(18):6186-93. PMID: 16669689.
      View in: PubMed
    60. Koch DM, Timerghazin QK, Peslherbe GH, Ladanyi BM, Hynes JT. Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics. J Phys Chem A. 2006 Feb 02; 110(4):1438-54. PMID: 16435804.
      View in: PubMed
    61. Bianco R, Hynes JT. Heterogeneous reactions important in atmospheric ozone depletion: a theoretical perspective. Acc Chem Res. 2006 Feb; 39(2):159-65. PMID: 16489736.
      View in: PubMed
    62. Laage D, Hynes JT. A molecular jump mechanism of water reorientation. Science. 2006 Feb 10; 311(5762):832-5. PMID: 16439623.
      View in: PubMed
    63. Bianco R, Wang S, Hynes JT. Theoretical study of the first acid dissociation of H2SO4 at a model aqueous surface. J Phys Chem B. 2005 Nov 17; 109(45):21313-21. PMID: 16853764.
      View in: PubMed
    64. Møller KB, Rey R, Masia M, Hynes JT. On the coupling between molecular diffusion and solvation shell exchange. J Chem Phys. 2005 Mar 15; 122(11):114508. PMID: 15836230.
      View in: PubMed
    65. Rey R, Møller KB, Hynes JT. Ultrafast vibrational population dynamics of water and related systems: a theoretical perspective. Chem Rev. 2004 Apr; 104(4):1915-28. PMID: 15080716.
      View in: PubMed
    66. Burghardt I, Cederbaum LS, Hynes JT. Environmental effects on a conical intersection: a model study. Faraday Discuss. 2004; 127:395-411. PMID: 15471356.
      View in: PubMed
    67. Laage D, Burghardt I, Sommerfeld T, Hynes JT. On the dissociation of aromatic radical anions in solution. Chemphyschem. 2003 Jan 13; 4(1):61-6. PMID: 12596466.
      View in: PubMed
    Hynes's Networks
    Click the "See All" links for more information and interactive visualizations!
    Concepts Expand Description
    _
    Co-Authors Expand Description
    _
    Similar People Expand Description
    _
    Same Department Expand Description
    Physical Neighbors Expand Description
    _

    Copyright © 2017 The Regents of the University of Colorado, a body corporate. All rights reserved. (Harvard PROFILES RNS software version: 2.10.0)