James T. HYNES

James T. HYNES

Professor

Office: Ekeley S152B
Office Phone: 303 492 6926
Lab: Ekeley S152
Lab Phone: 303 492 6489
Fax: 303 492 5894
Group Website:
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Molecular Biophysics Program

Ph.D.: Princeton University, 1969
Postdoctoral Fellow: NIH Fellow at Massachusetts Institute of Technology, 1970
Awards: ACS Fellow 2013, Distinguished Professor 2012, National Academy of Sciences 2011, American Academy of Arts and Sciences 2008, ACS Hildebrand Award in Theory and Experiment of Liquids 2005, Hirschfelder Prize in Theoretical Chemistry 2004, ISI Highly Cited Researcher for 1980-1999, Catholic University Distinguished Alumnus Award 1988, University of Colorado Research and Creative Work Lecturer 1988,SERC Research Fellow at Oxford 1985, ACS Nobel Laureate Signature Award 1983 (with D. J. Nesbitt and S. R. Leone), J. S. Guggenheim Fellow 1979, Alfred P. Sloan Fellow 1975-1977.

Theoretical Chemistry

Our research area is theoretical chemistry and, in particular, its application to reaction and relaxation problems in chemistry. The group’s work focuses on the theory of chemical reaction dynamics, mechanisms and rates in solution (especially water), at interfaces, and in biomolecules, as well as such related phenomena such as vibrational energy transfer. The methodologies employed include quantum chemistry, statistical mechanics, classical and quantum dynamics simulations and (our favorite) analytic theory, and mixtures of these.

While most chemical reactions occur in solution, much remains to be understood at the molecular level concerning the crucial influence of the solvent on reaction rates and mechanisms. The group has constructed theories of this influence for various reaction classes, and in recent years has focused on acid-base proton transfer (PT) reactions, among the most important in chemistry/biochemistry. Emphasis is on our quite nontraditional picture, in which the quantum mechanical character of the proton's motion is critical and in which the reaction coordinate and the reaction barrier are largely associated with the surrounding polar solvent molecules, and not the proton, as tradition would have it. Related ideas also apply in our other current research areas : photochemical PTs, biological reactions such as enzyme catalysis, and the formation of a peptide bond (for protein synthesis) in vivo.

A related research area of strong current focus is the mechanism of water splitting, a key reaction in solar energy conversion. We are trying to understand this complex, multiple electron and proton transfer reaction and how it can be catalyzed, an acceleration critical for solar energy to be viable. A similar study is underway for the catalyzed reduction of carbon dioxide to form fuels such as methanol, an important ‘solar fuel’ target.

Another reaction dynamics research area is conical intersections (CIs) in photochemical reactions--- very important 'funnels' for the rapid and efficient passage of the molecule from the excited electronic state to the ground state. We have already found that a surrounding polar solvent can drastically affect electronic deactivation ultrafast dynamics, and applications to both small molecules and photoactive biomolecules are underway.

The intramolecular and intermolecular flow of vibrational energy in molecules is central to chemical reactions and mode-selective laser chemistry. Reactions of particular interest under study are PTs and hydrogen bond breaking induced by infrared radiation. In related work, we have examined the ultrafast dynamics of water as probed by femtosecond infrared techniques, and a key part of the dynamics is the making and breaking of a hydrogen bond between water molecules. Current work is focused on related issues for the dynamics of water molecules in the hydration shells of ions, hydrophobes and amphiphiles such as amino acids, including reorientational dynamics, where we have found that the mechanism differs completely from the traditional view.

Heterogeneous reactions on ice and other aerosol surfaces are critical in many atmospheric contexts, including stratospheric ozone depletion (the Antarctic Ozone Hole.) We have determined the molecular level mechanisms of a number of these reactions, finding the water molecules of the surface are actually active participants in the reactions, due to previously unsuspected proton relay mechanisms. Current efforts focus on understanding heterogeneous reactions on aerosols in other atmospheric locales, including acid dissociation of sulfuric and nitric acids on aqueous aerosol surfaces. These are strong acids in solution, but we find that they can become quite weak at a water surface. Related work is underway in an astrobiological topic: amino acid synthesis on ice surfaces in the Interstellar Medium, possibly related to the origin of life on Earth.

Finally, in addition to the biochemically related reactions mentioned above, we are also currently attempting to understand the molecular mechanism of the intercalation of anti-cancer drugs into DNA. These drugs are large compared to the space into which they must insert, and the DNA dynamics must play a key role in this reaction.

(Prof. Hynes is also affiliated with the Department of Chemistry, Ecole Normale Supérieure, Paris).

Selected Publications

R.Bianco, P. J. Hay and J.T. Hynes,"Theoretical Study of O-O Single Bond Formation in the Oxidation of Water by the Ruthenium Blue Dimer”, J. Phys. Chem. A, 115, 8003 (2011).

J.Malhado, R. Spezia and J.T. Hynes, « Dynamical Friction Effects on the Photoisomerization of a Model Protonated Schiff Base in Solution », J. Phys. Chem. A, 115, 3720 (2011).

I. Tunon and J. T. Hynes, “A Simple Model for Barrier Frequencies for Enzymatic Reactions”, ChemPhysChem,  12, 184 (2011).

D. Laage, G. Stirnemann, F. Sterpone, R. Rey and J. T. Hynes, «  Reorientation and Allied Dynamics in Water and Aqueous Solutions », Annu. Rev. Phys. Chem., 62, 395 (2011).

 

S. Wang, R. Bianco and J. T. Hynes, « Dissociation of Nitric Acid at an Aqueous Surface: Large Amplitude Motions in the Contact Ion Pair to Solvent-Separated Ion Pair Conversion », PhysChemChemPhys, 12, 8241 (2010).

F. Sterpone, G. Stirnemann, J.T. Hynes and D.Laage, “Water Hydrogen Bond Dynamics around Amino Acids: the Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups”, J. Phys. Chem B.114,  2083 (2010).

S.Wang, R. Bianco and J.T. Hynes, “Depth-Dependent Dissociation of Nitric Acid at an Aqueous Surface: Car-Parrinello Dynamics”, J. Phys. Chem. A, 113, 1295 (2009).

R. Rey, F. Ingrosso, T. Elsaesser and J. T. Hynes, “Pathways for H2O Bend Vibrational Relaxation in Liquid Water”. J. Phys. Chem. A, 113, 8949 (2009).

D.M. Koch, C. Toubin, G. H. Peslherbe and J.T. Hynes, “Theoretical Study of the Formation of the AminoAcetonitrile Precursor of Glycine on Icy Grain Mantles in the Interstellar Medium”, J. Phys. Chem. C, 112, 12972 (2008).

A. Mukherjee, R. Lavery, B. Bagchi and J. T. Hynes, "On the Molecular Mechanism of Drug Intercalation into DNA : A Simulation Study of the Intercalation Pathway, Free Energy and DNA Structural Changes", J. Amer. Chem. Soc., 130, 9747 (2008).

National Academy of Sciences, 2011