Chemistry and Biochemistry

Andrew L. Cooksy

Associate Professor; Physical Chemistry.
Associate Director, Computational Sciences Research Center

Office: CSL-310 (office), CSL-307,312 (lab)
Office Phone: +1-619-594-5571 (office) 594-0891 (lab) 594-4634 (fax)
e-mail: acooksy@sciences.sdsu.edu

Curriculum Vita

• B.A., chemistry and physics, Harvard College, 1984;
• Ph.D., chemistry, University of California, Berkeley, 1990;
• Postdoctoral Research Associate, Harvard-Smithsonian Center for Astrophysics and Harvard University Department of Chemistry, 1990-1993;
• Asst. and Assoc. Professor, University of Mississippi Department of Chemistry, 1993-1999.

Recent Courses

• Chem 200: General Chemistry I
• Chem 410: Physical Chemistry
• Chem 417: Physical Chemistry Lab
• Chem 713: Quantum Chemistry

Research Interests

Pentadienyl/cyclopentenyl transition state.
(image by C. Cheng, instr. Spring 2006 CS689)

Reactive intermediates in combustion, interstellar chemistry, chemical synthesis, and biochemistry; investigated by laser spectroscopy and spectroscopic theory, and by computational quantum mechanics.

Molecular free radicals are crucial to the chemistry of combustion, the upper atmosphere, polymerization, and interstellar molecular clouds, and also figure in many biochemical electron transfer processes. We are interested in the physical and chemical properties of these molecules, particularly those containing conjugated π-electron systems, such as HC₃O and C₄H and the biochemical quinones, because the delocalized orbitals can confer surprising dynamic and reactive properties to these systems.

High Resolution Spectroscopy of Free Radicals

In our experimental work, we search for new spectra of small hydrocarbon or other first-row element free radicals in the visible or infrared regions of the spectrum in order to characterize these dynamic properties. Our mid-infrared diode laser spectrometer operates between 1800 and 2400 cm^-1, and uses a 2-meter electric discharge cell as the sample chamber. With this system we search for strong stretching transitions in the free radicals, and then probe the isomerization coordinate by examining hot band and combination band spectra to obtain measurements at high resolution of the interesting vibrational dynamics of these molecules. These studies were originally supported by one of the first NSF CAREER awards, and is currently funded by the Army Research Office. Erynn Kutzera and David Sagaz are currently working on this project.

Computational Studies of Free Radical Structures and Dynamics

We are engaged in concurrent ab initio computational studies of these and larger molecules to investigate the relative stability of the competing structures, and their effect on the chemistry. These ab initio calculations guide the laboratory measurements of the energy level structure, geometry, and chemistry of these molecules, as well as offering information for the kinetic models of the highly complex chemical environments found in combustion and interstellar space.

Previous work in our group along these lines included studies of the mechanisms behind the elctrocyclic ring-closure of cyclopentadienyl radical (C₅H₅) and the vibrational dynamics of cyclooctatetraenyl (C₈H₇), including its effective isomerization from one structure to another under specific vibrational excitations. We are presently applying similar approaches to problems in computational biochemistry, elucidating the reaction mechanisms underlying vitamin E regeneration and enzyme-mediated metabolism of small compounds.

Recognizing the need for a general, easily mastered way to study these complex vibrational dynamics, we've recently published a protocol for the integration of the vibrational Schrodinger equation on an arbitrary potential energy surface. This work formed the doctoral work of Dong Xu, one of SDSU's first two PhD students in Computational Sciences, and now a postdoctoral researcher at UCSD. A new PhD candidate, Peter Zajac, is joining NIW fellow Leo Arzu in pursuing these studies.

Organometallics

Current work with Prof. Doug Grotjahn strives to understand the activity of organometallic catalysts synthesized in his lab. To model the transformation of a ;pi-complexed alkyne into vinylidene on one of these catalysts, we mapped the reaction surface of the complex in two dimensions, finding an unexpected parallel in our previous work on multiple minima on vibrational surfaces of free radicals. We are in the midst of an exhaustive analysis of a system that catalyzes the formation of aldehyde from alkyne and water, finding that Grotjahn's signature heterocyclic ligands play a major role in the dynamics by providing a basic chemical environment to stabilize the relocation of hydrogen atoms. Undergraduates Amy Arita and Kirsten Ivey are hard at work on this project, which is funded by the National Science Foundation.

Bridging Experiment and Theory

The complex interactions among the spin and orbital magnetic fields of unpaired electrons and the rotational, vibrational, and nuclear angular momenta in these molecules also means that we sometimes work at the limits of present spectroscopic theory. Work from a sabbatical with Prof. John M. Brown at Oxford University involved the first combined analysis of the lowest vibrational bending states in the NCO radical. NCO is a prototype example of the Renner-Teller effect, in this case the strong interaction between the two electronic states formed when the Π state symmetry of the linear is broken upon bending. To complete this analysis, we used third-order perturbation theory to derive additional contributions to the effective Hamiltonian, which is still growing after 70 years.

We gratefully acknowledge funding for past and current work from the National Science Foundation, the Petroleum Research Fund of the American Chemical Society, the Exxon Education Foundation, the San Diego Foundation, and the Department of Defense.

Recent Publications

1. "Electron Transfer as a Potential Cause of Diacetyl Toxicity in Popcorn Lung Disease,"
   Peter Kovacic and Andrew L. Cooksy,
   Rev. Environ. Contam. Toxicol. 204 (in press) (2010).
2. "Solving the Vibrational Schrodinger Equation on an Arbitrary Multidimensional Potential Energy Surface by the Finite Element Method,"
   Dong Xu, Jernej Stare, and Andrew L. Cooksy,
   Comp. Phys. Commun. 180, 2079-2094 (2009). (DOI:10.1016/j.cpc.2009.06.010.)
3. "Finding the Proton in a Key Intermediate of anti-Markovnikov Alkyne Hydration by a Bifunctional Catalyst,"
   Douglas B. Grotjahn, Elijah J. Kragulj, Constantinos D. Zeinalipour-Yazdi, Valentin Miranda-Soto, Daniel A. Lev, and Andrew L. Cooksy,
   J. Am. Chem. Soc. 130, 10860-10861 (Communication) (2008). (DOI: 10.1021/ja803106z.)
4. "CO Adsorption on Transition Metal Clusters: Trends from Density Functional Theory,"
   Constantinos D. Zeinalipour-Yazdi, Andrew L. Cooksy, and Angelos M. Efstathiou,
   Surf. Sci. 602, 1858-1862 (2008). (DOI:10.1016/j.susc.2008.03.024.)
5. "Hydrogen Bond Acceptance of Bifunctional Ligands in an Alkyne-Metal π Complex,"
   Douglas B. Grotjahn, Valentin Miranda-Soto, Elijah J. Kragulj, Daniel A. Lev, Gulin Erdogan, Xi Zeng, and Andrew L. Cooksy,
   J. Am. Chem. Soc. 130, 20-21 (Communication) (2008). (DOI: 10.1021/ja0774616.)
6. "Study of CO Adsorption on Rh/γ-Al₂O₃: a DRIFTS and DFT Study,"
   Constantinos D. Zeinalipour-Yazdi, Andrew L. Cooksy, Angelos M. Efstathiou,
   J. Phys. Chem. C 111, 13872-13878 (2007). (DOI: 10.1021/jp074549x.)
7. "Wittig Reactions in Water Media Employing Stabilized Ylides with Aldehydes. Synthesis of α,β-Unsaturated Esters from Mixing Aldehydes, α-Bromoesters, and Ph₃P in Aqueous NaHCO₃,"
   Amer El-Batta, Changchun Jiang, Wen Zhao, Robert Anness, Andrew L. Cooksy and Mikael Bergdahl,
   J. Org. Chem. 72, 5244-5259 (2007). (DOI: 10.1021/jo070665k.)
8. "Experimental and Computational Study of the Transformation of Terminal Alkynes to Vinylidene Ligands on trans-(Chloro)bis(phosphine)Rh Fragments and Effects of Phosphine Substituents,"
   Douglas B. Grotjahn, Xi Zeng, Andrew L. Cooksy, W. Scott Kassel, Antonio G. DiPasquale, Lev. N. Zakharov, and Arnold L. Rheingold,
   Organomet. 26, 3385-3402 (2007). (DOI: 10.1021/om700355r.)
9. "Ab Initio Study of the Torsional Motion in Tolane,"
   Dong Xu and Andrew L. Cooksy,
   J. Molec. Struct. (THEOCHEM) 815, 119-125 (2007). (DOI: 10.1016/j.theochem.2007.03.028.)
10. "Laser Magnetic Resonance Spectroscopy. Fundamental Physics to Medical Analysis of Free Radicals,"
    Andrew L. Cooksy,
    G.I.T. Laboratory Journal 3-4, 54-55 (2007).
11. "Infrared Laser Magnetic Resonance Spectroscopy of the ν₃ Fundamental and Associated Hot Bands of the NCO Free Radical,"
    D. A. Gillett, A. L. Cooksy, and J. M. Brown,
    J. Mol. Spectrosc. 239, 190-200 (2006). (DOI:10.1016/j.jms.2006.07.00.)
12. "Computational Study of Aqueous Reactions in Tocopherol Regeneration,"
    R. Lui and A. L. Cooksy,
    J. Comp. Theor. Chem. 2, 1395-1402 (2006). (DOI: 10.1021/ct600161w.)
13. "Alkyne-to-Vinylidene Transformation on trans-(Cl)Rh(phosphine)₂: Acceleration by a Heterocyclic Ligand and Absence of Bimolecular Mechanism,"
    Douglas B. Grotjahn, Xi Zeng, and Andrew L. Cooksy,
    J. Am. Chem. Soc. 128, 2798-2799 (2006). (DOI: 10.1021/ja058736p.)

M.S. Theses and Ph.D. Dissertations

1. Dong Xu, Ph.D. 2007. FEMvib, an Ab Initio Multi-Dimensional Solver for Probing Vibrational Dynamics in Polyatomic Molecules and Free Radicals.
2. Christopher D. Uranga, M.S. 2007. Characterization of Spectrometers for Infrared Spectroscopy of Free Radicals.
3. Raymond L. Lui, M.S. 2005. Computational Study of Aqueous Reactions in Vitamin E Regeneration.
4. Christopher Hinton, M.S. 2004. Computational Study of Carbon Radicals: C₉H₉ and HC_nO.
5. Roger Wong, M.S. 2004. Construction and Characterization of an Infrared Laser Spectrometer for Free Radicals.
6. Dong Xu, M.S. 2003. Ab Initio Study of The Torsional Motion in Tolane
7. Claudia L. Parker, Ph.D. 2000. Ab Initio and Spectroscopic Examination of Butadienyl Free Radicals.
8. Haibo Wang, M.S. 1996. Ab Initio Calculations and Spectroscopy of Free Radicals.