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[photo]

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

Recent Courses

Research Interests

[C5H7 ts]
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 pi-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

lab photo
lab photo
lab photo

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.

Using a resistively heated tube of silicon carbide, precursor molecules are flash pyrolyzed into free radicals, which enter a vacuum chamber in a supersonic free jet. The supersonic jet provides a collisionless environment for the radicals and cools them to roughly 30 K, greatly simplifying the spectroscopy. The structure and internal dynamics of these systems are probed by direct absorption and laser-induced fluorescence spectroscopy using a tunable ring dye laser. We are upgrading this spectrometer to an extremely sensitive configuration employing frequency-modulation/magnetic resonance spectroscopy, a technique that detects only those signals originating from the free radicals and with nearly the maximum theoretical signal-to-noise ratio.

A second spectrometer is now operational, which uses a mid-infrared tunable diode laser between 1800 and 2400 cm-1 as the radiation source, and a 2-meter electric discharge cell as the sample chamber. With this system we hope to study at higher resolution some of the interesting vibrational dynamics of these molecules.

nco image

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. Recently completed 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 Pi 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.

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. diagram 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.

Recent work in our group along these lines has 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.

Research in our group has been funded by the Physical Chemistry and Academic Research Infrastructure programs of the National Science Foundation, by the Petroleum Research Fund of the American Chemical Society, the Exxon Education Foundation, and the San Diego Foundation.

Selected Publications

  1. "Finding the Proton in a Key Intermediate of anti-Markovnikov Alkyne Hydrati on by a Bifunctional Catalyst," Douglas B. Grotjahn, Elijah J. Kragulj, Constan tinos D. Zeinalipour-Yazdi, Valentin Miranda-Soto, Daniel A. Lev, and Andrew L. Cook sy, J. Am. Chem. Soc. (in press) (2008). (Full article.)
  2. "CO Adsorption on Transition Metal Clusters: Trends from Density Functional Theory," Constantinos D. Zeinalipour-Yazdi, Andrew L. Cooksy, and Angelos M. Efstathiou, Surf. Sci. (in press) (2008).
  3. "Hydrogen Bond Acceptance of Bifunctional Ligands in an Alkyne-Metal pi 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 (2008). (Full article)
  4. "Study of CO Adsorption on Rh/gamma-Al2O3: a DRIFTS and DFT Study," Constantinos D. Zeinalipour-Yazdi, Andrew L. Cooksy, Angelos M. Efstathiou, J. Phys. Chem. C 111, 13872-13878 (2007). (Full article)
  5. "Wittig Reactions in Water Media Employing Stabilized Ylides with Aldehydes. Synthesis of alpha,beta-Unsaturated Esters from Mixing Aldehydes, alpha-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). (Full article)
  6. "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). (Full article)
  7. "Ab Initio Study of the Torsional Motion in Tolane," Dong Xu and Andrew L. Cooksy, J. Molec. Struct. (THEOCHEM) 815, 119-125 DOI: 10.1016/j.theochem.2007.03.028 (2007).
  8. "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).
  9. "Infrared Laser Magnetic Resonance Spectroscopy of the nu3 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 DOI: 10.1016/j.jms.2006.07.005 (2006).
  10. "Computational Study of Aqueous Reactions in Tocopherol Regeneration," R. Lui and A. L. Cooksy, J. Comp. Theor. Chem. 2, 1395-1402 (2006). (Full article)
  11. "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). (Full article)

MS 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 Spectronmeters 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 HCnO.
  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.

Copyright © 2008. All rights reserved. Web editor: A. L. Cooksy. Page last modified: Wed 30 Jul 2008 10:07:29.