Rex Skodje

Office: Ekeley W145C
Lab: Cristol Chemistry
Lab Phone: 303-492-3507
Fax: 303-492-5894


Ph.D.: University of Minnesota, 1983

Areas of Expertise

Renewable Energy, Reaction Dynamics, Surface Chemistry, Theoretical Chemistry

Theoretical Chemistry: Kinetics and Dynamics

The application of theoretical models to important problems in chemistry is the focus of Professor Skodje's research program. Topics currently under study can be grouped into two broad categories: (1) small molecule chemical physics, and (2) the kinetics of surface processes. The typical Ph.D. thesis produced by Professor Skodje's students will contain a mix of computer simulations, analytical modeling, and an analysis of experimental data. For all the projects presently underway, there is a strong emphasis on interfacing with state-of-the-art experimental work. There is ample opportunity for motivated students to design all or part of their own program.

In small molecule chemical physics, areas of particular interest include: theory of chemical reactions in the gas phase, spectroscopy of the transition state, adiabatic theory, nonlinear dynamics and the theory of chaos, and dynamics of molecular collisions. In the last few years, the strongest emphasis of the research group has been on transition state spectroscopy. This is due in no small part to the influx of new high-quality experimental results requiring interpretation.

In transition state spectroscopy, one is, in essence, trying to assign quantum states which exist near the saddle point of a potential energy surface. Loosely speaking, these states reflect the vibrational and rotational modes of the activated complex. Thus, by studying a spectrum, we can learn a great deal about how a chemical reaction proceeds. Two theoretical techniques have proven especially useful: the spectral quantization method and variational spectral control. The spectral quantization technique provides a method to extract a quantum wave function associated with each spectral peak which is crucial for a correct assignment of the spectrum. In practice, spectral quantization involves extensive use of time-dependent wave packet methods. In the variational algorithm, the appearance of the spectrum is actually engineered to learn as much as possible about the transition state. For example, the uninteresting background component of the spectrum can be minimized in order to emphasize the peaks coming from the modes of the activated complex.

In the area of surface kinetics, topics under current study include: diffusion on surfaces, catalytic surface reactions, thin film growth, and the kinetics of aggregation. One project of particular interest is a detailed study of how clusters of atoms diffuse on surfaces. When atoms adsorb onto a surface, attractive interactions between the atoms typically cause them to congeal into clusters (or islands) on the surface. Diffusion may then occur as clusters move as an aggregate on the surface. Two mechanisms have been found to account for cluster diffusion. In one mechanism, atoms on the boundary of clusters evaporate into a two-dimensional gas phase and then re-condense onto other clusters. With each evaporation/condensation event, the cluster center of mass shifts, and with time the cluster undergoes a random walk. In the other mechanism, the clusters change shape due to movement of atoms around the periphery. This shape shifting allows the cluster to undergo an ameba-like diffusive motion on the surface.

When atomic clusters can move on a surface, they can also collide with each other and coalesce. Thus, with the passage of time, the average size of a cluster grows irreversibly larger and larger. This phenomena, known as coarsening (or ripening), presents a very interesting problem in kinetics. The kinetic equations are solved for distribution of cluster sizes, F(r,t), which represents the concentrations of the clusters. It appears that the correct theoretical picture of coarsening must involve the notions of fractals and renormalization. The theoretical work on thin film growth and coarsening is done in close collaboration with experimental groups. For example, the distribution of cluster sizes can be followed in situ with imaging techniques such as atomic force microscopy (AFM).

Resonances in Chemical Reactions

R.T. Skodje, "Resonances in Bimolecular Chemical Reactions", Advances in Quantum Chemistry63, 119-164 (2012).

R. T. Skodje, D. Skouteris, D. E. Manolopoulos, S.-H. Lee, F. Dong, and K. Liu,            ”F+HD-->HF+D:  A Resonance Mediated Reaction”, Phys. Rev. Lett85, 1206-1209 (2000).

M. Qiu, Z. Ren, L. Che, D. Dai, S. A. Harich, X. Wang, X.Yang, C. Xu, D. Xie, M. Gustafsson, R. T. Skodje, Z. Sun, and D. H. Zhang, “Observation of Feshbach Resonances in the       F+H2-->HF+H Reaction”, SCIENCE 311, 1440-1443 (2006).

Quantization of the Transition State Bottleneck

M. Gustafsson and R. T. Skodje, “The State-to-State-to-State Model of Direct Chemical Reactions:  Application to the D+H2 Reaction”, J. Chem. Phys124, 144311 (2006).

R. T. Skodje and X. M. Yang, "The Observation of Quantized Bottleneck States in Chemical Reactions", International Rev. in Phys. Chem., 23, 253-287 (2004).

D. Dai, C. C. Wang, S. A. Harich,  X. Yang,  S. D. Chao and R. T. Skodje, “Interference of Quantized Transition State Pathways in the H + D2  → D + HD Chemical Reaction”, SCIENCE 300, 1730-1734 (2003).

S. A. Harich, D. Dai, C. C. Wang, X. Yang, S. D. Chao, and R. T. Skodje, “Forward Scattering Due to Slow-Down of the Intermediate in the H+HD-->D+H2 Reaction”, NATURE 419, 281-284 (2002).

Chemical Kinetics

D. D. Y. Zhou, K. L. Han, P. Y. Zhang, L. B. Harding, M. J. Davis, and R. T. Skodje, “Theoretical Determination of the Rate Coefficient for the HO2+HO2-->H2O2+O2 Reaction: Adiabatic Treatment of Anharmonic Torsional Effects”, J. Phys. Chem. A, accepted (2012).

R. T. Skodje, A. S. Tomlin, S. J. Klippenstein, L. B. Harding, and M. J. Davis, “Theoretical Validation of Chemical Kinetic Mechanisms: Combustion of Methanol”, J. Phys. Chem. A. 114, 8286-8301 (2010).

M. J. Davis and R. T. Skodje, “Geometrical Investigation of Low-Dimensional Manifolds in Systems Approaching Equilibrium”, J. Chem. Phys. 111, 859-874 (1999).

Photochemistry, Photo-Catalysis, Water Clusters

Z. C. Kramer, K. Takahashi, and R. T. Skodje, “Water Catalysis and Anticatalysis in Photochemical Reactions: Observation of a Delayed Threshold Effect in the Reaction Quantum Yield”, J. Am. Chem. Soc. (communication) 132, 15154-15157 (2010).

K. Takahashi, K. L. Plath, R. T. Skodje, V. Vaida, “Dynamics of Vibrational Overtone Excited Pyruvic Acid in the Gas Phase:  Line Broadening Through Hydrogen-Atom Chattering”, J. Phys. Chem. A 112, 7321-7331 (2008).

Film Growth, Monte Carlo Simulation

D. N. Brunelli and R. T. Skodje, “The Coarsening of Multicomponent Thin Films”, Phys. Rev. B 69, 075406 (2004).