Research Nuggets



We are able to model the photoisomerization process in molecules like stilbene (above) and azobenzene. These molecule exist in two stable conformations: trans (top left) and cis (bottom left), and are converted from one configuration to the other when they are excited optically (middle panel). In our simulations, we perform ensembles to describe isomerization mechanism, time, and quantum yield (right panel). The photo switchable molecules have potential applications ranging from optical storage devices, photo-orientation of liquid crystals, control of peptide conformations, and control of CO2 adsorption in porous metal organic frameworks.

Amanda J. Neukirch, Logan C. Shamberger, Enrique Abad, Barry J. Haycock, Hong Wang, Jose Ortega, Oleg V. Prezhdo, and James P. Lewis. 2013. “Nonadiabatic ensemble simulations of cis-stilbene and cis-azobenzene photoisomerization” J. Chem. Theory Comp.  DOI: 10.1021/ct4009816

E. Abad, J.P. Lewis, V. Zobač, P. Hapala, P. Jelínek, and J. Ortega. 2013. “Calculation of non-adiabatic coupling vectors in a local-orbital basis set,” J. Chem. Phys. 138:154106. DOI: 10.1063/1.4801511

This work was supported by the Office of Science, Basic Energy Sciences in the US Department of Energy (Grant No.DE-SC0006527 ).




We explore the effect of crystallographic strain on the electronic configuration of materials such as CuGaO2 using high-throughput calculations. We can see how the crystal structure responds to iron substitution at the gallium sites and observe how the electronic transitions change as a result. We use very high-throughput calculations and data-mining techniques to determine the preferred crystal positions of the iron atoms relative to each other. We find that at a certain impurity level the disorder in the material becomes global, unlocking previously forbidden optoelectronic transitions throughout the material.

Barry Haycock, M. Kylee Underwood, Jonathan Lekse, Christopher Matranga, and James P. Lewis. 2013. "High-throughput calculations of transparent conducting oxide CuGa1-xFexO2 delafossite structures.", Comp. Mat. Sci. (accepted).

Jonathan W. Lekse, M. Kylee Underwood, James P. Lewis, and Christopher Matranga. 2012. "Synthesis, characterization, electronic structure, and photocatalytic behavior of CuGaO2 and CuGa1-xFexO2 (x = 0.05, 0.10, 0.15, 0.20) delafossites" J. Phys. Chem. C. 116 (2), 1865-1872. DOI: 10.1021/jp2087225

This work is supported by the National Science Foundation through NSF DMR 09-03225 and a subcontract from NETL (URS RES) for Work Activity 0004000.6.600.007.002.420.000.005 ARRA ICMI Project, Element 420, Photo Active Materials.


We combine computational and experimental effort together to explore the interaction between biomolecules and gold nanoparticles. Starting with small amino acid molecule, we have investigated the anchoring pattern for cysteine zwitterion attached on gold nanoparticle. Our results support the attaching mode recognized in solid state NMR studies, which indicate a double layer of L-cysteine molecules is the likely configuration.

We have expanded our studies to small peptide molecules with cysteine as terminated component. What we are curious herein is if the interaction will be different once cysteine presented as part of peptide. These computational results may be applicable to gain a better understanding of how peptides interact with gold nanoparticles.

Jessica A. Carr, Hong Wang, Anuji Abraham, Terry Gullion, and James P. Lewis. 2012. "l-Cysteine Interaction with Au55 Nanoparticles.",  J. Phys. Chem. C., 116 (49),  25816–25823. DOI: 10.1021/jp308215n

This work is supported by Grant PRF51290-ND6 from the American Chemical Society Petroleum Research Fund.



We predict possible material's that catalyze the photo-degradation of organic chemical pollutants using our high-throughput computational techniques. The removal of such chemicals from waste water in industrial processes' is a serious issue in many industries. For example,  we study a material that helps break down methylene blue in waste water by replacing indium sites in NaInO2 with iron

Jonathan W. Lekse, Barry Haycock, James P. Lewis, and Christopher Matranga. 2013. "The Effect of Electronic Structure Changes in NaInO2 and NaIn0.9Fe0.1O2 on the Photoreduction of Methylene Blue" In preparation.

This work is supported by the National Science Foundation through NETL (URS RES) for Work Activity 0004000.6.600.007.002.420.000.005 ARRA ICMI Project, Element 420, Photo Active Materials.