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Theoretical Modeling of Fluorescence Properties in Biological Systems

EMSL Project ID


In this project high level ab initio methods will be used to study photophysical properties of nucleic acid bases and their fluorescent analogs. The natural nucleobases have ultrashort excited state lifetimes and very short quantum yields for fluorescence. Small modifications in their structure renders them fluorescent. We seek to understand these effects by calculating potential energy surfaces (PESs) of the excited states of these systems and comparing their features. Conical intersections are of particular interest since they facilitate radiationless decay and fluorescence quenching. Multireference configuration interaction as implemented in the COLUMBUS suite of programs and completely renormalized equation-of-motion coupled cluster techniques as implemented in NWChem will be used to obtain accurate energies on PESs. Due to a large number of single point calculations that need to be performed in order to obtain a reliable characterization of the excited-state PESs for a wide variety of internuclear geometries, the use of highly scalable software is of paramount importance. Both of the computational packages that will be used satisfy this requirement. Monomers and pi-stacked dimers will be considered. A QM/MM approach will also be used to account for solvent and other environmental effects.

Project Details

Project type
Capability Research
Start Date
End Date


Principal Investigator

Spiridoula Matsika
Temple University

Team Members

Congyi Zhou
Temple University

JingXin Liang
Temple University

Zhen Lu
Temple University

Christopher Kozak
Temple University

Kurt Kistler
Pennsylvania State University

Karol Kowalski
Pacific Northwest National Laboratory

Marat Valiev
Environmental Molecular Sciences Laboratory

Related Publications

Christopher R. Kozak, Kurt A. Kistler, Zhen Lu, and Spiridoula Matsika. 2010. "Excited-State Energies and Electronic Couplings of DNA Base Dimers." J. Phys. Chem. B 2010, 114(4), 1674–1683.
Kotur M, TC Weinacht, C Zhou, and S Matsika. 2011. "Following Ultrafast Radiationless Relaxation Dynamics With Strong Field Dissociative Ionization: A Comparison Between Adenine, Uracil, and Cytosine." IEEE Journal of Quantum Electronics 18(1):187-197. doi:10.1109/JSTQE.2011.2107892
Kotur M, TC Weinacht, C Zhou, and S Matsika. 2011. "Strong-Field Molecular Ionization from Multiple Orbitals." Physical Review X 1:021010. doi:10.1103/PhysRevX.1.021010
Kotur M, TC Weinacht, C Zhou, KA Kistler, and S Matsika. 2011. "Distinguishing Between Relaxation Pathways by Combining Dissociative Ionization Pump Probe Spectroscopy and Ab Initio Calculations: A Case Study of Cytosine." Chinese Journal of Chemical Physics 134:184309. doi:10.1063/1.3586812
Kurt A. Kistler and Spiridoula Matsika. 2010. "Photophysical pathways of cytosine in aqueous solution." PCCP 12(19):5024-5031. DOI: 10.1039/b926125g
Liang J, and S Matsika. 2011. "Pathways for Fluorescence Quenching in 2-Aminopurine ?-Stacked with Pyrimidine Nucleobases." Journal of the American Chemical Society 133(17):6799-3808. doi:10.1021/ja2007998
Matsika S, C Zhou, M Kotur, and TC Weinacht. 2011. "Combining Dissociative Ionization Pump–Probe Spectroscopy and ab initio Calculations to Interpret Dynamics and Control Through Conical Intersections." Faraday Discussions 153:247-260. doi:10.1039/C1FD00044F
Zhou C, S Matsika, M Kotur, and TC Weinacht. 2012. "Fragmentation Pathways in the Uracil Radical Cation." Journal of Physical Chemistry A 116:9217?9227. doi:10.1021/jp209213e