This proposal describes theoretical studies of model porphyrin compounds and of the photosynthetic reaction center. The emphasis is on large scale ab initio electronic structure calculations for these systems using novel numerical techniques developed during the previous granting period which greatly reduce the computational effort needed to carry out high quality ab initio calculations for molecules containing 20-200 atoms. We will determine ground and excited state energies, redox potentials, equilibrium geometries, force fields, charge distributions, dispersion interactions, and-intermolecular electronic couplings for a wide variety of porphyrin moieties, including bacteriochlorophylls embedded in the reaction center protein environment. This information will then be used to calculate optical spectra and electron transfer dynamics in the photosynthetic reaction center, using theoretical methods for spectroscopic and quantum molecular dynamics simulations that we have developed over the past 10 years. We have proposed a simple physical model which explains the efficiency of charge separation in the reaction center and agrees qualitatively with the existing experimental data. The microscopic simulations described above will allow more quantitative models to be constructed, and will permit confirmation (or contradiction) of the basic picture that we have assembled on the basis of phenomenological modeling.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM040526-04
Application #
3298151
Study Section
Metallobiochemistry Study Section (BMT)
Project Start
1988-07-01
Project End
1995-06-30
Budget Start
1991-07-01
Budget End
1992-06-30
Support Year
4
Fiscal Year
1991
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Type
Other Domestic Higher Education
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10027
Friesner, Richard A; Abel, Robert; Goldfeld, Dahlia A et al. (2013) Computational methods for high resolution prediction and refinement of protein structures. Curr Opin Struct Biol 23:177-84
Zeiske, Tim; Stafford, Kate A; Friesner, Richard A et al. (2013) Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins 81:499-509
Miller, Edward B; Murrett, Colleen S; Zhu, Kai et al. (2013) Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. J Chem Theory Comput 9:1846-4864
Li, Jianing; Abel, Robert; Zhu, Kai et al. (2011) The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins 79:2794-812
Li, Jianing; Schneebeli, Severin T; Bylund, Joseph et al. (2011) IDSite: An accurate approach to predict P450-mediated drug metabolism. J Chem Theory Comput 7:3829-3845
Bochevarov, Arteum D; Li, Jianing; Song, Woon Ju et al. (2011) Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. J Am Chem Soc 133:7384-97
Wang, Lingle; Friesner, Richard A; Berne, B J (2011) Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115:9431-8
Bochevarov, Arteum D; Friesner, Richard A; Lippard, Stephen J (2010) The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study. J Chem Theory Comput 6:3735-3749
Schneebeli, Severin T; Hall, Michelle Lynn; Breslow, Ronald et al. (2009) Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations. J Am Chem Soc 131:3965-73
Tian, Li; Friesner, Richard A (2009) QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. J Chem Theory Comput 5:1421-1431

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