Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment
Abstract
We present molecular mechanics and spectroscopic calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker and Oregon Green 488, when these are attached at two different sites (104 and 123) on the TMV protein. The resulting geometric information shows that the extent of disorder and aggregation properties and therefore the optical properties of the TMV-templated chromophore assembly are highly dependent on both the choice of chromophores and the protein site to which they are bound. We use the results of the conformational search as geometric parameters together with an improved tight-binding Hamiltonian to simulate the linear absorption spectra and compare with experimental spectral measurements. The ideal dipole approximation to the Hamiltonian is not valid because the distance between chromophores can be very small. Finally, we found that using the geometries from the conformational search is necessary to reproduce the features of themore »
- Authors:
-
[1];
[2];
- Pohnag Univ. of Science and Technology (Korea); Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States); California State Univ., Easy Bay, CA (United States)
- Univ. of California, Berkeley, CA (United States); Kansas State Univ., Manhattan, KS (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); Defense Advanced Research Projects Agency (DARPA)
- OSTI Identifier:
- 1604660
- Grant/Contract Number:
- AC02-05CH11231; N66001-10-4068
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
- Additional Journal Information:
- Journal Volume: 122; Journal Issue: 51; Journal ID: ISSN 1520-6106
- Publisher:
- American Chemical Society
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; monomers; hamiltonians; chromophores; energy; mathematical methods
Citation Formats
Lee, Joonho, Lee, Donghyun, Kocherzhenko, Aleksey A., Greenman, Loren, Finley, Daniel T., Francis, Matthew B., and Whaley, K. Birgitta. Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment. United States: N. p., 2018.
Web. doi:10.1021/acs.jpcb.8b08858.
Lee, Joonho, Lee, Donghyun, Kocherzhenko, Aleksey A., Greenman, Loren, Finley, Daniel T., Francis, Matthew B., & Whaley, K. Birgitta. Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment. United States. https://doi.org/10.1021/acs.jpcb.8b08858
Lee, Joonho, Lee, Donghyun, Kocherzhenko, Aleksey A., Greenman, Loren, Finley, Daniel T., Francis, Matthew B., and Whaley, K. Birgitta. Tue .
"Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment". United States. https://doi.org/10.1021/acs.jpcb.8b08858. https://www.osti.gov/servlets/purl/1604660.
@article{osti_1604660,
title = {Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment},
author = {Lee, Joonho and Lee, Donghyun and Kocherzhenko, Aleksey A. and Greenman, Loren and Finley, Daniel T. and Francis, Matthew B. and Whaley, K. Birgitta},
abstractNote = {We present molecular mechanics and spectroscopic calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker and Oregon Green 488, when these are attached at two different sites (104 and 123) on the TMV protein. The resulting geometric information shows that the extent of disorder and aggregation properties and therefore the optical properties of the TMV-templated chromophore assembly are highly dependent on both the choice of chromophores and the protein site to which they are bound. We use the results of the conformational search as geometric parameters together with an improved tight-binding Hamiltonian to simulate the linear absorption spectra and compare with experimental spectral measurements. The ideal dipole approximation to the Hamiltonian is not valid because the distance between chromophores can be very small. Finally, we found that using the geometries from the conformational search is necessary to reproduce the features of the experimental spectral peaks.},
doi = {10.1021/acs.jpcb.8b08858},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 51,
volume = 122,
place = {United States},
year = {Tue Nov 20 00:00:00 EST 2018},
month = {Tue Nov 20 00:00:00 EST 2018}
}
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