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Title: Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution

Abstract

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well‐known codes—NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likelymore » coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.« less

Authors:
 [1];  [2];  [1];  [3];  [4]; ORCiD logo [4]
  1. Department of Chemistry and Biochemistry University of California San Diego 9500 Gilman Drive La Jolla California 92093
  2. San Diego Supercomputer Center, University of California San Diego 9500 Gilman Drive La Jolla California 92093
  3. Department of Chemistry and Biochemistry University of California San Diego 9500 Gilman Drive La Jolla California 92093, GlaxoSmithKline 1250 S. Collegeville Road Collegeville Pennsylvania 19426
  4. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory P. O. Box 999 Richland Washington 99352
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1401316
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Name: Journal of Computational Chemistry Journal Volume: 38 Journal Issue: 18; Journal ID: ISSN 0192-8651
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Pirojsirikul, Teerapong, Götz, Andreas W., Weare, John, Walker, Ross C., Kowalski, Karol, and Valiev, Marat. Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. United States: N. p., 2017. Web. doi:10.1002/jcc.24804.
Pirojsirikul, Teerapong, Götz, Andreas W., Weare, John, Walker, Ross C., Kowalski, Karol, & Valiev, Marat. Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. United States. https://doi.org/10.1002/jcc.24804
Pirojsirikul, Teerapong, Götz, Andreas W., Weare, John, Walker, Ross C., Kowalski, Karol, and Valiev, Marat. Wed . "Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution". United States. https://doi.org/10.1002/jcc.24804.
@article{osti_1401316,
title = {Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution},
author = {Pirojsirikul, Teerapong and Götz, Andreas W. and Weare, John and Walker, Ross C. and Kowalski, Karol and Valiev, Marat},
abstractNote = {Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well‐known codes—NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.},
doi = {10.1002/jcc.24804},
journal = {Journal of Computational Chemistry},
number = 18,
volume = 38,
place = {United States},
year = {Wed May 03 00:00:00 EDT 2017},
month = {Wed May 03 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
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https://doi.org/10.1002/jcc.24804

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