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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

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 Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1401316
Grant/Contract Number:
AC36-99GO-10337
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Volume: 38; Journal Issue: 18; Related Information: CHORUS Timestamp: 2017-10-20 16:34:06; 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. doi:10.1002/jcc.24804.
Pirojsirikul, Teerapong, Götz, Andreas W., Weare, John, Walker, Ross C., Kowalski, Karol, and Valiev, Marat. 2017. "Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution". United States. doi: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 = {},
doi = {10.1002/jcc.24804},
journal = {Journal of Computational Chemistry},
number = 18,
volume = 38,
place = {United States},
year = 2017,
month = 5
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on May 3, 2018
Publisher's Accepted Manuscript

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  • Green Fluorescent Protein (GFP) is a widely used fluorescent biomarker for the study of biological systems. Our investigation is focused on providing a reliable theoretical description of the GFP chromophore, the photochemical properties of which can be influenced through both the surrounding protein environment and pH levels. In this work we are specifically addressing the effect of an aqueous solvation environment , where a number of experimental measurements have been performed. Our approach is based on a combined quantum mechanics molecular mechanics (QM/MM) methodology, which incorporates high level coupled cluster theory for the analysis of excited states. It also presentsmore » the first application of the newly developed NWChem/AMBER QM/MM interface. Using a systematic approach, which involves comparison of gas phase and aqueous results for different protonation states and conformations, we have resolved existing uncertainties regarding theoretical interpretation of the experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts, but the magnitude of the effect is sensitive to charge 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 coupled description is essential for proper description of excited states of GFP.« less
  • The CH 2Cl 2 + OH - reaction in aqueous solution was investigated using combined quantum mechanical and molecular mechanics approach. We present analysis of the reactant, transition, and product state structures, and calculate the free energy reaction profile through the CCSD(T) level of the theory for the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process raising the reaction barrier by ~17 kcal/mol and the reaction energy by ~20 kcal/mol. While solvation effects play a predominant role, we also find sizable contributions from solvent-induced polarization effects.
  • Steady-state, time-resolved, and temperature-dependent fluorescence studies, together with molecular orbital calculations, have been used to investigate the photophysical behavior of the 2{prime}-naphthyldiene side chain of a novel fluorescent cholesterol analogue with the aim of establishing the utility of this molecule as a cell membrane probe. The photophysics is largely governed by the presence of two ground-state conformers, i.e., the s-cis and s-trans rotamers about the single bond adjacent to the naphthyl group. An excited-state viscosity-dependent process of the s-cis conformer also shows promise to be exploited to study membrane dynamics.
  • We have developed a hybrid approach based on a combination of integral equation theory of molecular liquids and QM/MM methodology in NorthWest computational Chemistry (NWChem) software package. We have split the evaluations into conse- quent QM/MM and statistical mechanics calculations based on the one-dimensional reference interaction site model, which allows us to reduce signicantly the time of computation. The method complements QM/MM capabilities existing in the NWChem package. The accuracy of the presented method was tested through com- putation of water structure around several organic solutes and their hydration free energies. We have also evaluated the solvent effect on themore » conformational equilibria. The applicability and limitations of the developed approach are discussed.« less
  • Using a combination of photoelectron spectroscopy measurements and quantum chemistry calculations, we have identified competing electron emission processes that contribute to the 350–315 nm photoelectron spectra of the deprotonated green fluorescent protein chromophore anion, p-hydroxybenzylidene-2,3-dimethylimidazolinone. As well as direct electron detachment from S{sub 0}, we observe resonant excitation of the 2{sup 1}ππ* state of the anion followed by autodetachment. The experimental photoelectron spectra are found to be significantly broader than photoelectron spectrum calculated using the Franck-Condon method and we attribute this to rapid (∼10 fs) vibrational decoherence, or intramolecular vibrational energy redistribution, within the neutral radical.