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 »
- Authors:
-
- Department of Chemistry and Biochemistry University of California San Diego 9500 Gilman Drive La Jolla California 92093
- San Diego Supercomputer Center, University of California San Diego 9500 Gilman Drive La Jolla California 92093
- 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
- 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}
}
https://doi.org/10.1002/jcc.24804
Web of Science
Works referenced in this record:
New coupled-cluster methods with singles, doubles, and noniterative triples for high accuracy calculations of excited electronic states
journal, January 2004
- Kowalski, Karol; Piecuch, Piotr
- The Journal of Chemical Physics, Vol. 120, Issue 4
Left-eigenstate completely renormalized equation-of-motion coupled-cluster methods: Review of key concepts, extension to excited states of open-shell systems, and comparison with electron-attached and ionized approaches
journal, November 2009
- Piecuch, Piotr; Gour, Jeffrey R.; Włoch, Marta
- International Journal of Quantum Chemistry, Vol. 109, Issue 14
Wavelength mutations and posttranslational autoxidation of green fluorescent protein.
journal, December 1994
- Heim, R.; Prasher, D. C.; Tsien, R. Y.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 26
Probing the Ground State Structure of the Green Fluorescent Protein Chromophore Using Raman Spectroscopy †
journal, April 2000
- Bell, Alasdair F.; He, Xiang; Wachter, Rebekka M.
- Biochemistry, Vol. 39, Issue 15
Quantum Chemistry Behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and Their Chromophores
journal, August 2011
- Bravaya, Ksenia B.; Grigorenko, Bella L.; Nemukhin, Alexander V.
- Accounts of Chemical Research, Vol. 45, Issue 2
Crystal Structure and Photodynamic Behavior of the Blue Emission Variant Y66H/Y145F of Green Fluorescent Protein †
journal, August 1997
- Wachter, Rebekka M.; King, Brett A.; Heim, Roger
- Biochemistry, Vol. 36, Issue 32
Understanding GFP Chromophore Biosynthesis: Controlling Backbone Cyclization and Modifying Post-translational Chemistry † , ‡
journal, February 2005
- Barondeau, David P.; Kassmann, Carey J.; Tainer, John A.
- Biochemistry, Vol. 44, Issue 6
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
journal, May 1976
- Warshel, A.; Levitt, M.
- Journal of Molecular Biology, Vol. 103, Issue 2
The Green Fluorescent Protein
journal, June 1998
- Tsien, Roger Y.
- Annual Review of Biochemistry, Vol. 67, Issue 1, p. 509-544
A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers
journal, December 1986
- Singh, U. Chandra; Kollman, Peter A.
- Journal of Computational Chemistry, Vol. 7, Issue 6
Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions
journal, December 2005
- Nemukhin, Alexander V.; Topol, Igor A.; Burt, Stanley K.
- Journal of Chemical Theory and Computation, Vol. 2, Issue 2
Quantum chemical modeling of structure and absorption spectra of the chromophore in green fluorescent proteins
journal, May 1998
- Voityuk, Alexander A.; Michel-Beyerle, Maria-Elisabeth; Rösch, Notker
- Chemical Physics, Vol. 231, Issue 1
Light-Driven Decarboxylation of Wild-Type Green Fluorescent Protein †
journal, June 2003
- Bell, Alasdair F.; Stoner-Ma, Deborah; Wachter, Rebekka M.
- Journal of the American Chemical Society, Vol. 125, Issue 23
Fluorescent proteins from nonbioluminescent Anthozoa species
journal, October 1999
- Matz, Mikhail V.; Fradkov, Arkady F.; Labas, Yulii A.
- Nature Biotechnology, Vol. 17, Issue 10
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
Chromophore Formation in Green Fluorescent Protein
journal, June 1997
- Reid, Brian G.; Flynn, Gregory C.
- Biochemistry, Vol. 36, Issue 22
Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein
journal, October 1998
- Wachter, Rebekka M.; Elsliger, Marc-André; Kallio, Karen
- Structure, Vol. 6, Issue 10
Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2. Cis − Trans Isomerization in Water
journal, June 2009
- Polyakov, Igor; Epifanovsky, Evgeny; Grigorenko, Bella
- Journal of Chemical Theory and Computation, Vol. 5, Issue 7
Understanding GFP Posttranslational Chemistry: Structures of Designed Variants that Achieve Backbone Fragmentation, Hydrolysis, and Decarboxylation
journal, April 2006
- Barondeau, David P.; Kassmann, Carey J.; Tainer, John A.
- Journal of the American Chemical Society, Vol. 128, Issue 14
Modeling environment effects on spectroscopies through QM/classical models
journal, January 2013
- Mennucci, Benedetta
- Physical Chemistry Chemical Physics, Vol. 15, Issue 18
Absorption Spectrum of the Green Fluorescent Protein Chromophore Anion In Vacuo
journal, November 2001
- Nielsen, S. B.; Lapierre, A.; Andersen, J. U.
- Physical Review Letters, Vol. 87, Issue 22
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins
journal, May 1999
- Weber, W.; Helms, V.; McCammon, J. A.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 11
Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase
journal, June 2009
- Epifanovsky, Evgeny; Polyakov, Igor; Grigorenko, Bella
- Journal of Chemical Theory and Computation, Vol. 5, Issue 7
On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein
journal, October 2015
- Faraji, Shirin; Krylov, Anna I.
- The Journal of Physical Chemistry B, Vol. 119, Issue 41
Properties of the Emitting State of the Green Fluorescent Protein Resolved at the CASPT2//CASSCF/CHARMM Level
journal, August 2005
- Sinicropi, Adalgisa; Andruniow, Tadeusz; Ferré, Nicolas
- Journal of the American Chemical Society, Vol. 127, Issue 33
Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics †
journal, March 2009
- Virshup, Aaron M.; Punwong, Chutintorn; Pogorelov, Taras V.
- The Journal of Physical Chemistry B, Vol. 113, Issue 11
Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein
journal, March 1997
- Brejc, K.; Sixma, T. K.; Kitts, P. A.
- Proceedings of the National Academy of Sciences, Vol. 94, Issue 6
Ground state isomerization of a model green fluorescent protein chromophore
journal, July 2003
- He, Xiang; Bell, Alasdair F.; Tonge, Peter J.
- FEBS Letters, Vol. 549, Issue 1-3
Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965
- Kohn, W.; Sham, L. J.
- Physical Review, Vol. 140, Issue 4A, p. A1133-A1138
Chemical nature of the light emitter of the Aequorea green fluorescent protein
journal, November 1996
- Niwa, H.; Inouye, S.; Hirano, T.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 24
Photoinduced proton transfer from the green fluorescent protein chromophore to a water molecule: analysis of the transfer coordinate
journal, September 2004
- Vendrell, Oriol; Gelabert, Ricard; Moreno, Miquel
- Chemical Physics Letters, Vol. 396, Issue 1-3
Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?
journal, March 2016
- Acharya, Atanu; Bogdanov, Alexey M.; Grigorenko, Bella L.
- Chemical Reviews, Vol. 117, Issue 2
Chromogenic Cross-Link Formation in Green Fluorescent Protein
journal, February 2007
- Wachter, Rebekka M.
- Accounts of Chemical Research, Vol. 40, Issue 2
Benchmarking the completely renormalised equation-of-motion coupled-cluster approaches for vertical excitation energies
journal, September 2015
- Piecuch, Piotr; Hansen, Jared A.; Ajala, Adeayo O.
- Molecular Physics, Vol. 113, Issue 19-20
Solvatochromism of the Green Fluorescence Protein Chromophore and Its Derivatives
journal, September 2006
- Dong, Jian; Solntsev, Kyril M.; Tolbert, Laren M.
- Journal of the American Chemical Society, Vol. 128, Issue 37
Chromophore–Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein
journal, September 2015
- Daday, Csaba; Curutchet, Carles; Sinicropi, Adalgisa
- Journal of Chemical Theory and Computation, Vol. 11, Issue 10
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
journal, July 1990
- Field, Martin J.; Bash, Paul A.; Karplus, Martin
- Journal of Computational Chemistry, Vol. 11, Issue 6
Spectral Perturbations of the Aequorea Green-Fluorescent Protein
journal, June 1982
- Ward, William W.; Prentice, Hugh J.; Roth, Amy F.
- Photochemistry and Photobiology, Vol. 35, Issue 6
The role of the tight-turn, broken hydrogen bonding, Glu222 and Arg96 in the post-translational green fluorescent protein chromophore formation
journal, June 2008
- Lemay, Nathan P.; Morgan, Alicia L.; Archer, Elizabeth J.
- Chemical Physics, Vol. 348, Issue 1-3
Resonantly Enhanced Multiphoton Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore
journal, September 2014
- Greenwood, Jason B.; Miles, Jordan; Camillis, Simone De
- The Journal of Physical Chemistry Letters, Vol. 5, Issue 20
Absorption spectra of the GFP chromophore in solution: comparison of theoretical and experimental results
journal, July 2001
- Voityuk, Alexander A.; Kummer, Andreas D.; Michel-Beyerle, Maria-Elisabeth
- Chemical Physics, Vol. 269, Issue 1-3
Photoabsorption of green and red fluorescent protein chromophore anions in vacuo
journal, September 2007
- Wan, Songbo; Liu, Shasha; Zhao, Guangjiu
- Biophysical Chemistry, Vol. 129, Issue 2-3
The equation-of-motion coupled-cluster method: Excitation energies of Be and CO
journal, December 1989
- Geertsen, Jan; Rittby, Magnus; Bartlett, Rodney J.
- Chemical Physics Letters, Vol. 164, Issue 1
Role of Zwitterions in Kindling Fluorescent Protein Photochemistry
journal, August 2014
- Mironov, Vladimir A.; Bravaya, Ksenia B.; Nemukhin, Alexander V.
- The Journal of Physical Chemistry B, Vol. 119, Issue 6
Reaction Progress of Chromophore Biogenesis in Green Fluorescent Protein
journal, April 2006
- Zhang, Liping; Patel, Hetal N.; Lappe, Jason W.
- Journal of the American Chemical Society, Vol. 128, Issue 14
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
journal, August 2011
- Gordon, Mark S.; Fedorov, Dmitri G.; Pruitt, Spencer R.
- Chemical Reviews, Vol. 112, Issue 1
Primary structure of the Aequorea victoria green-fluorescent protein
journal, February 1992
- Prasher, Douglas C.; Eckenrode, Virginia K.; Ward, William W.
- Gene, Vol. 111, Issue 2
Chromophores of the green fluorescent protein studied in the gas phase
journal, September 2002
- Andersen, L. H.; Lapierre, A.; Nielsen, S. B.
- The European Physical Journal D, Vol. 20, Issue 3
Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant
journal, May 2016
- Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree
- The Journal of Physical Chemistry B, Vol. 120, Issue 19
Excited state reactions in fluorescent proteins
journal, January 2009
- Meech, Stephen R.
- Chemical Society Reviews, Vol. 38, Issue 10
Extension of the method of moments of coupled-cluster equations to excited states: The triples and quadruples corrections to the equation-of-motion coupled-cluster singles and doubles energies
journal, May 2002
- Kowalski, Karol; Piecuch, Piotr
- The Journal of Chemical Physics, Vol. 116, Issue 17
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994
- Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.
- The Journal of Physical Chemistry, Vol. 98, Issue 45, p. 11623-11627
Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
journal, February 2000
- Zhang, Yingkai; Liu, Haiyan; Yang, Weitao
- The Journal of Chemical Physics, Vol. 112, Issue 8
Bond Selection in the Photoisomerization Reaction of Anionic Green Fluorescent Protein and Kindling Fluorescent Protein Chromophore Models
journal, July 2008
- Olsen, Seth; Smith, Sean C.
- Journal of the American Chemical Society, Vol. 130, Issue 27
Conical intersection dynamics in solution: The chromophore of Green Fluorescent Protein
journal, January 2004
- Toniolo, A.; Olsen, S.; Manohar, L.
- Faraday Discuss., Vol. 127
Solvent Effects on the Vibrational Activity and Photodynamics of the Green Fluorescent Protein Chromophore: A Quantum-Chemical Study
journal, March 2005
- Altoe', Piero; Bernardi, Fernando; Garavelli, Marco
- Journal of the American Chemical Society, Vol. 127, Issue 11
Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations
journal, December 2015
- Bhaskaran-Nair, Kiran; Valiev, Marat; Deng, S. H. M.
- The Journal of Chemical Physics, Vol. 143, Issue 22
Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein
journal, February 1993
- Cody, Chris W.; Prasher, Douglas C.; Westler, William M.
- Biochemistry, Vol. 32, Issue 5
On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein
journal, January 2013
- Petrone, Alessio; Caruso, Pasquale; Tenuta, Silvia
- Physical Chemistry Chemical Physics, Vol. 15, Issue 47
Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods?
journal, July 2009
- Filippi, Claudia; Zaccheddu, Maurizio; Buda, Francesco
- Journal of Chemical Theory and Computation, Vol. 5, Issue 8
Structural Evidence for an Enolate Intermediate in GFP Fluorophore Biosynthesis
journal, March 2006
- Barondeau, David P.; Tainer, John A.; Getzoff, Elizabeth D.
- Journal of the American Chemical Society, Vol. 128, Issue 10
Origin, Nature, and Fate of the Fluorescent State of the Green Fluorescent Protein Chromophore at the CASPT2//CASSCF Resolution
journal, May 2004
- Martin, María Elena; Negri, Fabrizia; Olivucci, Massimo
- Journal of the American Chemical Society, Vol. 126, Issue 17
Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo
journal, January 2009
- Rajput, J.; Rahbek, D. B.; Andersen, L. H.
- Physical Chemistry Chemical Physics, Vol. 11, Issue 43
Absorption of the green fluorescent protein chromophore anion in the gas phase studied by a combination of FTICR mass spectrometry with laser-induced photodissociation spectroscopy
journal, September 2011
- Chingin, Konstantin; Balabin, Roman M.; Frankevich, Vladimir
- International Journal of Mass Spectrometry, Vol. 306, Issue 2-3
Solvent effects on molecular spectra. III. Absorption to and emission from the lowest singlet ( n ,π*) state of dilute pyrimidine in water
journal, August 1993
- Zeng, J.; Hush, N. S.; Reimers, J. R.
- The Journal of Chemical Physics, Vol. 99, Issue 3
Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules
journal, January 1971
- Ditchfield, R.; Hehre, W. J.; Pople, J. A.
- The Journal of Chemical Physics, Vol. 54, Issue 2
COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient
journal, January 1993
- Klamt, A.; Schüürmann, G.
- J. Chem. Soc., Perkin Trans. 2, Issue 5
Solvent Effects on the Electronic Spectra of Transition Metal Complexes
journal, February 2000
- Hush, Noel S.; Reimers, Jeffrey R.
- Chemical Reviews, Vol. 100, Issue 2
The equation of motion coupled‐cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties
journal, May 1993
- Stanton, John F.; Bartlett, Rodney J.
- The Journal of Chemical Physics, Vol. 98, Issue 9
QM/MM Methods for Biomolecular Systems
journal, January 2009
- Senn, Hans Martin; Thiel, Walter
- Angewandte Chemie International Edition, Vol. 48, Issue 7
Insight into the Common Mechanism of the Chromophore Formation in the Red Fluorescent Proteins: The Elusive Blue Intermediate Revealed
journal, January 2012
- Bravaya, Ksenia B.; Subach, Oksana M.; Korovina, Nadezhda
- Journal of the American Chemical Society, Vol. 134, Issue 5
Electronic excitations of green fluorescent proteins: Protonation states of chromophore model compound in solutions
journal, November 2005
- Xie, Daiqian; Zeng, Jun
- Journal of Computational Chemistry, Vol. 26, Issue 14
Development and testing of a general amber force field
journal, January 2004
- Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
- Journal of Computational Chemistry, Vol. 25, Issue 9
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
journal, September 2010
- Valiev, M.; Bylaska, E. J.; Govind, N.
- Computer Physics Communications, Vol. 181, Issue 9, p. 1477-1489
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
journal, May 1995
- Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.
- Journal of the American Chemical Society, Vol. 117, Issue 19
Fluorescent properties of model chromophores of tyrosine-66 substituted mutants of Aequorea green fluorescent protein (GEP)
journal, July 1998
- Kojima, Satoshi; Ohkawa, Hiroko; Hirano, Takashi
- Tetrahedron Letters, Vol. 39, Issue 29
Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
journal, January 2005
- Weigend, Florian; Ahlrichs, Reinhart
- Physical Chemistry Chemical Physics, Vol. 7, Issue 18, p. 3297-3305
Optimized atomic radii for quantum dielectric continuum solvation models
journal, September 1995
- Stefanovich, Eugene V.; Truong, Thanh N.
- Chemical Physics Letters, Vol. 244, Issue 1-2
Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993
- Becke, Axel D.
- The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
Low-lying electronic excitations of the green fluorescent protein chromophore
journal, July 2000
- Helms, V.; Winstead, C.; Langhoff, P. W.
- Journal of Molecular Structure: THEOCHEM, Vol. 506, Issue 1-3
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package
journal, September 2012
- Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2
Improved green fluorescence
journal, February 1995
- Heim, Roger; Cubitt, Andrew B.; Tsien, Roger Y.
- Nature, Vol. 373, Issue 6516
Extension of the Effective Fragment Potential Method to Macromolecules
journal, June 2016
- Gurunathan, Pradeep Kumar; Acharya, Atanu; Ghosh, Debashree
- The Journal of Physical Chemistry B, Vol. 120, Issue 27
Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections
journal, July 2010
- Polyakov, I. V.; Grigorenko, B. L.; Epifanovsky, E. M.
- Journal of Chemical Theory and Computation, Vol. 6, Issue 8
Green Fluorescent Protein (GFP): Applications, Structure, and Related Photophysical Behavior
journal, March 2002
- Zimmer, Marc
- Chemical Reviews, Vol. 102, Issue 3
Electrostatic spectral tuning mechanism of the green fluorescent protein
journal, January 2013
- Kaila, Ville R. I.; Send, Robert; Sundholm, Dage
- Physical Chemistry Chemical Physics, Vol. 15, Issue 13
Relationship between structure and optical properties in green fluorescent proteins: a quantum mechanical study of the chromophore environment
journal, March 2004
- Laino, Teodoro; Nifosı̀, Riccardo; Tozzini, Valentina
- Chemical Physics, Vol. 298, Issue 1-3
Inhomogeneous Electron Gas
journal, November 1964
- Hohenberg, P.; Kohn, W.
- Physical Review, Vol. 136, Issue 3B, p. B864-B871
Unveiling How an Archetypal Fluorescent Protein Operates: Theoretical Perspective on the Ultrafast Excited State Dynamics of GFP Variant S65T/H148D
journal, August 2014
- Armengol, Pau; Gelabert, Ricard; Moreno, Miquel
- The Journal of Physical Chemistry B, Vol. 119, Issue 6
An extensible interface for QM/MM molecular dynamics simulations with AMBER
journal, October 2013
- Götz, Andreas W.; Clark, Matthew A.; Walker, Ross C.
- Journal of Computational Chemistry, Vol. 35, Issue 2
Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study
journal, July 2003
- Das, Abhijit K.; Hasegawa, Jun-Ya; Miyahara, Tomoo
- Journal of Computational Chemistry, Vol. 24, Issue 12
First-Principles Characterization of the Energy Landscape and Optical Spectra of Green Fluorescent Protein along the A→I→B Proton Transfer Route
journal, July 2013
- Grigorenko, Bella L.; Nemukhin, Alexander V.; Polyakov, Igor V.
- Journal of the American Chemical Society, Vol. 135, Issue 31
Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore
journal, June 2011
- Bravaya, Ksenia B.; Khrenova, Maria G.; Grigorenko, Bella L.
- The Journal of Physical Chemistry B, Vol. 115, Issue 25
Protonation effects on the chromophore of green fluorescent protein. Quantum chemical study of the absorption spectrum
journal, June 1997
- Voityuk, Alexander A.; Michel-Beyerle, Maria-Elisabeth; Rösch, Notker
- Chemical Physics Letters, Vol. 272, Issue 3-4
Modeling of the structure and electronic spectra of green fluorescent protein chromophore
journal, October 2008
- Bravaya, K. B.; Bochenkova, A. V.; Granovskii, A. A.
- Russian Journal of Physical Chemistry B, Vol. 2, Issue 5
Deactivation Pathways of an Isolated Green Fluorescent Protein Model Chromophore Studied by Electronic Action Spectroscopy
journal, December 2009
- Forbes, Matthew W.; Jockusch, Rebecca A.
- Journal of the American Chemical Society, Vol. 131, Issue 47
Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer
journal, April 2010
- Kowalski, Karol; Krishnamoorthy, Sriram; Villa, Oreste
- The Journal of Chemical Physics, Vol. 132, Issue 15