Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Insights into colour-tuning of chlorophyll optical response in green plants

Abstract

Here, we performed first-principles calculations within the framework of real-space time-dependent density functional theory for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9]
+ Show Author Affiliations
  1. Univ. de Barcelona, Barcelona (Spain)
  2. Univ. of the Basque Country, Donostia-San Sebastian (Spain)
  3. Univ. of the Basque Country, Donostia-San Sebastian (Spain); Univ. of Coimbra, Coimbra (Portugal)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Martin-Luther-Univ. Halle-Wittenberg, Halle (Germany)
  6. Univ. of Coimbra, Coimbra (Portugal)
  7. Univ. of Liege, Liege (Belgium)
  8. Stewart Computational Chemistry, Colorado Springs, CO (United States)
  9. Univ. of the Basque Country, Donostia-San Sebastian (Spain); Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Hamburg (Germany)
Publication Date:
Research Org.:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1263569
Grant/Contract Number:  
280879-2; CRONOS CP-7P7; 2010 BP-A2-00024; ERC-2010-AdG-267374; 2013081486; 1R44GM108085-01A1; IT395-10; IT578-13; CONT_DOUT/11/UC/405/10150/18/2008; CM1204; MP1306
Resource Type:
Accepted Manuscript
Journal Name:
Physical Chemistry Chemical Physics. PCCP
Additional Journal Information:
Journal Volume: 17; Journal Issue: 40; Journal ID: ISSN 1463-9076
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Jornet-Somoza, Joaquim, Alberdi-Rodriguez, Joseba, Milne, Bruce F., Andrade, Xavier, Marques, Miguel A. L., Nogueira, Fernando, Oliveira, Micael J. T., Stewart, James J. P., and Rubio, Angel. Insights into colour-tuning of chlorophyll optical response in green plants. United States: N. p., 2015. Web. doi:10.1039/c5cp03392f.
Copy to clipboard
Jornet-Somoza, Joaquim, Alberdi-Rodriguez, Joseba, Milne, Bruce F., Andrade, Xavier, Marques, Miguel A. L., Nogueira, Fernando, Oliveira, Micael J. T., Stewart, James J. P., & Rubio, Angel. Insights into colour-tuning of chlorophyll optical response in green plants. United States. https://doi.org/10.1039/c5cp03392f
Copy to clipboard
Jornet-Somoza, Joaquim, Alberdi-Rodriguez, Joseba, Milne, Bruce F., Andrade, Xavier, Marques, Miguel A. L., Nogueira, Fernando, Oliveira, Micael J. T., Stewart, James J. P., and Rubio, Angel. Fri . "Insights into colour-tuning of chlorophyll optical response in green plants". United States. https://doi.org/10.1039/c5cp03392f. https://www.osti.gov/servlets/purl/1263569.
Copy to clipboard
@article{osti_1263569,
title = {Insights into colour-tuning of chlorophyll optical response in green plants},
author = {Jornet-Somoza, Joaquim and Alberdi-Rodriguez, Joseba and Milne, Bruce F. and Andrade, Xavier and Marques, Miguel A. L. and Nogueira, Fernando and Oliveira, Micael J. T. and Stewart, James J. P. and Rubio, Angel},
abstractNote = {Here, we performed first-principles calculations within the framework of real-space time-dependent density functional theory for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex.},
doi = {10.1039/c5cp03392f},
journal = {Physical Chemistry Chemical Physics. PCCP},
number = 40,
volume = 17,
place = {United States},
year = {Fri Jul 17 00:00:00 EDT 2015},
month = {Fri Jul 17 00:00:00 EDT 2015}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1039/c5cp03392f
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 39 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Quantum coherence and its interplay with protein environments in photosynthetic electronic energy transfer
journal, January 2010

  • Ishizaki, Akihito; Calhoun, Tessa R.; Schlau-Cohen, Gabriela S.
  • Physical Chemistry Chemical Physics, Vol. 12, Issue 27
  • DOI: 10.1039/c003389h

Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature
journal, February 2010

  • Collini, Elisabetta; Wong, Cathy Y.; Wilk, Krystyna E.
  • Nature, Vol. 463, Issue 7281
  • DOI: 10.1038/nature08811

Natural light harvesting: principles and environmental trends
journal, January 2011

  • Ruban, Alexander V.; Johnson, Matthew P.; Duffy, Christopher D. P.
  • Energy & Environmental Science, Vol. 4, Issue 5
  • DOI: 10.1039/c0ee00578a

Concentration quenching in chlorophyll
journal, March 1976

Influence of Geometry Relaxation on the Energies of the S 1 and S 2 States of Violaxanthin, Zeaxanthin, and Lutein
journal, April 2006

  • Dreuw, Andreas
  • The Journal of Physical Chemistry A, Vol. 110, Issue 13
  • DOI: 10.1021/jp057385y

Carotenoids in photosynthesis. I. Location in photosynthetic membranes and light-harvesting function
journal, December 1985

  • Siefermann-Harms, Dorothes
  • Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, Vol. 811, Issue 4
  • DOI: 10.1016/0304-4173(85)90006-0

Superradiance and Exciton (De)localization in Light-Harvesting Complex II from Green Plants? †
journal, June 2002

  • Palacios, Miguel A.; de Weerd, Frank L.; Ihalainen, Janne A.
  • The Journal of Physical Chemistry B, Vol. 106, Issue 22
  • DOI: 10.1021/jp014078t

Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis
journal, January 2003

  • Fonseca Guerra, C�lia; Handgraaf, Jan-Willem; Baerends, Evert Jan
  • Journal of Computational Chemistry, Vol. 25, Issue 2
  • DOI: 10.1002/jcc.10351

octopus: a tool for the application of time-dependent density functional theory
journal, September 2006

  • Castro, Alberto; Appel, Heiko; Oliveira, Micael
  • physica status solidi (b), Vol. 243, Issue 11
  • DOI: 10.1002/pssb.200642067

Yield Trends Are Insufficient to Double Global Crop Production by 2050
journal, June 2013

Double excitations within time-dependent density functional theory linear response
journal, April 2004

  • Maitra, Neepa T.; Zhang, Fan; Cave, Robert J.
  • The Journal of Chemical Physics, Vol. 120, Issue 13
  • DOI: 10.1063/1.1651060

Excitation Energy Transfer and Charge Separation in Photosystem II Membranes Revisited
journal, November 2006

  • Broess, Koen; Trinkunas, Gediminas; van der Weij-de Wit, Chantal D.
  • Biophysical Journal, Vol. 91, Issue 10
  • DOI: 10.1529/biophysj.106.085068

Critical analysis and extension of the Hirshfeld atoms in molecules
journal, April 2007

  • Bultinck, Patrick; Van Alsenoy, Christian; Ayers, Paul W.
  • The Journal of Chemical Physics, Vol. 126, Issue 14
  • DOI: 10.1063/1.2715563

Will energy crop yields meet expectations?
journal, June 2014

Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence
journal, June 2007

Excitation energy transfer in the LHC-II trimer: a model based on the new 2.72 Å structure
journal, February 2006

  • Linnanto, Juha; Martiskainen, Jari; Lehtovuori, Viivi
  • Photosynthesis Research, Vol. 87, Issue 3
  • DOI: 10.1007/s11120-005-9004-1

Zwischenmolekulare Energiewanderung und Fluoreszenz
journal, January 1948

Ultrafast Dynamics of Carotenoid Excited States−From Solution to Natural and Artificial Systems
journal, April 2004

  • Polívka, Tomáš; Sundström, Villy
  • Chemical Reviews, Vol. 104, Issue 4
  • DOI: 10.1021/cr020674n

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Electronic Spectra of Structurally Deformed Lutein
journal, October 2012

  • Macernis, Mindaugas; Sulskus, Juozas; Duffy, Christopher D. P.
  • The Journal of Physical Chemistry A, Vol. 116, Issue 40
  • DOI: 10.1021/jp304363q

Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution
journal, March 2004

  • Liu, Zhenfeng; Yan, Hanchi; Wang, Kebin
  • Nature, Vol. 428, Issue 6980
  • DOI: 10.1038/nature02373

Intra- and inter-monomeric transfers in the light harvesting LHCII complex: the Redfield–Förster picture
journal, January 2011

  • Novoderezhkin, Vladimir; Marin, Alessandro; van Grondelle, Rienk
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 38
  • DOI: 10.1039/c1cp21079c

Solar light harvesting by energy transfer: from ecology to coherence
journal, January 2012

  • Scholes, Gregory D.; Mirkovic, Tihana; Turner, Daniel B.
  • Energy & Environmental Science, Vol. 5, Issue 11
  • DOI: 10.1039/c2ee23013e

Carotenoids in Photosynthesis
journal, March 1996

Quantum Coherence Enabled Determination of the Energy Landscape in Light-Harvesting Complex II
journal, December 2009

  • Calhoun, Tessa R.; Ginsberg, Naomi S.; Schlau-Cohen, Gabriela S.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 51
  • DOI: 10.1021/jp908300c

A general and efficient pseudopotential Fourier filtering scheme for real space methods using mask functions
journal, May 2006

  • Tafipolsky, Maxim; Schmid, Rochus
  • The Journal of Chemical Physics, Vol. 124, Issue 17
  • DOI: 10.1063/1.2193514

Photosynthetic Hydrogen Production by a Hybrid Complex of Photosystem I and [NiFe]-Hydrogenase
journal, November 2009

  • Krassen, Henning; Schwarze, Alexander; Friedrich, Bärbel
  • ACS Nano, Vol. 3, Issue 12
  • DOI: 10.1021/nn900748j

Energy transfer in photosynthesis: experimental insights and quantitative models
journal, January 2006

  • van Grondelle, Rienk; Novoderezhkin, Vladimir I.
  • Phys. Chem. Chem. Phys., Vol. 8, Issue 7
  • DOI: 10.1039/b514032c

Carotenoids as a Shortcut for Chlorophyll Soret-to-Q Band Energy Flow
journal, September 2014

  • Götze, Jan P.; Kröner, Dominik; Banerjee, Shiladitya
  • ChemPhysChem, Vol. 15, Issue 15
  • DOI: 10.1002/cphc.201402233

A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations
journal, November 2013

  • García-Risueño, Pablo; Alberdi-Rodriguez, Joseba; Oliveira, Micael J. T.
  • Journal of Computational Chemistry, Vol. 35, Issue 6
  • DOI: 10.1002/jcc.23487

Bonded-atom fragments for describing molecular charge densities
journal, January 1977

First-principles calculation of electronic spectra of light-harvesting complex II
journal, January 2011

  • König, Carolin; Neugebauer, Johannes
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 22
  • DOI: 10.1039/c0cp02808h

Photosynthetic hydrogen production
journal, September 2010

  • Allakhverdiev, Suleyman I.; Thavasi, Velmurugan; Kreslavski, Vladimir D.
  • Journal of Photochemistry and Photobiology C: Photochemistry Reviews, Vol. 11, Issue 2-3
  • DOI: 10.1016/j.jphotochemrev.2010.07.002

Unraveling the Intrinsic Color of Chlorophyll
journal, December 2014

  • Milne, Bruce F.; Toker, Yoni; Rubio, Angel
  • Angewandte Chemie International Edition, Vol. 54, Issue 7
  • DOI: 10.1002/anie.201410899

Modeling of Fluorescence Quenching by Lutein in the Plant Light-Harvesting Complex LHCII
journal, December 2012

  • Duffy, C. D. P.; Chmeliov, J.; Macernis, M.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 38
  • DOI: 10.1021/jp3110997

Comparison of self-interaction-corrections for metal clusters
journal, February 2002

  • Legrand, C.; Suraud, E.; Reinhard, P-G
  • Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 35, Issue 4
  • DOI: 10.1088/0953-4075/35/4/333

Design principles of photosynthetic light-harvesting
journal, January 2012

  • Fleming, Graham R.; Schlau-Cohen, Gabriela S.; Amarnath, Kapil
  • Faraday Discuss., Vol. 155
  • DOI: 10.1039/C1FD00078K

Molecular artificial photosynthesis
journal, January 2014

  • Berardi, Serena; Drouet, Samuel; Francàs, Laia
  • Chem. Soc. Rev., Vol. 43, Issue 22
  • DOI: 10.1039/C3CS60405E

Loop currents in chlorophyll a
journal, January 1982

Density-Functional Theory for Time-Dependent Systems
journal, March 1984

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems
journal, January 2015

  • Andrade, Xavier; Strubbe, David; De Giovannini, Umberto
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 47
  • DOI: 10.1039/C5CP00351B

octopus: a first-principles tool for excited electron–ion dynamics
journal, March 2003

Generalized Gradient Approximation Made Simple
journal, October 1996

  • Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
  • Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
  • DOI: 10.1103/PhysRevLett.77.3865

Principle of stationary action and the definition of a proper open system
journal, May 1994

The Soret absorption band of isolated chlorophyll a and b tagged with quaternary ammonium ions
journal, January 2015

  • Stockett, Mark H.; Musbat, Lihi; Kjær, Christina
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 39
  • DOI: 10.1039/C5CP01513H

An ‘all pigment’ model of excitation quenching in LHCII
journal, January 2015

  • Chmeliov, Jevgenij; Bricker, William P.; Lo, Cynthia
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 24
  • DOI: 10.1039/C5CP01905B

Unraveling the Intrinsic Color of Chlorophyll
journal, December 2014

Ultrafast Dynamics of Carotenoid Excited States — From Solution to Natural and Artificial Systems
journal, June 2004

Computational exploration of copper catalyzed vinylogous aerobic oxidation of unsaturated compounds
journal, January 2021

Density-functional theory for time-dependent systems
journal, January 1987

A survey of the parallel performance and the accuracy of Poisson solvers for electronic structure calculations
preprint, January 2012

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Applications of large-scale density functional theory in biology
    journal, August 2016

    Optical excitations of chlorophyll a and b monomers and dimers
    journal, November 2019

    • Preciado-Rivas, María Rosa; Mowbray, Duncan John; Lyon, Keenan
    • The Journal of Chemical Physics, Vol. 151, Issue 17
    • DOI: 10.1063/1.5121721

    Ultranonlocality and accurate band gaps from a meta-generalized gradient approximation
    journal, November 2019

    Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2
    journal, October 2019

    • Schelter, Ingo; Foerster, Johannes M.; Gardiner, Alastair T.
    • The Journal of Chemical Physics, Vol. 151, Issue 13
    • DOI: 10.1063/1.5116779

    From green to red: large-scale transcriptome comparison of a bud sport in poplar (Populus deltoides)
    journal, September 2016

    Perspective: Fundamental aspects of time-dependent density functional theory
    journal, June 2016

    • Maitra, Neepa T.
    • The Journal of Chemical Physics, Vol. 144, Issue 22
    • DOI: 10.1063/1.4953039

    Time-dependent density functional theory for charge-transfer dynamics: review of the causes of failure and success*
    journal, November 2016

    Applications of Large-Scale Density Functional Theory in Biology
    text, January 2016

    • Cole, Daniel J.; Hine, Nicholas D. M.
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.1266

    Challenging Density Functional Theory Calculations with Hemes and Porphyrins
    journal, April 2016

    • de Visser, Sam; Stillman, Martin
    • International Journal of Molecular Sciences, Vol. 17, Issue 4
    • DOI: 10.3390/ijms17040519
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: