liu.seSearch for publications in DiVA
Change search
Refine search result
1 - 11 of 11
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Begum, Shamima
    et al.
    University of Manchester, England.
    Cianci, Michele
    DESY, Germany.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Haedener, Alfons
    University of Manchester, England.
    Helliwell, John R.
    University of Manchester, England.
    Helliwell, Madeleine
    University of Manchester, England.
    Regan, Andrew C.
    University of Manchester, England.
    Watt, Ian F.
    University of Manchester, England.
    On the origin and variation of colors in lobster carapace2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 26, p. 16723-16732Article in journal (Refereed)
    Abstract [en]

    The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

  • 2.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Computational Studies of Photobiological Keto-Enol Reactions and Chromophores2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents computational chemistry studies of keto-enol reactions and chromophores of photobiological signicance.

    The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.

    The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.

    The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.

    The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.

    Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and  flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.

    List of papers
    1. On the origin and variation of colors in lobster carapace
    Open this publication in new window or tab >>On the origin and variation of colors in lobster carapace
    Show others...
    2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 26, p. 16723-16732Article in journal (Refereed) Published
    Abstract [en]

    The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2015
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:liu:diva-120247 (URN)10.1039/c4cp06124a (DOI)000356874000010 ()25797168 (PubMedID)
    Note

    Funding Agencies|Bildungs- und Kultur-departement des Kantons Luzern, Switzerland; Swedish Research Council; Olle Engkvist Foundation; Nuffield Foundation; School of Chemistry, University of Manchester; European Molecular Biology Laboratory

    Available from: 2015-07-21 Created: 2015-07-20 Last updated: 2017-12-04
    2. Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants
    Open this publication in new window or tab >>Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants
    2014 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 30, p. 2184-2194Article in journal (Refereed) Published
    Abstract [en]

    Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.

    Place, publisher, year, edition, pages
    Wiley: 12 months, 2014
    Keywords
    light emission; tautomerism; protonation state; Born-Haber cycle; density functional theory
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-112610 (URN)10.1002/jcc.23735 (DOI)000344173700003 ()25226816 (PubMedID)
    Note

    Funding Agencies|Linkoping University; Swedish Research Council; Olle Engkvist Foundation; Wenner-Gren Foundations

    Available from: 2014-12-10 Created: 2014-12-05 Last updated: 2017-12-05
    3. Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin
    Open this publication in new window or tab >>Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin
    2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed) Published
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2015
    Keywords
    Inter-excited state transition dipole moments, Radiative transitions, Nonradiative transitions, Response theory, Time-dependent density functional theory, Flavin chromophores
    National Category
    Chemical Sciences Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-122743 (URN)10.1021/acs.jpca.5b08908 (DOI)000366339400016 ()
    Note

    Vid tiden för disputation förelåg publikationen som manuskript

    Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2017-12-01Bibliographically approved
    4. Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    Open this publication in new window or tab >>Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    2013 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 19-28Article in journal (Refereed) Published
    Abstract [en]

    Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keywords
    bilin chromophores, photoreceptor proteins, fluorescent proteins, excited states, quantum chemistry
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-96694 (URN)10.1016/j.chemphys.2013.07.018 (DOI)000327443700003 ()
    Note

    Funding agencies|Linkoping University||Swedish Research Council||Olle Engkvist Foundation||Wenner-Gren Foundations||

    Available from: 2013-08-23 Created: 2013-08-23 Last updated: 2017-12-06Bibliographically approved
    5. Modeling of phytochrome absorption spectra
    Open this publication in new window or tab >>Modeling of phytochrome absorption spectra
    2013 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, p. 1363-1374Article in journal (Refereed) Published
    Abstract [en]

    Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2013
    Keywords
    photosensory proteins, bilin chromophores, QM/MM methods, time-dependent density functional theory
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-92393 (URN)10.1002/jcc.23265 (DOI)000318696800001 ()
    Available from: 2013-05-10 Created: 2013-05-10 Last updated: 2017-12-06Bibliographically approved
    6. QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome
    Open this publication in new window or tab >>QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome
    2015 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

    National Category
    Chemical Sciences Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-122744 (URN)
    Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2015-11-26Bibliographically approved
  • 3.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This licentiate thesis presents computational chemistry studies on photochemical properties of phytochrome and firefly luciferase chromophores.

    Phytochromes are bilin-containing proteins that based on the ambient light environment regulate a number of physiological and developmental processes in bacteria, cyanobacteria, fungi and plants. From the viewpoint of computational modeling, however, only a few studies have been devoted to these systems. In this thesis, two systematic studies comparing calculated and experimental UV-vis spectra of bilin chromophores in protein and solution environments are presented. The rst study focuses on how hybrid quantum mechanics/molecular mechanics methods are best applied to calculate absorption spectra of a bacteriophytochrome. The second study, in turn, investigates the performance of a number of quantum chemical methods in calculating absorption and emission spectra of sterically locked bilin chromophores.

    Firefly luciferase catalyzes a chemical reaction in which the electronically excited oxyluciferin is formed and subsequently emits light. Depending on the conditions, oxyluciferin can exist in a number of dierent chemical forms. To date, there is no consensus regarding which of these that most signicantly contributes to the light emission. In this thesis, the most probable form of the light emitter is predicted by calculating excited-state pKE and pKa values, in aqueous solution, of the various equilibrium reactions relevant for the oxyluciferin system.

    List of papers
    1. Modeling of phytochrome absorption spectra
    Open this publication in new window or tab >>Modeling of phytochrome absorption spectra
    2013 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, p. 1363-1374Article in journal (Refereed) Published
    Abstract [en]

    Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2013
    Keywords
    photosensory proteins, bilin chromophores, QM/MM methods, time-dependent density functional theory
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-92393 (URN)10.1002/jcc.23265 (DOI)000318696800001 ()
    Available from: 2013-05-10 Created: 2013-05-10 Last updated: 2017-12-06Bibliographically approved
    2. Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    Open this publication in new window or tab >>Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    2013 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 19-28Article in journal (Refereed) Published
    Abstract [en]

    Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keywords
    bilin chromophores, photoreceptor proteins, fluorescent proteins, excited states, quantum chemistry
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-96694 (URN)10.1016/j.chemphys.2013.07.018 (DOI)000327443700003 ()
    Note

    Funding agencies|Linkoping University||Swedish Research Council||Olle Engkvist Foundation||Wenner-Gren Foundations||

    Available from: 2013-08-23 Created: 2013-08-23 Last updated: 2017-12-06Bibliographically approved
    3. Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants
    Open this publication in new window or tab >>Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants
    2013 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    This study investigates the excited-state equilibria of the chemiexcited oxyluciferin light emitter responsible for the emission of light in firefly bioluminescence. To date, there is no consensus regarding which of the possible chemical forms connected by excited-state keto-enol and acid-base equilibrium reactions that is the main contributor to the light emission. Using a hybrid cluster-continuum approach, we perform quantum chemical calculations to obtain the relevant excited-state pKE and pKa values in aqueous solution. As such, we gain insight into the intrinsic tendency of the chemiexcited oxyluciferin light emitter to prefer a particular form.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-103337 (URN)
    Available from: 2014-01-17 Created: 2014-01-17 Last updated: 2014-01-17Bibliographically approved
  • 4.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited-State Proton Transfer in Bacteriophytochromes2018In: ChemPhotoChem, ISSN 2367-0932, Vol. 2, no 6, p. 453-457Article in journal (Refereed)
    Abstract [en]

    The engineering of bacteriophytochrome photoreceptors into near-infrared fluorescent proteins is a promising route toward deep-tissue imaging of living cells with many challenges ahead. One key objective is to increase the fluorescence quantum yields, which are limited by competing non-radiative relaxation processes involving not only the well-known double-bond photoisomerization of the tetrapyrrole chromophore, but also a potential excited-state proton transfer from the chromophore to the protein. Motivated by the lack of mechanistic knowledge about this proton transfer, we here use hybrid quantum mechanics/molecular mechanics methods to investigate three possible scenarios for how the process is initiated. Through calculated excited-state pKa values of the chromophore inside the protein matrix of Deinococcus radiodurans bacteriophytochrome, it is found that pyrrole ring C is a much more likely donor for excited-state proton transfer than rings A and B, which are also possible donors discussed in the literature. This finding offers a starting point for establishing a strategy to strengthen the fluorescence of engineered bacteriophytochromes through biochemical inhibition of the proton transfer.

  • 5.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants2013Manuscript (preprint) (Other academic)
    Abstract [en]

    This study investigates the excited-state equilibria of the chemiexcited oxyluciferin light emitter responsible for the emission of light in firefly bioluminescence. To date, there is no consensus regarding which of the possible chemical forms connected by excited-state keto-enol and acid-base equilibrium reactions that is the main contributor to the light emission. Using a hybrid cluster-continuum approach, we perform quantum chemical calculations to obtain the relevant excited-state pKE and pKa values in aqueous solution. As such, we gain insight into the intrinsic tendency of the chemiexcited oxyluciferin light emitter to prefer a particular form.

  • 6.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 30, p. 2184-2194Article in journal (Refereed)
    Abstract [en]

    Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.

  • 7.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Modeling of phytochrome absorption spectra2013In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, p. 1363-1374Article in journal (Refereed)
    Abstract [en]

    Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

  • 8.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome2015Manuscript (preprint) (Other academic)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

  • 9.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 19-28Article in journal (Refereed)
    Abstract [en]

    Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

  • 10.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Steric Effects Govern the Photoactivation of Phytochromes2016In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 7, p. 954-957Article in journal (Refereed)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins existing in two forms that absorb red (Pr) and far-red (Pfr) light. Although it is well-known that the conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the linear tetrapyrrole chromophore, direct evidence is scarce as to why this reaction always occurs at the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics calculations based on a high-resolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions render photoisomerizations at the AB and BC bridges much less probable than photoisomerization at the CD bridge.

  • 11.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed)
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

1 - 11 of 11
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf