liu.seSearch for publications in DiVA
Change search
CiteExportLink to record
Permanent link

Direct 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
Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
2015 (English)Doctoral 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.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. , 76 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1713
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:liu:diva-122614DOI: 10.3384/diss.diva-122614ISBN: 978-91-7685-922-3 (print)OAI: oai:DiVA.org:liu-122614DiVA: diva2:872576
Public defence
2015-12-18, Nobel (BL32), B-huset, Campus Valla, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2015-11-19 Created: 2015-11-11 Last updated: 2017-01-03Bibliographically approved
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, 16723-16732 p.Article 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, 2184-2194 p.Article 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
Keyword
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, 11911-11921 p.Article 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
Keyword
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, 19-28 p.Article 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
Keyword
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, 1363-1374 p.Article 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
Keyword
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

Open Access in DiVA

fulltext(1877 kB)176 downloads
File information
File name FULLTEXT01.pdfFile size 1877 kBChecksum SHA-512
801d4bc68492c5a89b1aafd54a35b958067777b9521f4da3343b0431af1e1d33b8aa66158c8d0eb79c787742f7e3a61a23f1affbfc5ce652b367f9856f135f74
Type fulltextMimetype application/pdf
omslag(1318 kB)1104 downloads
File information
File name COVER01.pdfFile size 1318 kBChecksum SHA-512
ccc0e4fe903e549bd216f631f0c236db0c5ef11e64391f09bfb2452f526bfda8b141aec7a1f4db7a687a6d60576374d403f3f4aefc91c0b9df1273a2e00737c5
Type coverMimetype application/pdf

Other links

Publisher's full text

Authority records BETA

Falklöf, Olle

Search in DiVA

By author/editor
Falklöf, Olle
By organisation
Theoretical ChemistryFaculty of Science & Engineering
Theoretical Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 176 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
isbn
urn-nbn

Altmetric score

doi
isbn
urn-nbn
Total: 1382 hits
CiteExportLink to record
Permanent link

Direct 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