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Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2008. , p. 61
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 394
Keywords [en]
Quantum chemistry, Quantum Chemistry, Halogenated Arenes, Phytochromobilin, Phytochrome, Ruthenium, 6-4 photoadducts, Photochemistry
Keywords [sv]
Kvantkemi
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-8469ISBN: 978-91-554-7096-8 (print)OAI: oai:DiVA.org:uu-8469DiVA, id: diva2:171449
Public defence
2008-03-19, Häggsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2011-03-14Bibliographically approved
List of papers
1. Photochemistry of Bromofluorobenzenes
Open this publication in new window or tab >>Photochemistry of Bromofluorobenzenes
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2006 (English)In: Journal of Physical Chemistry A, Vol. 110, p. 7045-Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-96758 (URN)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
2. A singlet mechanism for photodissociation of bromofluorobenzenes
Open this publication in new window or tab >>A singlet mechanism for photodissociation of bromofluorobenzenes
2007 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 436, no 1-3, p. 57-62Article in journal (Refereed) Published
Abstract [en]

The C-Br photo-fragmentation of bromo-3,5-difluorobenzene (Br-3,5-diFBz) has been investigated using ab initio methods. A reaction coordinate combining a carbon-bromine bond stretch and a bromine out-of-plane bending on the S1 surface has been found with an activation energy of 2.96 kcal/mol, compatible with the observed picosecond time scale.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96759 (URN)10.1016/j.cplett.2007.01.035 (DOI)000244946400011 ()
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
3. Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
Open this publication in new window or tab >>Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
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2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 3, p. 034307-Article in journal (Refereed) Published
Abstract [en]

The UV photodissociation of bromo-3-fluorobenzene under collisionless conditions has been studied as a function of the excitation wavelength between 255 and 265 nm. The experiments were performed using ultrafast pump-probe laser spectroscopy. To aid in the interpretation of the results, it was necessary to extend the theoretical framework substantially compared to previous studies, to also include quantum dynamical simulations employing a two-dimensional nuclear Hamiltonian. The nonadiabatic potential energy surfaces (PES) were parameterized against high-level MS-CASTP2 quantum chemical calculations, using both the C–Br distance and the out-of-plane bending of the bromine as nuclear parameters. We show that the wavelength dependence of the photodissociation via the S01ππ*1πσ* channel, accessible with a ∼ 260 nm pulse, is captured in this model. We thereby present the first correlation between experiments and theory within the quantitative regime.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96760 (URN)10.1063/1.2819093 (DOI)000252471100017 ()
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
4. The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
Open this publication in new window or tab >>The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
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(English)In: Chemical Physics LettersArticle in journal (Refereed) Submitted
Identifiers
urn:nbn:se:uu:diva-96761 (URN)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
5. Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
Open this publication in new window or tab >>Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
2004 (English)In: Physical Chemistry Chemical Physics, Vol. 6, p. 5066-Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-96762 (URN)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
6. Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
Open this publication in new window or tab >>Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
2005 (English)In: Chemical Physics Letters, Vol. 416, p. 83-Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-96763 (URN)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
7. Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational StudyRelative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study
Open this publication in new window or tab >>Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational StudyRelative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study
2007 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 39, p. 11554-11565Article in journal (Refereed) Published
Abstract [en]

The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z→ E photoisomerization of its phytochromobilin chromophore. In recent years, the question whether the photoactivation involves a change in chromophore protonation state has been the subject of many experimental studies. Here, we have used quantum chemical methods to calculate relative ground and excited-state pKa values of the different pyrrole moieties of phytochromobilin in a protein-like environment. Assuming (based on experimental data) a Pr ZaZsZa chromophore and considering isomerizations at C15 and C5, it is found that moieties B and C are the strongest acids both in the ground state and in the bright first singlet excited state, which is rationalized in simple geometric and electronic terms. It is also shown that neither light absorption nor isomerization increases the acidity of phytochromobilin relative to the reference Pr state with all pyrrolenic nitrogens protonated. Hence, provided that the subset of chromophore geometries under investigation is biologically relevant, there appears to be no intrinsic driving force for a proton-transfer event. In a series of benchmark calculations, the performance of ab initio and time-dependent density functional theory methods for excited-state studies of phytochromobilin is evaluated in light of available experimental data.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96764 (URN)10.1021/jp0727953 (DOI)000249838600031 ()
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
8. Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
Open this publication in new window or tab >>Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
2008 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 18, p. 2528-2537Article in journal (Refereed) Published
Abstract [en]

Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z --> E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKa s of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr --> Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKa s relative to their Pr values are identified: (i) a thermal Z,anti --> Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96765 (URN)10.1039/b719190a (DOI)000255449200011 ()18446253 (PubMedID)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
9. A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
Open this publication in new window or tab >>A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
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2008 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 19, p. 4470-4476Article in journal (Refereed) Published
Abstract [en]

The potential energy surfaces of the first excited triplet state of some ruthenium polypyridyl complexes were investigated by means of density functional theory. Focus was placed on the interaction between the geometrical changes accompanying the photoactivity of these complexes when used as antenna complexes in artificial photosynthesis and dye-sensitized solar cells and the accompanying changes in electronic structure. The loss process (3)MLCT --> (3)MC can be understood by means of ligand-field splitting, traced down to the coordination of the central ruthenium atom.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-96766 (URN)10.1021/jp8000702 (DOI)000255649300011 ()18426189 (PubMedID)
Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
10. Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
Open this publication in new window or tab >>Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
2007 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed) Published
Abstract [en]

The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:uu:diva-92096 (URN)10.1021/jp0676383 (DOI)000245083600013 ()17388321 (PubMedID)
Available from: 2004-09-03 Created: 2004-09-03 Last updated: 2017-12-14Bibliographically approved

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