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Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts
Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
2008 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Uppsala: Acta Universitatis Upsaliensis , 2008. , s. 61
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 394
Nyckelord [en]
Quantum chemistry, Quantum Chemistry, Halogenated Arenes, Phytochromobilin, Phytochrome, Ruthenium, 6-4 photoadducts, Photochemistry
Nyckelord [sv]
Kvantkemi
Nationell ämneskategori
Teoretisk kemi
Identifikatorer
URN: urn:nbn:se:uu:diva-8469ISBN: 978-91-554-7096-8 (tryckt)OAI: oai:DiVA.org:uu-8469DiVA, id: diva2:171449
Disputation
2008-03-19, Häggsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 10:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2011-03-14Bibliografiskt granskad
Delarbeten
1. Photochemistry of Bromofluorobenzenes
Öppna denna publikation i ny flik eller fönster >>Photochemistry of Bromofluorobenzenes
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2006 (Engelska)Ingår i: Journal of Physical Chemistry A, Vol. 110, s. 7045-Artikel i tidskrift (Refereegranskat) Published
Identifikatorer
urn:nbn:se:uu:diva-96758 (URN)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
2. A singlet mechanism for photodissociation of bromofluorobenzenes
Öppna denna publikation i ny flik eller fönster >>A singlet mechanism for photodissociation of bromofluorobenzenes
2007 (Engelska)Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 436, nr 1-3, s. 57-62Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-96759 (URN)10.1016/j.cplett.2007.01.035 (DOI)000244946400011 ()
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
3. Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
Öppna denna publikation i ny flik eller fönster >>Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
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2008 (Engelska)Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, nr 3, s. 034307-Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-96760 (URN)10.1063/1.2819093 (DOI)000252471100017 ()
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
4. The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
Öppna denna publikation i ny flik eller fönster >>The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
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(Engelska)Ingår i: Chemical Physics LettersArtikel i tidskrift (Refereegranskat) Submitted
Identifikatorer
urn:nbn:se:uu:diva-96761 (URN)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
5. Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
Öppna denna publikation i ny flik eller fönster >>Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
2004 (Engelska)Ingår i: Physical Chemistry Chemical Physics, Vol. 6, s. 5066-Artikel i tidskrift (Refereegranskat) Published
Identifikatorer
urn:nbn:se:uu:diva-96762 (URN)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
6. Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
Öppna denna publikation i ny flik eller fönster >>Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
2005 (Engelska)Ingår i: Chemical Physics Letters, Vol. 416, s. 83-Artikel i tidskrift (Refereegranskat) Published
Identifikatorer
urn:nbn:se:uu:diva-96763 (URN)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>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 (Engelska)Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 39, s. 11554-11565Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-96764 (URN)10.1021/jp0727953 (DOI)000249838600031 ()
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
8. Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
Öppna denna publikation i ny flik eller fönster >>Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
2008 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, nr 18, s. 2528-2537Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-96765 (URN)10.1039/b719190a (DOI)000255449200011 ()18446253 (PubMedID)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
9. A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
Öppna denna publikation i ny flik eller fönster >>A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
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2008 (Engelska)Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 19, s. 4470-4476Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-96766 (URN)10.1021/jp8000702 (DOI)000255649300011 ()18426189 (PubMedID)
Tillgänglig från: 2008-02-26 Skapad: 2008-02-26 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
10. Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
Öppna denna publikation i ny flik eller fönster >>Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
2007 (Engelska)Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 12, s. 2351-2361Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Kemi
Identifikatorer
urn:nbn:se:uu:diva-92096 (URN)10.1021/jp0676383 (DOI)000245083600013 ()17388321 (PubMedID)
Tillgänglig från: 2004-09-03 Skapad: 2004-09-03 Senast uppdaterad: 2017-12-14Bibliografiskt granskad

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