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Quantum Chemical Studies of Protein-Bound Chromophores, UV-Light Induced DNA Damages, and Lignin Formation
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical Chemistry, Quantum Chemistry.
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin.

The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.

The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed.

DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.

Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2004. , p. 81
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 1010
Keyword [en]
Quantum chemistry, quantum chemistry, calculations, density functional theory, excited states, photochemistry, chromophores, absorption spectra, bathochromic shift, isomerization, UV radiation, DNA damages, cycloaddition reactions, photoenzymic repair, electron transfer, lignin, polymerization, phenoxy radicals, dilignols
Keyword [sv]
Kvantkemi
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-4531ISBN: 91-554-6030-5 (print)OAI: oai:DiVA.org:uu-4531DiVA, id: diva2:165056
Public defence
2004-09-30, Siegbahnsalen, Ångströmlaboratoriet, Uppsala, 13:15
Opponent
Supervisors
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
List of papers
1. On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study
Open this publication in new window or tab >>On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study
2003 In: Chemical Physics Letters, ISSN 0009-2614, Vol. 375, no 1-2, p. 30-38Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92091 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
2. Conformational dependence of the electronic absorption by astaxanthin and its implications for the bathochromic shift in crustacyanin
Open this publication in new window or tab >>Conformational dependence of the electronic absorption by astaxanthin and its implications for the bathochromic shift in crustacyanin
2004 In: Physical Chemistry Chemical Physics, ISSN 1463-9076, Vol. 6, p. 4190-4198Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92092 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
3. Phytochromobilin C15-Z,syn to C15-E,anti isomerization - concerted or stepwise?
Open this publication in new window or tab >>Phytochromobilin C15-Z,syn to C15-E,anti isomerization - concerted or stepwise?
Article in journal (Refereed) Submitted
Identifiers
urn:nbn:se:uu:diva-92093 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
4. Thermodynamics of the photoenzymic repair mechanism studied by density functional theory
Open this publication in new window or tab >>Thermodynamics of the photoenzymic repair mechanism studied by density functional theory
2000 In: Journal of the American Chemical Society, ISSN 0002-7863, Vol. 122, no 41, p. 10126-10132Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92094 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
5. On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive?
Open this publication in new window or tab >>On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive?
2003 In: Photochemistry and Photobiology, ISSN 0031-8655, Vol. 78, no 2, p. 159-167Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92095 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
6. 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
7. A density functional theory study of coniferyl alcohol intermonomeric linkages in lignin - three-dimensional structures, stabilities and the thermodynamic control hypothesis
Open this publication in new window or tab >>A density functional theory study of coniferyl alcohol intermonomeric linkages in lignin - three-dimensional structures, stabilities and the thermodynamic control hypothesis
2003 In: Holzforschung, ISSN 0018-3830, Vol. 57, no 2, p. 150-164Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92097 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
8. Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals
Open this publication in new window or tab >>Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals
2003 In: Holzforschung, ISSN 0018-3830, Vol. 57, no 1, p. 59-61Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92098 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved
9. Formation of β-O-4 lignin models - a theoretical study
Open this publication in new window or tab >>Formation of β-O-4 lignin models - a theoretical study
2003 In: Holzforschung, ISSN 0018-3830, Vol. 57, no 5, p. 466-478Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-92099 (URN)
Available from: 2004-09-03 Created: 2004-09-03Bibliographically approved

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