Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • 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
Theoretical Studies on Magnetic and Photochemical Properties of Organic Molecules
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The present thesis is concerned with the theoretical studies on magnetic and photochemical properties of organic molecules. The ab initio and first principles theories were employed to investigate the vibrational effects on the isotropic hyperfine coupling constant (HFCC) known as the critical parameter in electron paramagnetic resonance spectrum, the theoretical simulations of the vibronically resolved molecular spectra, the photo-induced reaction mechanism of α-santonin and the spin-forbidden reaction of triplet-state dioxygen with cofactor-free enzyme. The theoretical predictions shed light on the interpretation of experimental observations, the understanding of reaction mechanism, and importantly the guideline and perspective in respect of the popularized applications.

We focused on the vibrational corrections to the isotropic HFCCs of hydrogen and carbon atoms in organic radicals. The calculations indicate that the vibrational contributions induce or enhance the effect of spin polarization. A set of rules were stated to guide experimentalist and theoretician in identification of the contributions from the molecular vibrations to HFCCs. And the coupling of spin density with vibrational modes in the backbone is significant and provides the insight into the spin density transfer mechanism in organic π radicals.

The spectral characters of the intermediates in solid-state photoarrangement of α-santonin were investigated in order to well understand the underlying experimental spectra. The molecular spectra simulated with Franck-Condon principle show that the positions of the absorption and emission bands of photosantonic acid well match with the experimental observations and the absorption spectrum has a vibrationally resolved character.

α-Santonin is the first found organic molecule that has the photoreaction activities. The photorearrangement mechanism is theoretically predicted that the low-lying excited state 1(nπ*) undergoing an intersystem crossing process decays to 3(ππ*) state in the Franck-Condon region. A pathway which is favored in the solid-state reaction requires less space and dynamic advantage on the excited-state potential energy surface (PES). And the other pathway is predominant in the weak polar solvent due to the thermodynamical and dynamical preferences. Lumisantonin is a critical intermediate derived from α-santonin photoreaction. The 3(ππ*) state plays a key role in lumisantonin photolysis. The photolytic pathway is in advantage of dynamics and thermodynamics on the triplet-state PES. In contrast, the other reaction pathway is facile for pyrolysis ascribed to a stable intermediate formed on the ground-state PES.

 The mechanism of the oxidation reaction involving cofactor-free enzyme and triplet-state dioxygen were studied. The theoretical calculations show that the charge-transfer mechanism is not a sole way to make a spin-forbidden oxidation allowed. It is more likely to take place in the reactant consisting of a non-conjugated substrate. The other mechanism involving the surface hopping between the triplet- and singlet-state PESs via a minimum energy crossing point (MECP) without a significant charge migration. The electronic state of MECP exhibits a mixed characteristic of the singlet and triplet states. The enhanced conjugation of the substrate slows down the spin-flip rate, and this step can in fact control the rate of the reaction that a dioxygen attaches to a substrate.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2011. , xvi, 62 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2012:2
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-52818ISBN: 978-91-7501-227-8 (print)OAI: oai:DiVA.org:kth-52818DiVA: diva2:467777
Public defence
2012-01-18, F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20111220Available from: 2011-12-20 Created: 2011-12-19 Last updated: 2012-01-20Bibliographically approved
List of papers
1. Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules
Open this publication in new window or tab >>Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules
Show others...
2011 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 2, 696-707 p.Article in journal (Refereed) Published
Abstract [en]

The present work addresses isotropic hyperfine coupling constants in polyatomic systems with a particular emphasis on a largely neglected, but a posteriori significant, effect, namely zero-point vibrational corrections. Using the density functional restricted-unrestricted approach, the zero-point vibrational corrections are evaluated for the allyl radical and four of its derivatives. In addition for establishing the numerical size of the zero-point vibrational corrections to the isotropic hyperfine coupling constants, we present simple guidelines useful for identifying hydrogens for which such corrections are significant. Based on our findings, we critically re-examine the computational procedures used for the determination of hyperfine coupling constants in general as well as the practice of using experimental hyperfine coupling constants as reference data when benchmarking and optimizing exchange-correlation functionals and basis sets for such calculations.

Place, publisher, year, edition, pages
RSC Publishing, 2011
National Category
Physical Chemistry Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-25886 (URN)10.1039/c0cp01443e (DOI)000285390400041 ()21063618 (PubMedID)2-s2.0-79953248258 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note
QC 20101103. Updated from manuscript to article in journal. 20111220 The published version of this article is deposited in DiVA by permission of the publisher. The pdf may however by no means be further made available or distributed.Available from: 2010-11-03 Created: 2010-11-03 Last updated: 2017-12-12Bibliographically approved
2. Vibrationally induced carbon hyperfine coupling constants: a reinterpretation of the McConnell relation
Open this publication in new window or tab >>Vibrationally induced carbon hyperfine coupling constants: a reinterpretation of the McConnell relation
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-52821 (URN)
Note
QS 2011Available from: 2011-12-19 Created: 2011-12-19 Last updated: 2011-12-20Bibliographically approved
3. Spectral character of intermediate state in solid-state photoarrangement of alpha-santonin
Open this publication in new window or tab >>Spectral character of intermediate state in solid-state photoarrangement of alpha-santonin
Show others...
2012 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 405, 40-45 p.Article in journal (Refereed) Published
Abstract [en]

The vibronically resolved spectra of an intermediate and a product involved in the photoreaction of alpha-santonin have been explored by the density functional theory and the post-SCF methodologies, and a detailed comparison of theory with experiment was conducted to obtain reliable assignments to the observed spectra. The predicted emission energies of photosantonic acid and a topochemical product are found to match with the experimental values reasonably. The further calculations manifest that the absorption spectrum of photosantonic acid exhibits vibrationally resolved features, while the absorption band of topochemical product without vibrational resolution is opposite to the experimental observation. These new computational findings lead to a revised assignment to the observed bands and provide a basis for experimentalists to draw a convinced reaction mechanism for the alpha-santonin photorearrangement.

Keyword
Vibronically resolved spectra, Simulation, alpha-Santonin, Spectral assignment
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-52822 (URN)10.1016/j.chemphys.2012.06.004 (DOI)000308720500007 ()2-s2.0-84866059119 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20121008. Updated from manuscript to article in journal.

Available from: 2011-12-19 Created: 2011-12-19 Last updated: 2017-12-08Bibliographically approved
4. Theoretical studies on the mechanism of α-santonin photo-induced rearrangement
Open this publication in new window or tab >>Theoretical studies on the mechanism of α-santonin photo-induced rearrangement
Show others...
2012 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 13, no 1, 353-362 p.Article in journal (Refereed) Published
Abstract [en]

α-Santonin is the first organic compound observed to feature a photoinduced rearrangement and is now known to undergo a series of photochemical processes under UV irradiation. On the basis of the considerable interest of this system as a prototype, and of the yet limited insights reached for the basic photo mechanisms, we calculate the high-level electronic structures and explore the potential energy surfaces (PES) of α-santonin in the ground and lowest-lying excited states, their couplings, and the possible photoinduced isomerization pathways. The calculations identify the low-lying singlet excited state 1(nπ*) accessible under light irradiation, which decays to the low-energy 3(ππ*) state through an intersystem crossing in the Franck–Condon region to initiate the photoinduced rearrangement. The initial reaction from the C3C5 bond coupling, which takes place on the 3(ππ*) state potential energy surface, leads to a three-membered alkyl-ring compound intermediate state INT. The following photochemical reactions have the possibility to arise from two distinct CC bond cleavages, C4C5 and C3C4, denoted as path A and path B. Path A is favored both dynamically on the excited-state PES and thermodynamically on the ground-state PES in vacuo. Experiments show that it also becomes the dominant photoinduced rearrangement process in the crystal, which can be explained by considering the requirement for less space and the stacking effect under the confined environment. Path B is dynamical advantaged both on the ground- and excited-state PESs in a weak polar solvent, such as dioxane. Once the biradical intermediate B-INT is accessible on the ground-state PES, the formation of the product B-P is almost barrier free.

Place, publisher, year, edition, pages
Germany: John Wiley & Sons, 2012
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-52823 (URN)10.1002/cphc.201100451 (DOI)000298913500047 ()22120926 (PubMedID)2-s2.0-84862958847 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20120227

Available from: 2011-12-19 Created: 2011-12-19 Last updated: 2017-12-08Bibliographically approved
5. Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies
Open this publication in new window or tab >>Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies
Show others...
2011 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 26, 7815-7822 p.Article in journal (Refereed) Published
Abstract [en]

The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the (n pi*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the (3)(pi pi*) state through intersystem crossing in the region of minimum surface crossings with a notable spin-orbital coupling constant. The 3(pi pi*) state, derived from the promotion of an electron from the pi-type orbital mixed with the sigma orbital localized on the C-C bond in the three-membered alkyl ring to the pi* orbital of conjugation carbon atoms, plays a critical role in C-C bond cleavage. Based on the different C-C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1-C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5-C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-37160 (URN)10.1021/jp203369b (DOI)000292281300047 ()2-s2.0-79959795779 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note
QC 20110803Available from: 2011-08-03 Created: 2011-08-02 Last updated: 2017-12-08Bibliographically approved
6. Theoretical studies on reaction of cofactor-free enzyme with triplet oxygen molecule
Open this publication in new window or tab >>Theoretical studies on reaction of cofactor-free enzyme with triplet oxygen molecule
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-52825 (URN)
Note
QS 2011Available from: 2011-12-19 Created: 2011-12-19 Last updated: 2011-12-20Bibliographically approved

Open Access in DiVA

fulltext(1707 kB)742 downloads
File information
File name FULLTEXT02.pdfFile size 1707 kBChecksum SHA-512
e8bb097fdfd8da1b005cf0d833a9d4344c63b11c6a0d854560621c896b704cc4a485d3d8a802f2c72f4b86a857997aecc59a8391df1724f4d8bbc2ce3e0e247c
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Chen, Xing
By organisation
Theoretical Chemistry and Biology
Theoretical Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 742 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

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 273 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • 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