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Theoretical studies of EPR parameters of spin-labels incomplex environments
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis encloses quantum chemical calculations performed in the framework of density functional response theory for evaluating electron paramagnetic resonance (EPR) spin Hamiltonian parameters of various spin-labels in different environments. These parameters are the well known electronic g-tensor and the nitrogen hyperfine coupling constants, which are extensively explored in this work for various systems. A special attention was devoted to the relationships that form between the structural and spectroscopic properties that can be accounted for as an environmental inuence. Such environmental effects were addressed either within a fully quantum mechanical formalism, involving simplified model structures that still capture the physical properties of the extended system, or by employing a quantum mechanics/molecular mechanics (QM/MM) approach. The latter implies that the nitroxide spin label is treated quantum mechanically, while the environment is treated in a classical discrete manner, with appropriate force fields employed for its description. The state-of- the art techniques employed in this work allow for an optimum accounting of the environmental effects that play an important role for the behaviour of EPR properties of nitroxides spin labels. One achievement presented in this thesis includes the first theoretical con_rmation of an empirical assumption that is usually made for inter-molecular distance measurement experiments in deoxyribonucleic acid (DNA), involving pulsed electron-electron double resonance (PELDOR) and site-directed spin labeling (SDSL) techniques. This refers to the fact that the EPR parameters of the spin-labels are not affected by their interaction with the nucleobases from which DNA is constituted. Another important result presented deals with the inuence of a supramolecular complex on the EPR properties of an encapsulated nitroxide spin-label. The enclusion complex affects the hydrogen bonding topology that forms around the R2NO moiety of the nitroxide. This, on the other hand has a major impact on its structure which further on governs the magnitude of the spectroscopic properties. The projects and results presented in this thesis offer an example of successful usage of modern quantum chemistry techniques for the investigation of EPR parameters of spin-labels in complex systems.

 

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. , iv, 57 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2013:6
Keyword [en]
EPR, DFT, spin-labels, QM/MM, Breit-Pauli Hamiltonian
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-119515ISBN: 978-91-7501-681-8 (print)OAI: oai:DiVA.org:kth-119515DiVA: diva2:611241
Public defence
2013-04-05, FB 54, AlbaNova University Center, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20130318

Available from: 2013-03-18 Created: 2013-03-15 Last updated: 2013-03-18Bibliographically approved
List of papers
1. π –stacking effects on the EPR parameters of a prototypical DNA spin label
Open this publication in new window or tab >>π –stacking effects on the EPR parameters of a prototypical DNA spin label
2013 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, 10466-10471 p.Article in journal (Refereed) Published
Abstract [en]

The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

Place, publisher, year, edition, pages
RSC Publishing, 2013
Keyword
EPR, spin labels, DNA
National Category
Theoretical Chemistry
Research subject
SRA - E-Science (SeRC)
Identifiers
urn:nbn:se:kth:diva-119514 (URN)10.1039/C3CP51129D (DOI)000319943200050 ()2-s2.0-84881088674 (Scopus ID)
Funder
EU, FP7, Seventh Framework Programme, RI-283493Swedish e‐Science Research Center
Note

This work was granted access to the HPC resources of MonteRosa/Swiss National High-Performance Centre made avail-able within the Distributed European Computing Initiative bythe PRACE-2IP, receiving funding from the European Com-munity Seventh Framework Programme (FP7/2007-2013) un-der grant agreement no. RI-283493.

QC 20130422

Available from: 2013-05-07 Created: 2013-03-15 Last updated: 2017-12-06Bibliographically approved
2. EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology
Open this publication in new window or tab >>EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology
Show others...
2013 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 7, 2427-2434 p.Article in journal (Refereed) Published
Abstract [en]

Encapsulation of spin-labels into "host'' compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound'' complexes.

Keyword
Accurate Prediction, Condensed Phases, Exact Exchange, G-Tensors, Density, Nitroxides, Radicals, Inclusion, Probes, Approximation
National Category
Physical Sciences Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-118627 (URN)10.1039/c2cp43951d (DOI)000313891400022 ()2-s2.0-84873020192 (Scopus ID)
Funder
EU, FP7, Seventh Framework Programme, RI-283493Swedish e‐Science Research Center
Note

QC 20130221

Available from: 2013-02-21 Created: 2013-02-21 Last updated: 2017-12-06Bibliographically approved
3. Encapsulation Influence on EPR Parameters of Spin-Labels: 2,2,6,6-Tetramethyl-4-methoxypiperidine-1-oxyl in Cucurbit[8]uril
Open this publication in new window or tab >>Encapsulation Influence on EPR Parameters of Spin-Labels: 2,2,6,6-Tetramethyl-4-methoxypiperidine-1-oxyl in Cucurbit[8]uril
Show others...
2012 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 1, 257-263 p.Article in journal (Refereed) Published
Abstract [en]

Encapsulation of a nitroxide spin label into a host cavity can prolong the lifetime of the spin label in biological tissues and other environments. Although such paramagnetic supramolecular complexes have been extensively studied experimentally, there is yet little understanding of the role of the encapsulation on the magnetic properties of the spin labels and their performance at the atomistic level. In this work, we approach this problem by modeling encapsulation induced changes of the magnetic properties of spin labels for a prototypical paramagnetic guest host complex, 2,2,6,6-tetramethyl-4-methoxypiperidine-1-oxyl, enclosed in the hydrophobic cavity of cucurbit[8]uril, using state-of-the-art hybrid quantum mechanics/molecular mechanics methodology. The results allow a decomposition of the encapsulation shift of the electronic g-tensor and the nitrogen isotropic hyperfine coupling constant of nitroxide radical into a set of distinct contributions associated with the host cavity confinement and with changes of the local solvent environment of the spin label upon encapsulation. It is found that the hydrophobic cavity of cucurbit[8]uril only weakly influences the electronic g-tensor of the 2,2,6,6-tetramethyl-4-methoxypiperidine-1-oxyl but induces a significant encapsulation shift of the nitrogen hyperfine coupling constant. The latter is caused by the change of topology of the hydrogen bonding network and the nature of the hydrogen bonds around the spin label induced by the hydrophobic cavity of the inclusion host. This indirect effect is found to be more important than the direct influence of the cavity exerted on the radical. The ramification of this finding for the use of approximate methods for computing electron paramagnetic resonance spectra of spin labels and for designing optimal spin labels based on guest-host templates is discussed.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-75528 (URN)10.1021/ct200816z (DOI)000298908500027 ()2-s2.0-84855660084 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20120206

Available from: 2012-02-06 Created: 2012-02-06 Last updated: 2017-12-08Bibliographically approved
4. Density Functional Restricted-Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution
Open this publication in new window or tab >>Density Functional Restricted-Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution
Show others...
2011 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 10, 3261-3271 p.Article in journal (Refereed) Published
Abstract [en]

A density functional restricted unrestricted approach, capable of evaluating hyperfine coupling constants with the inclusion of spin polarization effects in a spin-restricted Kohn-Sham method, has been extended to incorporate environmental effects. This is accomplished by means of a hybrid quantum mechanics/molecular mechanics formalism which allows for a granular representation of the polarization and electrostatic interactions with the classically described medium. By this technique, it is possible to trace the physical origin of hyperfine coupling constants in terms of spin polarization and spin density contributions and disentangle the dependence of these contributions on molecular geometry and solvent environment, something that increases the prospects for optimal design of spin labels for particular applications. A demonstration is given for the nitrogen isotropic hyperfine coupling constant in di-tert-butyl nitroxide solvated in water. The results indicate that the direct spin density contribution is about 5 times smaller than the spin polarization contribution to the nitrogen isotropic hyperfine coupling constant and that the latter contribution is solely responsible for the solvent shift of the constant. The developed approach is found capable of achieving satisfactory accuracy in prediction of the hyperfine coupling constants of solvated di-tert-butyl nitroxide and other similar nitroxides without the inclusion of solvent molecules in the quantum region provided polarizable force fields are used for the description of these molecules.

Keyword
NITROXIDE SPIN-LABEL, ELECTRONIC G-TENSORS, INTEGRATED COMPUTATIONAL APPROACH, LARGE FREE-RADICALS, CAR-PARRINELLO, MAGNETIC-PROPERTIES, SOLVATED MOLECULES, DYNAMICS SIMULATIONS, SOLVENT POLARITY, AQUEOUS-SOLUTION
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-47984 (URN)10.1021/ct2003572 (DOI)000295655000023 ()2-s2.0-80053960691 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note

QC 20111116

Available from: 2011-11-16 Created: 2011-11-15 Last updated: 2017-12-08Bibliographically approved

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