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Molecular dynamics effects on luminescence properties of oligothiophene derivatives: a molecular mechanics-response theory study based on the CHARMM force field and density functional theory
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
2011 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 39, 17532-17542 p.Article in journal (Refereed) Published
Abstract [en]

CHARMM force field parameter values for a class of oligothiophene derivatives have been derived with reference to density functional theory/B3LYP potential energy surfaces. The force field parametrization of these luminescent conjugated polyelectrolytes includes the electronic ground state as well as the strongly light absorbing first excited state. In conjunction with quantum chemical response theory calculations of transition state properties, a molecular dynamical model of the Stokes shift is obtained. The theoretical model is benchmarked against experimental data recorded at room temperature which refer to sodium salts of p-HTAA and p-FTAA with distilled water as a solvent. For p-HTAA the theoretically predicted Stokes shift of 112 nm is in good agreement with the experimental result of 124 nm, given the approximations about exciton localization that were introduced to obtain a force field for the excited state.

Place, publisher, year, edition, pages
Royal Society of Chemistry , 2011. Vol. 13, no 39, 17532-17542 p.
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:liu:diva-71564DOI: 10.1039/c1cp21252dISI: 000295377700012OAI: oai:DiVA.org:liu-71564DiVA: diva2:450511
Note
Funding Agencies|Swedish Research Council|621-2010-5014 |National Supercomputer Centre (NSC), Sweden||Swedish e-Science Research Center||Available from: 2011-10-21 Created: 2011-10-21 Last updated: 2017-12-08
In thesis
1. Luminescence properties of flexible conjugated dyes
Open this publication in new window or tab >>Luminescence properties of flexible conjugated dyes
2012 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease.

MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm.

In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2012. 50 p.
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1522
Keyword
force field, molecular dynamics, linear absorption, QM/MM, absorption spectrum, emission spectrum, water solvation, stokes shift
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:liu:diva-75191 (URN)LIU-TEK-LIC-2012:7 (Local ID)978-91-7519-948-1 (ISBN)LIU-TEK-LIC-2012:7 (Archive number)LIU-TEK-LIC-2012:7 (OAI)
Presentation
2012-03-28, Planck, Fysikhuset, Campus Valla, Linköpings universitet, Linköping, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council, 621-2010-5014
Available from: 2012-03-06 Created: 2012-02-20 Last updated: 2012-03-06Bibliographically approved
2. Light interactions in flexible conjugated dyes
Open this publication in new window or tab >>Light interactions in flexible conjugated dyes
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations.

The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. For absorption and fluorescence spectroscopies a form of conformational averaging is used, where the final spectrum is obtained as an average of spectra calculated for geometries extracted from ground and excited state MD simulations. For infrared and Raman spectroscopies averaged spectra are calculated based on individual spectra, obtained for zero-temperature optimized molecular structures, weighted by conformational statistics from MD trajectories. Statistics for structural properties are also used in both cases to gain additional information about the systems, allowing more efficient utilization of computational resources. As it is essential that the molecular mechanics description of the system is highly accurate for methods of this nature to be effective, high quality force field parameters have been derived, describing the molecules of interest in either the MM3 or CHARMM force fields.

These methods have been employed in the study of three systems. The first is a platinum(II) actylide chromophore used in optical power limiting materials, for which a ultraviolet/visible absorption spectrum has been calculated. The second is a family of molecular probes called luminescent conjugated oligothiophenes, used to detect and characterize amyloid proteins, for which both absorption and fluorescence spectra have been calculated. Finally, infrared and Raman spectra have been calculated for a group of branched oligothiophenes used in organic solar cells.

In addition, solvation effects have been studied for conjugated poly\-eletrolytes in water, resulting in the development of two solvation models suitable for this class of molecules. The first uses a quantum meachanics/molecular mechanics (QM/MM) description, in which the solute mole\-cule is described using accurate quantum mechanical methods while the surrounding water molecules are described using point charges and polarizable point dipoles. The second discards the water entirely and removes the ionic groups of the solute. The QM/MM model provides highly accurate results while the cut-down model gives results of slightly lower quality but at a much reduced computational cost.

Finally, a study of protein-dye interactions has been performed, with the goal of explaining changes in the luminescence properties of the LCO chromophores when in the presence of amyloid proteins. Results were less than conclusive.

Place, publisher, year, edition, pages
Linköping, Sweden: Linköping University Electronic Press, 2014. 63 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1608
Keyword
force field, molecular dynamics, QM/MM, solvation effects, absorption spectroscopy, fluorescence spectrosocopy, infrared spectroscopy, Raman spectroscopy, stokes shift, conjugated polyelectrolytes
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-109011 (URN)10.3384/diss.diva-109011 (DOI)978-91-7519-282-6 (ISBN)
Public defence
2014-09-12, Planck, Fysikhuset, Campus Valla, Linköpings universitet, Linköping, 10:00 (English)
Opponent
Supervisors
Available from: 2014-08-28 Created: 2014-07-26 Last updated: 2014-08-28Bibliographically approved

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Sjöqvist, JonasLinares, MathieuLindgren, MikaelNorman, Patrick

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