liu.seSearch for publications in DiVA
Change search
ReferencesLink to record
Permanent link

Direct link
QM/MM-MD Simulations of Conjugated Polyelectrolytes: A Study of Luminescent Conjugated Oligothiophenes for Use as Biophysical Probes
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.
University of Copenhagen, Denmark .
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
2014 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 19, 3419-3428 p.Article in journal (Refereed) Published
Abstract [en]

A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (in) ii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

Place, publisher, year, edition, pages
American Chemical Society , 2014. Vol. 118, no 19, 3419-3428 p.
National Category
Engineering and Technology
URN: urn:nbn:se:liu:diva-107448DOI: 10.1021/jp5009835ISI: 000336199500004OAI: diva2:724325
Available from: 2014-06-12 Created: 2014-06-12 Last updated: 2014-08-28
In thesis
1. 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.
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1608
force field, molecular dynamics, QM/MM, solvation effects, absorption spectroscopy, fluorescence spectrosocopy, infrared spectroscopy, Raman spectroscopy, stokes shift, conjugated polyelectrolytes
National Category
Theoretical Chemistry
urn:nbn:se:liu:diva-109011 (URN)10.3384/diss.diva-109011 (DOI)978-91-7519-282-6 (print) (ISBN)
Public defence
2014-09-12, Planck, Fysikhuset, Campus Valla, Linköpings universitet, Linköping, 10:00 (English)
Available from: 2014-08-28 Created: 2014-07-26 Last updated: 2014-08-28Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Sjöqvist, JonasLinares, MathieuNorman, Patrick
By organisation
Computational PhysicsThe Institute of Technology
In the same journal
Journal of Physical Chemistry A
Engineering and Technology

Search outside of DiVA

GoogleGoogle Scholar
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

Altmetric score

Total: 242 hits
ReferencesLink to record
Permanent link

Direct link