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Light interactions in flexible conjugated dyes
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
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 [en]
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: urn:nbn:se:liu:diva-109011DOI: 10.3384/diss.diva-109011ISBN: 978-91-7519-282-6 (print)OAI: oai:DiVA.org:liu-109011DiVA: diva2:737026
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
List of papers
1. Platinum(II) and Phosphorus MM3 Force Field Parametrization for Chromophore Absorption Spectra at Room Temperature
Open this publication in new window or tab >>Platinum(II) and Phosphorus MM3 Force Field Parametrization for Chromophore Absorption Spectra at Room Temperature
2010 (English)In: JOURNAL OF PHYSICAL CHEMISTRY A, ISSN 1089-5639, Vol. 114, no 14, 4981-4987 p.Article in journal (Refereed) Published
Abstract [en]

Platinum(II) and phosphine MM3 force field parameters are derived from fits to the ground state potential energy surface at the level of Kohn-Sham density functional theory with employment of the B3LYP exchange-correlation functional. The parametrization includes bond stretch, angle bend, and torsional parameters for a planar platinum(II) center with phosphine and ethynyl ligands. The force field is used to study the dynamics of a fifth-generation dendrimer-coated platinum(II)organic compound in tetrahydrofurane solution at room temperature, and, based on a selection of conformations from the molecular dynamics simulation, the averaged linear absorption spectrum is determined with use of the CAM-B3LYP functional. The main absorption peak in the theoretical absorption spectrum is found at a transition wavelength of 325 nm with a full-width at half-maximum of 26 am clue to conformational broadening.

Place, publisher, year, edition, pages
American Chemical Society, 2010
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-55051 (URN)10.1021/jp911046u (DOI)000276341300039 ()
Available from: 2010-04-28 Created: 2010-04-28 Last updated: 2014-08-28
2. 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
Open this publication in new window or tab >>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
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
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-71564 (URN)10.1039/c1cp21252d (DOI)000295377700012 ()
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
3. QM/MM-MD Simulations of Conjugated Polyelectrolytes: A Study of Luminescent Conjugated Oligothiophenes for Use as Biophysical Probes
Open this publication in new window or tab >>QM/MM-MD Simulations of Conjugated Polyelectrolytes: A Study of Luminescent Conjugated Oligothiophenes for Use as Biophysical Probes
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
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-107448 (URN)10.1021/jp5009835 (DOI)000336199500004 ()
Available from: 2014-06-12 Created: 2014-06-12 Last updated: 2017-12-05
4. Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes
Open this publication in new window or tab >>Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes
Show others...
2014 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 42, 9820-9827 p.Article in journal (Refereed) Published
Abstract [en]

Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2014
Keyword
UV/vis absorption spectra, density functional theory, QM/MM, molecular dynamics
National Category
Theoretical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:liu:diva-109095 (URN)10.1021/jp506797j (DOI)000343741100004 ()
Note

At the time for thesis presentation publication was in status: Manuscript

Funding agencies: We acknowledge financial support from the Swedish Research Council (Grant No. 621-2010-5014) as well as a grant for computing time at the National Supercomputer Centre (NSC), Sweden. M.L. thanks the Swedish e-Science Research Center (SeRC) for financial support. Our work is supported by the Swedish Foundation for Strategic Research (K.P.R.N., R.A.S.). K.P.R.N. is financed by an ERC Starting Independent Researcher Grant (Project: MUMID) from the European Research Council. R.A.S. is enrolled in the doctoral program Forum Scientum. M.L. is grateful to Linkoping University for a guest professorship. Parts of this work were supported by the LUPAS project supported by the EU FP7 program.

Available from: 2014-08-11 Created: 2014-08-07 Last updated: 2017-12-05Bibliographically approved
5. A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes
Open this publication in new window or tab >>A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes
Show others...
2014 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 45, 24841-24852 p.Article in journal (Refereed) Published
Abstract [en]

Infrared (IR) absorption and vibrational Raman spectra of a family of branched oligothiophenes have been determined experimentally as well as theoretically. The molecular spectra have been compared to those of the linear analogues, with identification made of spectral features due to structural properties that are valued in organic solar cell applications. The theoretical spectra have been obtained through a newly developed method in which individual conformer spectra, calculated at the time-dependent DFT level in this work, are weighted by statistics extracted from classical molecular dynamics trajectories. The agreement with experiment for the resulting averaged spectra is at least as good as, and often better than, what is observed for Boltzmann-weighted spectra. As the weights are available before the costly step of spectrum calculation, the method has the additional advantage of enabling efficient approximations. For simulating the molecular dynamics of the studied α,β-linked thiophenes and 2-methylthiophenes, high quality parameters have been derived for the CHARMM force field. Furthermore, the temperature dependence of the IR and Raman spectra have been investigated, both experimentally and theoretically.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2014
Keyword
organic solar cells, time-dependent density functional theory, CHARMM, IR spectroscopy, Raman spectroscopy
National Category
Theoretical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:liu:diva-109096 (URN)10.1039/c4cp03365e (DOI)000344464800023 ()25319050 (PubMedID)
Available from: 2014-08-11 Created: 2014-08-07 Last updated: 2017-12-05Bibliographically approved

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