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Osella, S. & Knippenberg, S. (2019). Environmental effects on the charge transfer properties of Graphene quantum dot based interfaces. International Journal of Quantum Chemistry, 119(10), Article ID e25882.
Open this publication in new window or tab >>Environmental effects on the charge transfer properties of Graphene quantum dot based interfaces
2019 (English)In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 119, no 10, article id e25882Article in journal (Refereed) Published
Abstract [en]

Graphene quantum dots (GQD) are interesting materials due to the confined sizes which allow to exploit their optoelectronic properties, especially when they interface with organic molecules through physisorption. In particular, when interfaces are formed, charge transfer (CT) processes can occur, in which electrons can flow either from the GQD to the absorbed molecule, or vice versa. These processes are accessible by modeling and computational analysis. Yet, the presence of different environments can strongly affect the outcome of such simulations which, in turn, can lead to wrong results if not taken into account. In this multiscale study, we assess the sensibility of the computational approach and compute the CT, calculated at interfaces composed by GQD and amino-acene derivatives. The hole transfer is strongly affected by dynamic disorder and the nature of the environment, and imposes stringent descriptions of the modeled systems to ensure enhanced accuracy of the transfer of charges.

Place, publisher, year, edition, pages
Wiley, 2019
Keywords
amino-acenes, charge transfer, dynamic disorder, graphene quantum dots, multiscale modeling
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-249845 (URN)10.1002/qua.25882 (DOI)000462571800002 ()2-s2.0-85058979292 (Scopus ID)
Note

QC 20190424

Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-04-24Bibliographically approved
$$$Paloncyova, M., Ameloot, M. & Knippenberg, S. (2019). Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments. Physical Chemistry, Chemical Physics - PCCP, 21(14), 7594-7604
Open this publication in new window or tab >>Orientational distribution of DPH in lipid membranes: a comparison of molecular dynamics calculations and experimental time-resolved anisotropy experiments
2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 14, p. 7594-7604Article in journal (Refereed) Published
Abstract [en]

Characterization of the membrane phases is a crucial task in cell biology. Cells differ in composition of the lipids and consequently in adopted phases. The phases can be discriminated based upon lipid ordering and molecular diffusion and their identification could be used for characterization of cell membranes. Here we used molecular dynamics (MD) simulations to study the behavior of the fluorescent reporter molecule diphenylhexatriene (DPH) in different lipid phases - liquid disordered (L-d), liquid ordered (L-o), and solid ordered (S-o) composed of phosphatidylcholines (L-d and S-o) or a sphingomyelin/cholesterol (SM/Chol) mixture (L-o). To the best of our knowledge, this is the first simulation of DPH in L-o SM/Chol and S-o DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the L-o phase we observed a significant fraction of DPH positioned in between membrane leaflets, which agrees with experimental findings, but which has not been observed in previous MD simulations of DPH in phosphatidylcholine membranes. Further, we calculated rotational autocorrelation functions (ROTACF) from our MD simulations in order to model the time-resolved fluorescence anisotropy decay. We observed that order parameters P-2 and P-4 are sufficient to fully describe the orientation distribution of DPH. We analyzed the ROTACFs by a so-called general model for the time-resolved fluorescence anisotropy [W. van der Meer et al., Biophys. J., 1984, 46, 515] and observed an overestimation of P-4. We suggest a rescaling of the recovered P-4 yielding an orientation distribution of DPH close to the one observed in our MD simulations.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-251488 (URN)10.1039/c8cp07754a (DOI)000464580600035 ()30900721 (PubMedID)2-s2.0-85063982254 (Scopus ID)
Note

QC 20190522

Available from: 2019-05-22 Created: 2019-05-22 Last updated: 2019-05-22Bibliographically approved
Osella, S., Di Meo, F., Natarajan Arul, M., Fabre, G., Ameloot, M., Trouillas, P. & Knippenberg, S. (2018). Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition. Journal of Chemical Theory and Computation, 14(10), 5350-5359
Open this publication in new window or tab >>Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 10, p. 5350-5359Article in journal (Refereed) Published
Abstract [en]

The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as one-photon absorption (OPA), two-photon absorption (TPA), and second harmonic generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (dioleoyl-sn-glycero-3-phosphocholine, room temperature) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of sphingomyelin and cholesterol. By means of extensive hybrid quantum mechanics molecular mechanics calculations and based upon the (non)linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as a versatile probe for phase recognition. In particular, the SHG data obtained by means of hyper-Rayleigh scattering and by electric field induced second harmonic generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar headgroup region of the 2:1 SM:Chol mixture in the liquid ordered phase.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-238130 (URN)10.1021/acs.jctc.8b00553 (DOI)000447238500031 ()30216061 (PubMedID)2-s2.0-85054346528 (Scopus ID)
Note

QC 20181113

Available from: 2018-11-13 Created: 2018-11-13 Last updated: 2018-11-13Bibliographically approved
Osella, S. & Knippenberg, S. (2017). Triggering On/Off States of Photoswitchable Probes in Biological Environments. Journal of the American Chemical Society, 139(12), 4418-4428
Open this publication in new window or tab >>Triggering On/Off States of Photoswitchable Probes in Biological Environments
2017 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 12, p. 4418-4428Article in journal (Refereed) Published
Abstract [en]

The use of hybrid systems for which the change in properties of one component triggers the change in properties of the other is of outmost importance when "on/off' states are needed. For such a reason, azobenzene compounds are one of the most used probes due to their high photoswitching efficiency. In this study, we consider a new derivative of azobenzene interacting with different lipid membrane phases as a versatile fluorescent probe for phase recognition. By means of a multiscale approach, we found that the cis and trans conformers have different positions and orientations in the different lipid membranes (DOPC for the liquid disordered phase and DPPC for the gel phase), and these have a profound effect on the optical properties of the system, for both one and two photon absorption. In fact, we found that the cis state is the "on" state when the probe is inserted into the DOPC membrane, while it is in the "off' state in the DPPC membrane. This behavior enhances the selectivity of this probe for phase recognition, since the different environments will generate different responses on the same conformer of the probe. The same effect is found for the fluorescence anisotropy analysis, for which the trans (cis) isomer in DOPC (DPPC) presents a fast decay time. Due to the "on/off' effect it is possible to screen the different membrane phases via fluorescence decay time analysis, making this new probe versatile for phase detection.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-205450 (URN)10.1021/jacs.6b13024 (DOI)000398247100038 ()28252300 (PubMedID)2-s2.0-85016257716 (Scopus ID)
Note

QC 20170523

Available from: 2017-05-23 Created: 2017-05-23 Last updated: 2017-06-30Bibliographically approved
Bacalum, M., Wang, L., Boodts, S., Yuan, P., Leen, V., Smisdom, N., . . . Ameloot, M. (2016). A Blue-Light-Emitting BODIPY Probe for Lipid Membranes. Langmuir, 32(14), 3495-3505
Open this publication in new window or tab >>A Blue-Light-Emitting BODIPY Probe for Lipid Membranes
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2016 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 32, no 14, p. 3495-3505Article in journal (Refereed) Published
Abstract [en]

Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C,8, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5 -positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single -exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C-18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C-18. The directions of the absorption and transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70 degrees, which is comparable with the value reported for al DiI-C-18.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-186623 (URN)10.1021/acs.langmuir.6b00478 (DOI)000374196700020 ()27003513 (PubMedID)2-s2.0-84964699618 (Scopus ID)
Note

QC 20160601

Available from: 2016-06-01 Created: 2016-05-13 Last updated: 2017-11-30Bibliographically approved
Knippenberg, S., Gieseking, R. L., Rehn, D. R., Mukhopadhyay, S., Dreuw, A. & Bredas, J.-L. (2016). Benchmarking Post-Hartree-Fock Methods To Describe the Nonlinear Optical Properties of Polymethines: An Investigation of the Accuracy of Algebraic Diagrammatic Construction (ADC) Approaches. Journal of Chemical Theory and Computation, 12(11), 5465-5476
Open this publication in new window or tab >>Benchmarking Post-Hartree-Fock Methods To Describe the Nonlinear Optical Properties of Polymethines: An Investigation of the Accuracy of Algebraic Diagrammatic Construction (ADC) Approaches
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2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 11, p. 5465-5476Article in journal (Refereed) Published
Abstract [en]

Third-order nonlinear optical (NLO) properties of polymethine dyes have been widely studied for applications such as all-optical switching. However, the limited accuracy of the current computational methodologies has prevented a comprehensive understanding of the nature of the lowest excited states and their influence on the molecular optical and NLO properties. Here, attention is paid to the lowest excited-state energies and their energetic ratio, as these characteristics impact the figure-of-merit for all-optical switching. For a series of model polymethines, we compare several algebraic diagrammatic construction (ADC) schemes for the polarization propagator with approximate second-order coupled cluster (CC2) theory, the widely used INDO/MRDCI approach and the symmetry adapted cluster configuration interaction (SAC-CI) algorithm incorporating singles and doubles linked excitation operators (SAC-CI SD-R). We focus in particular on the ground-to-excited state transition dipole moments and the corresponding state dipole moments, since these quantities are found to be of utmost importance for an effective description of the third-order polarizability gamma and two-photon absorption spectra. A sum-overstates expression has been used, which is, found to quickly converge. While ADC(3/2) has been found to be the most appropriate method to calculate these properties, CC2 performs poorly.

Place, publisher, year, edition, pages
American Chemical Society, 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-197779 (URN)10.1021/acs.jctc.6b00615 (DOI)000387519400022 ()2-s2.0-84994700971 (Scopus ID)
Note

QC 20161228

Available from: 2016-12-28 Created: 2016-12-08 Last updated: 2017-11-29Bibliographically approved
Osella, S., Murugan, N. A., Jena, N. K. & Knippenberg, S. (2016). Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives. Journal of Chemical Theory and Computation, 12(12), 6169-6181
Open this publication in new window or tab >>Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives
2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 12, p. 6169-6181Article in journal (Refereed) Published
Abstract [en]

The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50 degrees between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70-80 degrees with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-199503 (URN)10.1021/acs.jctc.6b00906 (DOI)000389866500041 ()2-s2.0-85006010884 (Scopus ID)
Note

QC 20170117

Available from: 2017-01-17 Created: 2017-01-09 Last updated: 2017-11-29Bibliographically approved
Knippenberg, S., Bohnwagner, M. V., Harbach, P. H. & Dreuw, A. (2015). Strong Electronic Coupling Dominates the Absorption and Fluorescence Spectra of Covalently Bound BisBODIPYs. Journal of Physical Chemistry A, 119(8), 1323-1331
Open this publication in new window or tab >>Strong Electronic Coupling Dominates the Absorption and Fluorescence Spectra of Covalently Bound BisBODIPYs
2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 8, p. 1323-1331Article in journal (Refereed) Published
Abstract [en]

The absorption spectrum of a representative BisBODIPY molecule is investigated using high-level quantum chemical methodology; the results are compared with experimental data. The S1 and S2 excited states are examined in detail to illuminate and to understand the electronic coupling between them. With the help of model systems in which the distance between the BODIPY monomers is increased or in which the dihedral angle between the subunits is changed, the electronic coupling is quantified, and its influence on energetics and oscillator strengths is highlighted. For the explanation of the experimental spectrum, orbital interaction effects are found to be important. Because of the large experimental Stokes shift of BisBODIPY, the nature of the emissive state is investigated and found to remain C2 symmetric as the ground state, and no localization of the excitation on one BODIPY subunit occurs. The excitonic coupling is in BisBODIPY still larger than the geometry relaxation energy, which explains the absence of a pseudo-Jahn-Teller effect.

Keywords
Absorption spectroscopy, Dihedral angle, Excited states, Geometry, Ground state, Quantum chemistry, Absorption and fluorescence spectra, Electronic coupling, Excitonic coupling, Experimental spectra, Geometry relaxation, Orbital interaction, Oscillator strengths, Quantum chemical methodology
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-163469 (URN)10.1021/acs.jpca.5b00637 (DOI)000350328800011 ()25635754 (PubMedID)2-s2.0-84923863264 (Scopus ID)
Note

QC 20150407

Available from: 2015-04-07 Created: 2015-04-07 Last updated: 2017-12-04Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4527-2566

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