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Karaush, N. N., Baryshnikov, G. V., Ågren, H. & Minaev, B. F. (2018). A theoretical study of new representatives of closed- and open-circle benzofuran and benzocyclopentadienone oligomers. New Journal of Chemistry, 42(14), 11493-11505
Open this publication in new window or tab >>A theoretical study of new representatives of closed- and open-circle benzofuran and benzocyclopentadienone oligomers
2018 (English)In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 42, no 14, p. 11493-11505Article in journal (Refereed) Published
Abstract [en]

Owing to their potential use as materials for strong optical rotation, circular dichroism and circularly polarized luminescence, the structure and energetic stability of novel closed- and open-circle benzofuran and benzocyclopentadienone oligomers have been studied computationally using the DFT method. It is found that an extension of the macrocycle size (n = 10-30) for the closed-circle species leads to a gradual transformation of their structure from saddle- to helical- and then to a wing-like shape. At the same time, the smaller closed-circle representatives with n = 4 and 6 exhibit a bowl-shaped structure due to the high energy strain of their molecular structures. Application of the NICS (nucleus-independent chemical shift) criterion to the here studied open-circle benzofuran and benzocyclopentadienone species with planar linear, planar fan-shape and helical molecular topology indicates that for the planar benzofuran series the inner benzene ring is more aromatic than the outer hexagons, while the aromaticity of the outer and inner furan rings is insensitive to the molecular size variations. The replacement of the aromatic furan rings by antiaromatic cyclopentadienone fragments for the planar linear species leads to a decrease of aromaticity of the benzene rings from the edge to the center of the benzocyclopentadienone chain. On the other hand, for the planar fan-shape benzocyclopentadienone series a zigzag trend in the NICS values is observed for the benzene rings. Loss of planarity only slightly affects the aromaticity of the helical open-circle benzofuran and benzocyclopentadienone oligomers. We propose that an increase of the NICS indices for the outer and inner rings of the macromolecular helical species is due to the magnetic couplings between the superimposed benzene and furan/cyclopentadienone rings.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2018
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-232758 (URN)10.1039/c8nj00601f (DOI)000438394800034 ()2-s2.0-85049737696 (Scopus ID)
Funder
Swedish National Infrastructure for Computing (SNIC)Carl Tryggers foundation , CTS 17:514
Note

QC 20180803

Available from: 2018-08-03 Created: 2018-08-03 Last updated: 2018-08-03Bibliographically approved
Natarajan Arul, M., Nordberg, A. & Ågren, H. (2018). Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling. ACS Chemical Neuroscience, 9(7), 1757-1767
Open this publication in new window or tab >>Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling
2018 (English)In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 9, no 7, p. 1757-1767Article in journal (Refereed) Published
Abstract [en]

Using the recently reported cryo-EM structure for the tau fibril [Fitzpatrick et al. (2017) Nature 547, 185-190], which is a potential target concerning Alzheimer's disease, we present the first molecular modeling studies on its interaction with various positron emission tomography (PET) tracers. Experimentally, based on the binding assay studies, at least three different high affinity binding sites have been reported for tracers in the tau fibril. Herein, through integrated modeling using molecular docking, molecular dynamics, and binding free energy calculations, we provide insight into the binding patterns of various tracers to the tau fibril. We suggest that there are four different high affinity binding sites available for many of the studied tracers showing varying binding affinity to different binding sites. Thus, PBB3 binds most strongly to site 4, and interestingly, this site is not a preferable site for any other tracers. For THIC5351, our data show that it strongly binds to sites 3 and 1, the former one being more preferable. We also find that MK6240 and T807 bind to site 1 specifically. The modeling data also give some insight into whether a tracer bound to a specific site can be replaced by others or not. For example, the displacement of T807 by PBB3 as reported experimentally can also be explained and attributed to the larger binding affinity of the latter compound in all binding sites. The binding free energy results explain very well the small binding affinity of THK523 compared to all the aryl quinoline moieties containing THK tracers. The ability of certain tau tracers, like FDDNP and THK523, to bind to amyloid fibrils has also been investigated. Furthermore, such off-target interaction of tau tracers with amyloid beta fibrils has been validated using a quantum mechanical fragmentation approach.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-232912 (URN)10.1021/acschemneuro.8b00093 (DOI)000439531400024 ()29630333 (PubMedID)2-s2.0-85050285842 (Scopus ID)
Note

QC 20180808

Available from: 2018-08-08 Created: 2018-08-08 Last updated: 2018-08-08Bibliographically approved
Karaush, N. N., Minaeva, V. A., Baryshnikov, G. V., Minaev, B. F. & Ågren, H. (2018). Identification of tautomeric intermediates of a novel thiazolylazonaphthol dye - A density functional theory study. Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, 203, 324-332
Open this publication in new window or tab >>Identification of tautomeric intermediates of a novel thiazolylazonaphthol dye - A density functional theory study
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2018 (English)In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 203, p. 324-332Article in journal (Refereed) Published
Abstract [en]

The recently synthesized thiazolylazo dye, 1-(5-benzy1-1,3-thiazol-2-yl)diazenyllnaphthalene-2-ol called shortly BnTAN, is studied by density functional theory (DFT) in three tautomeric forms in order to explain the available H-1 NMR, UV-Vis and FTIR spectra. An experimentally observed IR band at 1678 cm(-1), assigned to the C=O bond stretching vibration, supports the notion that BnTAN retains in the less stable keto-form even in the solid state due to an ultrafast single-coordinate intramolecular proton transfer. This finding is also in a good agreement with an X-ray crystallography analysis which indicates an intermediate position of the proton between the OH and -N=N-groups. Calculations also show that some experimentally observed H-I NMR signals could be considered as being averaged values between theoretically calculated chemical shifts for the corresponding protons in the keto- and enol-tautomers. At the same time the UV-Vis spectra are almost insensitive to the tautomerization processes as the main single band absorption at 500 nm is present in all tautomers according to our TD DFT simulations. The minor differences in spectral features of the long-wavelength visible region are also noted and discussed with respect to the manifestation of the less stable tautomer form.

Place, publisher, year, edition, pages
Pergamon Press, 2018
Keywords
Tautomers, FTIR spectra, UV-vis spectra, NMR spectra, DFT calculations
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:kth:diva-232582 (URN)10.1016/j.saa.2018.05.096 (DOI)000437816000040 ()29879648 (PubMedID)2-s2.0-85047933840 (Scopus ID)
Funder
Carl Tryggers foundation , CTS 17:514Stiftelsen Olle Engkvist Byggmästare, 189-0223
Note

QC 20180727

Available from: 2018-07-27 Created: 2018-07-27 Last updated: 2018-07-27Bibliographically approved
Li, D., Ågren, H. & Chen, G. (2018). Near infrared harvesting dye-sensitized solar cells enabled by rare-earth upconversion materials. Dalton Transactions, 47(26), 8526-8537
Open this publication in new window or tab >>Near infrared harvesting dye-sensitized solar cells enabled by rare-earth upconversion materials
2018 (English)In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 47, no 26, p. 8526-8537Article, review/survey (Refereed) Published
Abstract [en]

Dye-sensitized solar cells (DSSCs) have been deemed as promising alternatives to silicon solar cells for the conversion of clean sunlight energy into electricity. A major limitation to their conversion efficiency is their inability to utilize light in the infrared (IR) spectral range, which constitutes almost half the energy of the sun's radiation. This fact has elicited motivations and endeavors to extend the response wavelength of DSSCs to the IR range. Photon upconversion through rare-earth ions constitutes one of the most promising approaches toward the goal of converting near-IR (NIR) or IR light into visible or ultraviolet light, where DSSCs typically have high sensitivity. In the present review, we summarize recent progress based on the utilization of various upconversion materials and device structures to improve the performance of dye-sensitized solar cells.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2018
National Category
Energy Systems
Identifiers
urn:nbn:se:kth:diva-232388 (URN)10.1039/c7dt04461e (DOI)000437317700004 ()29388652 (PubMedID)2-s2.0-85049430338 (Scopus ID)
Note

QC 20180727

Available from: 2018-07-27 Created: 2018-07-27 Last updated: 2018-07-27Bibliographically approved
Zakomirnyi, V., Rasskazov, I. L., Gerasimov, V. S., Ershov, A. E., Polyutov, S. P., Karpov, S. V. & Ågren, H. (2018). Titanium nitride nanoparticles as an alternative platform for plasmonic waveguides in the visible and telecommunication wavelength ranges. Photonics and Nanostructures - Fundamentals and Applications, 30, 50-56
Open this publication in new window or tab >>Titanium nitride nanoparticles as an alternative platform for plasmonic waveguides in the visible and telecommunication wavelength ranges
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2018 (English)In: Photonics and Nanostructures - Fundamentals and Applications, ISSN 1569-4410, Vol. 30, p. 50-56Article in journal (Refereed) Published
Abstract [en]

We propose to utilize titanium nitride (TiN) as an alternative material for linear periodic chains (LPCs) of nanoparticles (NPs) which support surface plasmon polariton (SPP) propagation. Dispersion and transmission properties of LPCs have been examined within the framework of the dipole approximation for NPs with various shapes: spheres, prolate and oblate spheroids. It is shown that LPCs of TiN NPs support high-Q eigenmodes for an SPP attenuation that is comparable with LPCs from conventional plasmonic materials such as Au or Ag, with the advantage that the refractory properties and cheap fabrication of TiN nanostructures are more preferable in practical implementations compared to Au and Ag. We show that the SPP decay in TiN LPCs remains almost the same even at extremely high temperatures which is impossible to reach with conventional plasmonic materials. Finally, we show that the bandwidth of TiN LPCs from non-spherical particles can be tuned from the visible to the telecommunication wavelength range by switching the SPP polarization, which is an attractive feature for integrating these structures into modern photonic devices.

Place, publisher, year, edition, pages
Elsevier, 2018
Keywords
Nanoparticle, Plasmon waveguide, Refractory plasmonics, Surface plasmon polariton, Titanium nitride
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-229236 (URN)10.1016/j.photonics.2018.04.005 (DOI)2-s2.0-85046117367 (Scopus ID)
Note

QC 20180601

Available from: 2018-06-01 Created: 2018-06-01 Last updated: 2018-06-01Bibliographically approved
Baryshnikov, G. V., Valiev, R. R., Minaev, B. F. & Ågren, H. (2017). A computational study of aromaticity and photophysical properties of unsymmetrical azatrioxa[8]circulenes. New Journal of Chemistry, 41(7), 2717-2723
Open this publication in new window or tab >>A computational study of aromaticity and photophysical properties of unsymmetrical azatrioxa[8]circulenes
2017 (English)In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, no 7, p. 2717-2723Article in journal (Refereed) Published
Abstract [en]

Owing to their potential use in organic light-emitting diodes and field-effect transistors we present a theoretical study of a series of unsymmetrical azatrioxa[8]circulenes in order to explain the impact of outer substituents and benzoannelation on photophysical constants and aromaticity of these compounds in terms of spin-orbit coupling perturbation and magnetically-induced ring currents. It is argued that the S1-Tn inter-system crossing processes constitute the main deactivation pathways for the fluorescence quenching, something that is supported by a good agreement obtained with experimental data on fluorescence quantum yields. The concept of the gauge-including magnetically induced currents has been applied in order to estimate the role of substituents and benzoannelated fragments on the aromaticity and particularly on the overall balance between the diatropic “aromatic” and paratropic “antiaromatic” current strengths. While a variation of the substituents in the outer perimeter of the studied circulenes does not provide a clear effect on their aromaticity, it is demonstrated that an additional benzoannelation (π-extension) of the azatrioxa[8]circulene macrocycle induces a significant aromaticity enhancement.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-207398 (URN)10.1039/c6nj03925a (DOI)000401528400021 ()2-s2.0-85016316941 (Scopus ID)
Note

Funding details: 0115U000637, MESU, Ministry of Education and Science of Ukraine; Funding text: The calculations were performed using the computational resources provided by the Swedish National Infrastructure for Computing (SNIC) at the Parallel Computer Center (PDC) through the project “Multiphysics Modeling of Molecular Materials” SNIC 020/11-23. This work has been supported by the Academy of Finland through project 275845. CSC, Finnish IT Center for Science, is acknowledged for computer time. This research was also supported by the Ministry of Education and Science of Ukraine (project number 0115U000637).

QC 20170608

Available from: 2017-06-08 Created: 2017-06-08 Last updated: 2017-06-08Bibliographically approved
Shao, W., Chen, G., Ohulchanskyy, T. Y., Yang, C., Ågren, H. & Prasad, P. N. (2017). A core-multiple shell nanostructure enabling concurrent upconversion and quantum cutting for photon management. Nanoscale, 9(5), 1934-1941
Open this publication in new window or tab >>A core-multiple shell nanostructure enabling concurrent upconversion and quantum cutting for photon management
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2017 (English)In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 5, p. 1934-1941Article in journal (Refereed) Published
Abstract [en]

Photon management enables the manipulation of the number of input photons by conversion of two or more light quanta into one (upconversion) or vice versa (quantum cutting). Simultaneous realization of both these processes in a single unit provides unique opportunities of efficient utilization of photons throughout a broad spectral range. Yet, concurrent realization of these two parallel optical processes in one single unit remains elusive, limiting its impact on many existing or possible future applications such as for panchromatic photovoltaics. Here, we describe an epitaxial active core/inert shell/active shell/inert shell fluoride nanostructure to implement upconversion and quantum cutting within spatially confined and isolated rare-earth-doped active domains. The core area transforms infrared photons through trivalent erbium (Er3+) ions into three-and two-photon upconverted visible and near infrared luminescence, while the second shell domain splits an excitation photon into two near infrared photons through cooperative quantum cutting from one trivalent terbium ion (Tb3+) to two trivalent ytterbium ions (Yb3+). The inert layer in between the active domains is able to effectively suppress the destructive interference between upconversion and quantum cutting, while the outermost inert shell is able to eliminate surfacerelated quenching. This design enables the colloidal core/multishell nanoparticles to have an upconversion quantum yield of similar to 1.6%, and to have a luminescence yield of the quantum cutting process as high as similar to 130%. This work constitutes a solid step for flexible photon management in a single nanostructure, and has an implication for photonic applications beyond photovoltaics.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-204732 (URN)10.1039/c6nr09713h (DOI)000395594300022 ()28098308 (PubMedID)2-s2.0-85011387426 (Scopus ID)
Note

QC 20170601

Available from: 2017-06-01 Created: 2017-06-01 Last updated: 2017-06-01Bibliographically approved
Vaz da Cruz, V., Ertan, E., C. Couto, R., Eckert, S., Fondell, M., Dantz, M., . . . Kimberg, V. (2017). A study of the water molecule using frequency control over nuclear dynamics in resonant X-ray scattering. Physical Chemistry, Chemical Physics - PCCP, 19(30), 19573-19589
Open this publication in new window or tab >>A study of the water molecule using frequency control over nuclear dynamics in resonant X-ray scattering
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2017 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 30, p. 19573-19589Article in journal (Refereed) Published
Abstract [en]

In this combined theoretical and experimental study we report a full analysis of the resonant inelastic X-ray scattering (RIXS) spectra of H2O, D2O and HDO. We demonstrate that electronically-elastic RIXS has an inherent capability to map the potential energy surface and to perform vibrational analysis of the electronic ground state in multimode systems. We show that the control and selection of vibrational excitation can be performed by tuning the X-ray frequency across core-excited molecular bands and that this is clearly reflected in the RIXS spectra. Using high level ab initio electronic structure and quantum nuclear wave packet calculations together with high resolution RIXS measurements, we discuss in detail the mode coupling, mode localization and anharmonicity in the studied systems.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017
Keywords
RIXS, water, quantum dynamics, x-ray
National Category
Atom and Molecular Physics and Optics
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-187012 (URN)10.1039/C7CP01215B (DOI)000407053000006 ()28352891 (PubMedID)2-s2.0-85027313711 (Scopus ID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Carl Tryggers foundation , CTS 15:266Swedish Research Council
Note

QC 20160516

Available from: 2016-05-16 Created: 2016-05-16 Last updated: 2018-05-15Bibliographically approved
Bu, L., Chen, J., Wei, X., Li, X., Ågren, H. & Xie, Y. (2017). An AIE and ICT based NIR florescent probe for cysteine and homocysteine. Dyes and pigments, 136, 724-731
Open this publication in new window or tab >>An AIE and ICT based NIR florescent probe for cysteine and homocysteine
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2017 (English)In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 136, p. 724-731Article in journal (Refereed) Published
Abstract [en]

A combination of aggregation-induced emission and intramolecular charge transfer was achieved by using a triphenylamine analogue and a dicyanovinyl moiety as the electron donating and accepting units, respectively. Hence, we designed and synthesized a probe with a D-π-A framework as a near-infrared fluorescence turn-on probe for biothiols (cysteine and homocysteine). Owing to the remarkable intramolecular charge transfer effect as well as intramolecular rotations associated with the donor moiety, the probe exhibits extremely weak fluorescence, which becomes a good starting point for developing fluorescence “turn-on” probes. Upon reaction with cysteine or homocysteine utilizing the dicyanovinyl moiety, the intramolecular charge transfer character was weakened, and the reacting products were observed to aggregate in aqueous solutions, resulting in the aggregation-induced emission effect with red fluorescence at 651 and 656 nm, respectively. Hence, the probe could be used as a fluorescence “turn-on” sensor for cysteine and homocysteine, with the sensing time of less than 4 min and the detection limits of 8.4 μM and 5.7 μM towards cysteine and homocysteine, respectively. The probe could distinguish cysteine and homocysteine from glutathione. The sensing mechanism was systematically investigated by employing high resolution mass spectrometry, 1H NMR and density functional theory calculations as well as checking the solvent viscosity dependent fluorescence, and thus the nucleophilic addition products, the intramolecular charge transfer character, and the aggregation-induced emission behaviour were clearly elucidated. It is noteworthy that the low cytotoxicity, the intrinsic aggregation-induced emission nature and near-infrared emissions enable the application of the probe in living cell imaging. © 2016 Elsevier Ltd

Keywords
AIE, Biothiols, Cell imaging, Fluorescent probes, ICT, Addition reactions, Amino acids, Charge transfer, Density functional theory, Fluorescence, Infrared devices, Lanthanum compounds, Mass spectrometry, Solutions, Aggregation-induced emissions, High resolution mass spectrometry, Intra-molecular charge transfer, Near-infrared emissions, Near-infrared fluorescence, Probes
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-195127 (URN)10.1016/j.dyepig.2016.09.032 (DOI)000387837200087 ()2-s2.0-84988524950 (Scopus ID)
Note

Funding Details: 91227201, NSFC, National Natural Science Foundation of China. QC 20161107

Available from: 2016-11-07 Created: 2016-11-02 Last updated: 2017-11-29Bibliographically approved
Jena, N. K., Lyne, Å., Natarajan Arul, M., Ågren, H. & Birgisson, B. (2017). Atomic level simulations of the interaction of asphaltene with quartz surfaces: role of chemical modifications and aqueous environment. Materials and Structures, 50(1), Article ID 99.
Open this publication in new window or tab >>Atomic level simulations of the interaction of asphaltene with quartz surfaces: role of chemical modifications and aqueous environment
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2017 (English)In: Materials and Structures, ISSN 1359-5997, E-ISSN 1871-6873, Vol. 50, no 1, article id 99Article in journal (Refereed) Published
Abstract [en]

Understanding the properties of bitumen and its interaction with mineral aggregates is crucial for future strategies to improve roads and highways. Knowledge of basic molecular and electronic structures of bitumen, one out of the two main components of asphalt, poses a major step towards achieving such a goal. In the present work we employ atomistic simulation techniques to study the interaction of asphaltenes, a major constituent of bitumen, with quartz surfaces. As an effective means to tune adhesion or cohesion properties of asphaltenes and mineral surfaces, we propose chemical modification of the pristine asphaltene structure. By the choice of substituent and site of substitution we find that adhesion between the asphaltene molecule and the quartz surface can easily be improved at the same time as the cohesive interaction between the asphaltene units is reduced, while other substituents may lead to the opposite effect. We also provide insight at the molecular level into how water molecules affect interactions between asphaltenes and quartz. Our approach emphasizes a future role for advanced atomistic modeling to understand the properties of bitumen and suggest further improvements.

Place, publisher, year, edition, pages
Kluwer Academic Publishers, 2017
Keywords
Adhesion, Bitumen, Cohesion, Molecular dynamics, Quartz, Bituminous materials, Chemical modification, Electronic structure, Molecules, Aqueous environment, Atomic level simulations, Atomistic modeling, Atomistic simulations, Cohesion properties, Cohesive interactions, Asphaltenes
National Category
Materials Engineering
Identifiers
urn:nbn:se:kth:diva-201948 (URN)10.1617/s11527-016-0880-y (DOI)000405071300013 ()2-s2.0-84994500697 (Scopus ID)
Note

QC 20170306

Available from: 2017-03-06 Created: 2017-03-06 Last updated: 2017-08-01Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-1763-9383

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