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TV visited our lab

TVP Nauka (the science sub-channel of the main TV channel in Poland) visited our lab. Adam and Gosia gave an interview explaining what happens in the CoopCat lab. Below is a teaser. We will post here the final movie once it appears in TV. Stay tuned!

PNAS paper published!

We continue great collaboration with Kris Palczewski lab at the University of California Irvine.

Chromophore hydrolysis and release from photoactivated rhodopsin in native membranes

John D Hong, David Salom, Michał Andrzej Kochman, Adam Kubas, Philip D Kiser, Krzysztof Palczewski

For sustained vision, photoactivated rhodopsin (Rho*) must undergo hydrolysis and release of all-trans-retinal, producing substrate for the visual cycle and apo-opsin available for regeneration with 11-cis-retinal. The kinetics of this hydrolysis has yet to be described for rhodopsin in its native membrane environment. We developed a method consisting of simultaneous denaturation and chromophore trapping by isopropanol/borohydride, followed by exhaustive protein digestion, complete extraction, and liquid chromatography–mass spectrometry. Using our method, we tracked Rho* hydrolysis, the subsequent formation of N-retinylidene-phosphatidylethanolamine (N-ret-PE) adducts with the released all-trans-retinal, and the reduction of all-trans-retinal to all-trans-retinol. We found that hydrolysis occurred faster in native membranes than in detergent micelles typically used to study membrane proteins. The activation energy of the hydrolysis in native membranes was determined to be 17.7 ± 2.4 kcal/mol. Our data support the interpretation that metarhodopsin II, the signaling state of rhodopsin, is the primary species undergoing hydrolysis and release of its all-trans-retinal. In the absence of NADPH, free all-trans-retinal reacts with phosphatidylethanolamine (PE), forming a substantial amount of N-ret-PE (∼40% of total all-trans-retinal at physiological pH), at a rate that is an order of magnitude faster than Rho* hydrolysis. However, N-ret-PE formation was highly attenuated by NADPH-dependent reduction of all-trans-retinal to all-trans-retinol. Neither N-ret-PE formation nor all-trans-retinal reduction affected the rate of hydrolysis of Rho*. Our study provides a comprehensive picture of the hydrolysis of Rho* and the release of all-trans-retinal and its reentry into the visual cycle, a process in which alteration can lead to severe retinopathies.

Two new papers are out!

Tandem rigidification and π-extension as a key tool for the development of a narrow linewidth yellow hyperfluorescent OLED system

by Krzysztof Bartkowski, Paola Zimmermann Crocomo, Michał Andrzej Kochman, Dharmandra Kumar, Adam Kubas, Przemysław Data, Marcin Lindner

Hyperfluorescence (HF), a relatively new phenomenon utilizing the transfer of excitons between two luminophores, requires careful pairwise tuning of molecular energy levels and is proposed to be the crucial step towards the development of new, highly effective OLED systems. To date, barely few HF yellow emitters with desired narrowband emission but moderate external quantum efficiency (EQE < 20%) have been reported. This is because a systematic strategy embracing both Förster resonance energy transfer (FRET) and triplet to singlet (TTS) transition as complementary mechanisms for effective exciton transfer has not yet been proposed. Herein, we present a rational approach, which allows, through subtle structural modification, a pair of compounds built from the same donor and acceptor subunits, but with varied communication between these ambipolar fragments, to be obtained. The TADF-active dopant is based on a naphthalimide scaffold linked to the nitrogen of a carbazole moiety, which through the introduction of an additional bond leads not only to π-cloud enlargement, but also rigidifies and inhibits the rotation of the donor. This structural change prevents TADF, and guides bandgaps and excited state energies to simultaneously pursue FRET and TTS processes. New OLED devices utilizing the presented emitters show excellent external quantum efficiency (up to 27%) and a narrow full width at half maximum (40 nm), which is a consequence of very good alignment of energy levels. The presented design principles prove that only a minor structural modification is needed to obtain commercially applicable dyes for HF OLED devices.

Understanding structure–properties relationships of porphyrin linked to graphene oxide through π–π-stacking or covalent amide bonds

Anna Lewandowska-Andralojc, Ewelina Gacka, Tomasz Pedzinski, Gotard Burdzinski, Aleksandra Lindner, Jessica M O’Brien, Mathias O Senge, Aleksandra Siklitskaya, Adam Kubas, Bronislaw Marciniak, Justyna Walkowiak-Kulikowska

Two graphene oxide nanoassemblies using 5-(4-(aminophenyl)-10,15,20-triphenylporphyrin (TPPNH2) were fabricated by two synthetic methods: covalent (GO-CONHTPP) and noncovalent bonding. GO-CONHTPP was achieved through amide formation at the periphery of GO sheets and the hybrid material was fully characterized by FTIR, XPS, Raman spectroscopy, and SEM. Spectroscopic measurements together with theoretical calculations demonstrated that assembling TPPNH2 on the GO surface in DMF-H2O (1:2, v/v) via non-covalent interactions causes changes in the absorption spectra of porphyrin, as well as efficient quenching of its emission. Interestingly, covalent binding to GO does not affect notably neither the porphyrin absorption nor its fluorescence. Theoretical calculations indicates that close proximity and π–π-stacking of the porphyrin molecule with the GO sheet is possible only for the non-covalent functionalization. Femtosecond pump–probe experiments revealed that only the non-covalent assembly of TPPNH2 and GO enhances the efficiency of the photoinduced electron transfer from porphyrin to GO. In contrast to the non-covalent hybrid, the covalent GO-CONHTPP material can generate singlet oxygen with quantum yields efficiency (ΦΔ = 0.20) comparable to that of free TPPNH2 (ΦΔ = 0.26), indicating the possible use of covalent hybrid materials in photodynamic/photothermal therapy. The spectroscopic studies combined with detailed quantum-chemical analysis provide invaluable information that can guide the fabrication of hybrid materials with desired properties for specific applications.

Two new papers from our group are out!

These are results of Darek’s and Magda’s collaborations:

Metal-free oxoammonium salt-mediated C(sp3)–H oxidative Ugi-azide multicomponent reaction
Niklas Lohmann, Vesna Milovanović, Dariusz G. Piekarski and Olga García Mancheño
In this work, an efficient oxidative C(sp3)–H Ugi-azide multicomponent reaction of cyclic benzylic amines to the corresponding α-tetrazolo compounds using a TEMPO salt as mild hydride abstractor-type oxidant is reported. This simple one-pot approach allows the direct functionalization of N-heterocycles such as tetrahydroisoquinolines with a variety of isocyanides and NaN3 as a practical azide source. The reaction proceeds at room temperature and without the need of acid additives, allowing for the use of sensitive substrates, while minimizing isocyanide polymerization to provide the desired heterocycle-tetrazole products in synthetically useful yields (up to 99%).

Oxidized Multiwalled Carbon Nanotubes as Components and Oxidant Agents in the Formation of Multiwalled Carbon Nanotube/Polyazulene Composites
Emilia Grądzka, Joanna Breczko, Magdalena Bonarowska, Monika Wysocka-Żołopa, Anna Basa and Krzysztof Winkler
This work describes the practical and facile synthesis of oxidized multiwalled carbon nanotube/polyazulene (ox-MWCNT/PAZ) composites. In the proposed procedure, oxidized multiwalled carbon nanotubes were used both as components and oxidant agents in the formed composite material, which eliminated the use of conventional oxidizing agents such as ferric chloride. The properties and morphology of composite materials depend on the synthesis conditions, such as monomer concentration, synthesis time and synthesis temperature. The composite material is much more stable at high temperatures than pristine polyazulene. Additionally, the electrochemical performance of composite materials is better than that of pure polymeric materials. The highest specific capacitance of the ox-MWCNT/PAZ composite equals 381 F gPAZ−1. This value is approximately 5 times higher than the specific capacitance of pristine polyazulene. This high value results from the larger surface area of the composite material and its easier penetration by counterions of the supporting electrolyte during the oxidation process. Apart from the traditional doping process by counterions, the composite material is additionally codoped by hexafluorophosphate anions of the supporting electrolyte, which form hydrogen bonds with surface hydroxyl groups of ox-MWCNTs.

Our first work within OPUS20 is out!

We are delighted to share great news: our first work related to OPUS 20 grant CatVis that we recently started has just been accepted for publication in J. Phys. Chem. A!

“Theoretical Study of the Photoisomerization Mechanism of All-Trans-Retinyl Acetate”

by M. Kochman, K. Palczewski and A. Kubas


The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor to 9-cis-retinal, which has potential application in the treatment of some hereditary diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the readily available all-trans-RAc. In the present study, we examine the mechanism of the photoisomerization reaction with the use of state-of-the-art electronic structure calculations for two polyenic model compounds: tEtEt-octatetraene and tEtEtEc-2,6-dimethyl-1,3,5,7,9-decapentaene. The occurrence of photoisomerization is attributed to a chain-kinking mechanism, whereby a series of S1/S0 conical intersections associated with kinking deformations at different positions along the polyenic chain mediate internal conversion to the S0 state, and subsequent isomerization around one of the double bonds. Two other possible photoisomerization mechanisms are taken into account, but they are rejected as incompatible with simulation results and/or the available spectroscopic data.

Michal’s work on transient absorption spectra of DMABN published in JPC A

Fantastic news – Michal’s work “Simulation and Analysis of the Transient Absorption Spectrum of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Acetonitrile” was accepted for publication in J. Phys. Chem. A!


4-(N,N-Dimethylamino)benzonitrile (DMABN) is a well-known model compound for dual fluorescence—in sufficiently polar solvents, it exhibits two distinct fluorescence emission bands. The interpretation of its transient absorption (TA) spectrum in the visible range is the subject of a long-standing controversy. In the present study, we resolve this issue by calculating the TA spectrum on the basis of nonadiabatic molecular dynamics simulations. An unambiguous assignment of spectral signals to specific excited-state structures is achieved by breaking down the calculated spectrum into contributions from twisted and nontwisted molecular geometries. In particular, the much-discussed excited-state absorption band near 1.7 eV (ca. 700 nm) is attributed to the near-planar locally excited (LE) minimum on the S1 state. On the technical side, our study demonstrates that the second-order approximate coupled cluster singles and doubles (CC2) method can be used successfully to calculate the TA spectra of moderately large organic molecules, provided that the system in question does not approach a crossing between the lowest excited state and the singlet ground state within the time frame of the simulation.

Paper co-authored by Magda is online!

Congrats to Magda Bonarowska on publishing the following work in the ECS Journal of Solid State Science and Technology:

Capacitance Properties of Chemically Prepared Carbon Nanostructure/Polyazulene Composites

Emilia Grądzka, Gian Andrea Rizzi, Magdalena Bonarowska and Piotr Dłużewski

This work describes the chemical formation of composites based on different carbon nanostructures, such as single-walled carbon nanotubes, multi-walled carbon nanotubes, single-layer graphene oxide and p-type conducting polyazulene. The composite materials were synthesized in ethanol solution containing an appropriate amount of carbon nanostructures, azulene and ferric chloride as an oxidizing agent. The main attention was given to the electrochemical properties of these materials and their capacitance performance. The type of nanostructures influenced the morphology of the synthesized polyazulene. Thus, the relationship between the type of nanostructures present in the composite and its morphology and the electrochemical and stability properties were studied. The highest specific capacitance of 649 F g-1 was obtained for the SWCNT/PAZ composite. This value is nine times higher than the specific capacitance of pristine polyazulene synthesized under the same conditions. The SLGO/PAZ composite exhibited the lowest specific capacitance of 53 F g-1. However, this value was improved by approximately 77% by thermal treatment of the composite material at high temperature, resulting in an increase in the BET surface area as well as an increase in conductivity after heat treatment.

Paper co-authored by Gosia published in Int. J. Mol. Sci.!

Congratulations to Gosia! Her paper entitled “Synthesis and Structure of Novel Copper(II) Complexes with N,O- or N,N-Donors as Radical Scavengers and a Functional Model of the Active Sites in Metalloenzymes” was published in the International Journal of Molecular Sciences. Congratulations!

To evaluate the antioxidant activity of potential synthetic enzyme mimetics, we prepared new five copper(II) complexes via a self-assembly method and named them [Cu(2-(HOCH2)py)3](ClO4)2 (1), [Cu(2-(HOCH2)py)2(H2O)2]SiF6 (2), [Cu2(2-(HOCH2CH2)py)2(2-(OCH2CH2)py)2](ClO4)2 (3), [Cu(pyBIm)3](BF4)2·1.5H2O (4) and [Cu(py2C(OH)2)2](ClO4)2 (5). The synthetic protocol involved N,O- or N,N-donors: 2-(hydroxymethyl)pyridine (2-(HOCH2)py), 2-(hydroxyethyl)pyridine (2-(HOCH2CH2)py), 2-(2-pyridyl)benzimidazole (pyBIm), di(2-pyridyl)ketone (py2CO). The obtained Cu(II) complexes were fully characterised by elemental analysis, FTIR, EPR, UV-Vis, single-crystal X-ray diffraction and Hirshfeld surface analysis. Crystallographic and spectroscopic analyses confirmed chromophores of both monomeric ({CuN3O3} (1), {CuN2O4} (2), {CuN6} (4), {CuN4O2} (5)) and dimeric complex ({CuN2O3} (3)). Most of the obtained species possessed a distorted octahedral environment, except dimer 3, which consisted of two copper centres with square pyramidal geometries. The water-soluble compounds (13 and 5) were selected for biological testing. The results of the study revealed that complex 1 in solutions displayed better radical scavenging activity than complexes 35 and free ligands. Therefore, complex 1 has been selected for further studies to test its activity as an enzyme mimetic. The chosen compound was tested on the erythrocyte lysate of two groups of patients after undergoing chemotherapy and chemoradiotherapy. The effect of the tested compound (1) on enzyme activity levels (TAS, SOD and CAT) suggests that the selected complex can be treated as a functional mimetic of the enzymes.