Category Archives

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 work “Lerf–Klinowski-type models of graphene oxide and reduced graphene oxide are robust in analyzing non-covalent functionalization with porphyrins” is among 100 most downloaded chemistry papers in Scientific reports journal.

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

Abstract

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.

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!

Abstract

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.

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

Abstract
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.

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!

https://www.mdpi.com/1422-0067/22/14/7286

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 (1, 3 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 3, 5 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.

We are happy to anounce that our project entitled “Combined experimental and theoretical studies of the catalytic activity of RPE65 enzyme using biomimetic active centre models (CatVis)” (PI: A. Kubas) received funding under National Science Centre Opus 20 call (ca. 690 kPLN / 150 kEUR).

Adam’s milestone paper on electronic couplings dependency on spin states has just been published in the Journal of Chemical Theory and Computation: “How the Donor/Acceptor Spin States Affect the Electronic Couplings in Molecular Charge-Transfer Processes?”

Abstract:

The electronic coupling matrix element H_AB is an essential ingredient of most electron-transfer theories. H_AB depends on the overlap between donor and acceptor wave functions and is affected by the involved states’ spin. We classify the spin-state effects into three categories: orbital occupation, spin-dependent electron density, and density delocalization. The orbital occupancy reflects the diverse chemical nature and reactivity of the spin states of interest. The effect of spin-dependent density is related to a more compact electron density cloud at lower spin states due to decreased exchange interactions between electrons. Density delocalization is strongly connected with the covalency concept that increases the spatial extent of the diabatic state’s electron density in specific directions. We illustrate these effects with high-level ab initio calculations on model direct donor–acceptor systems relevant to metal oxide materials and biological electron transfer. Obtained results can be used to benchmark existing methods for H_AB calculations in complicated cases such as spin-crossover materials or antiferromagnetically coupled systems.

Read it online free:

https://pubs.acs.org/doi/10.1021/acs.jctc.1c00126

Our paper “Lerf–Klinowski-type models of graphene oxide and reduced graphene oxide are robust in analyzing non-covalent functionalization with porphyrins” is online! This is excellent collaboration between CoopCat team, AMU team in Poznan and WUT in Warsaw.

Abstract:

Graphene-based nanohybrids are good candidates for various applications. However, graphene exhibits some unwanted features such as low solubility in an aqueous solution or tendency to aggregate, limiting its potential applications. On the contrary, its derivatives, such as graphene oxide (GO) and reduced graphene oxide (RGO), have excellent properties and can be easily produced in large quantities. GO/RGO nanohybrids with porphyrins were shown to possess great potential in the field of photocatalytic hydrogen production, pollutant photodegradation, optical sensing, or drug delivery. Despite the rapid progress in experimental research on the porphyrin-graphene hybrids some fundamental questions about the structures and the interaction between components in these systems still remain open. In this work, we combine detailed experimental and theoretical studies to investigate the nature of the interaction between the GO/RGO and two metal-free porphyrins 5,10,15,20-tetrakis(4-aminophenyl) porphyrin (TAPP) and 5,10,15,20-tetrakis(4-hydroxyphenyl) porphyrin (TPPH)]. The two porphyrins form stable nanohybrids with GO/RGO support, although both porphyrins exhibited a slightly higher affinity to RGO. We validated finite, Lerf–Klinowski-type (Lerf et al. in J Phys Chem B 102:4477, 1998) structural models of GO and RGO and successfully used them in ab initio absorption spectra simulations to track back the origin of experimentally observed spectral features. We also investigated the nature of low-lying excited states with high-level wavefunction-based methods and shown that states’ density becomes denser upon nanohybrid formation. The studied nanohybrids are non-emissive, and our study suggests that this is due to excited states that gain significant charge-transfer character. The presented efficient simulation protocol may ease the properties screening of new GO/RGO-nanohybrids.

Check online:

https://www.nature.com/articles/s41598-021-86880-1

We look for potential candidates for Post-Doc application under the PASIFIC programme coordinated by the Polish Academy of Sciences. Check more details in the JOBS section.