The windmill, the dragon, and the frog: geometry control over the spectral, magnetic, and electrochemical properties of cobalt phthalocyanine regioisomers.

For the first time, we have prepared non-aggregating phthalocyanine cobalt complexes as a set of resolved positional isomers. These compounds comprise a unique test bed for the structure-properties studies, as their optical and electrochemical properties are influenced by the planarity of the phthalocyanine macrocycle, which can be controlled by the positional isomerism of the bulky aromatic substituents at the α-phthalo sites. We support our conclusions with molecular modelling studies, which show a perfect match between the calculated and experimentally determined spectral/electrochemical values. We challenge a common perception that the NMR spectra of cobalt phthalocyanines cannot be measured due to the paramagnetic nature of Co(II). We suggest instead that the key factors affecting the NMR spectral resolution are molecular aggregation and π-π stacking. These interactions are suppressed by the bulky peripheral substituents on the cobalt phthalocyanines prepared, making these isomeric compounds an excellent tool for paramagnetic NMR studies.

Phototoxicity of BODIPY in long-term imaging can be reduced by intramolecular motion.

For long-term live-cell fluorescence imaging and biosensing, it is crucial to work with a dye that has high fluorescence quantum yield and photostability without being detrimental to the cells. In this paper, we demonstrate that neutral boron-dipyrromethene (BODIPY)-based molecular rotors have great properties for high-light-dosage demanding live-cell fluorescence imaging applications that require repetitive illuminations. In molecular rotors, an intramolecular rotation (IMR) allows an alternative route for the decay of the singlet excited state (S1) via the formation of an intramolecular charge transfer state (CT). The occurrence of IMR reduces the probability of the formation of a triplet state (T1) which could further react with molecular oxygen (3O2) to form cytotoxic reactive oxygen species, e.g., singlet oxygen (1O2). We demonstrate that the oxygen-related nature of the phototoxicity for BODIPY derivatives can be significantly reduced if a neutral molecular rotor is used as a probe. The studied neutral molecular rotor probe shows remarkably lower phototoxicity when compared with both the non-rotating BODIPY derivative and the cationic BODIPY-based molecular rotor in different light dosages and dye concentrations. It is also evident that the charge and localization of the fluorescent probe are as significant as the IMR in terms of the phototoxicity in a long-term live-cell imaging.

Agonists in the Extended Conformation Stabilize the Active State of ß-Adrenoceptors.

In this study, we conducted a comparative analysis of the structure of agonists and antagonists of transmembrane (TM) ß-adrenoceptors (ß-ARs) and their interactions with the ß-ARs and proposed the mechanism of receptor activation. A characteristic feature of agonist and antagonist molecules is the presence of a hydrophobic head (most often, one or two aromatic rings) and a tail with a positively charged amino group. All ß-adrenergic agonists have two carbon atoms between the aromatic ring of the head and the nitrogen atom of the amino group. In antagonist molecules, this fragment can be either reduced or increased to four atoms due to the additional carbon and oxygen atoms. The agonist head, as a rule, has two H-bond donors or acceptors in the para- and meta-positions of the aromatic rings, while in the antagonist heads, these donors/acceptors are absent or located in other positions. Analysis of known three-dimensional structures of ß-AR complexes with agonists showed that the agonist head forms two H-bonds with the TM5 helix, and the tail forms an ionic bond with the D3.32 residue of the TM3 helix and one or two H-bonds with the TM7 helix. The tail of the antagonist can form similar bonds, but the interaction between the head and the TM5 helix is much weaker. As a result of these interactions, the agonist molecule acquires an extended "strained string" conformation, in contrast to the antagonist molecule, which has a longer, bended, and flexible tail. The "strained string" of the agonist interacts with the TM6 helix (primarily with the W6.48 residue) and turns it, which leads to the opening of the G protein-binding site on the intracellular side of the receptor, while flexible and larger antagonist molecules do not have the same effect on the receptor.

3ß-Corner Stability by Comparative Molecular Dynamics Simulations.

This study explored the mechanisms by which the stability of super-secondary structures of the 3ß-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3ß-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3ß-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3ß-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or "ready-made" building block in protein folding. The 3ß-corner can also be considered as an independent object for study in field of structural biology.

Electron transfer in oriented donor-acceptor dyads, intralayer charge migration, and formation of interlayer charge separated states in multi-layered Langmuir-Schäfer films.

Photoinduced intra- and interlayer electron transfer (ET) of doubly bridged donor-acceptor molecule, porphyrin-fullerene dyad (PF), was studied in single- and multi-layered Langmuir-Schäfer (LS) films and in LS films, where PF and an efficient electron donating polymer polyhexyltiophene (PHT) formed a bilayer PHT/PF and multi-layered PHT/PF structures. The ET through layers were investigated by a method, which measures the photovoltaic (PV) response proportional to the number of charge-separated (CS) states and to the CS distance between the electrons and holes formed in pulsed photo-excitation. Primary conclusions were, that ET starts as formations of CS dyads (P+F-) in single-layers, continues as long-range intra-layer charge migrations following interlayer CS between two adjacent monolayers. Quantitative conclusions were, that the interlayer ET efficiency is 100% in the bi-layered PF structure (2PF), where two CS dyads in adjacent layers forms CS complexes (P+F/PF-) and that the probability to form longer or higher order of CS complexes follows an expression of a convergent geometric series, with a converting factor of 2/3. In the PHT/PF bilayer structure the ET efficiency was one order of magnitude higher, than that for the 2PF structure due to the ET from the CS dyads to ground state electron donor PHT, with an acceptor density, much higher than that of (P+F-).

Structural motifs in which ß-strands are clipped together with the П-like module.

In this study, the structural motifs that can be represented as combinations of small motifs such as ß-hairpins, S-, and Z-like ß-sheets and ßαß-units, and the П-like module are described and analyzed. The П-module consists of connected elements of the ß-strand-loop-ß-strand type arranged in space so that its overall fold resembles a clip or the Greek letter П. In proteins, the П-module itself and the structural motifs containing it exhibit unique overall folds and have specific sequence patterns of the key hydrophobic, hydrophilic and glycine residues. All this together enables us to conclude that these structural motifs can fold independently of the remaining part of the molecule and can act as nuclei and/or "ready-made" building blocks in protein folding.

Tailored Fabrication of Transferable and Hollow Weblike Titanium Dioxide Structures.

The preparation of weblike titanium dioxide thin films by atomic layer deposition on cellulose biotemplates is reported. The method produces a TiO2 web, which is flexible and transferable from the deposition substrate to that of the end application. Removal of the cellulose template by calcination converts the amorphous titania to crystalline anatase and gives the structure a hollow morphology. The TiO2 webs are thoroughly characterized using electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy to give new insight into manufacturing of porous titanium dioxide structures by means of template-based methods. Functionality and integrity of the TiO2 hollow weblike thin films were successfully confirmed by applying them as electrodes in dye-sensitized solar cells.

Color Bricks: Building Highly Organized and Strongly Absorbing Multicomponent Arrays of Terpyridyl Perylenes on Metal Oxide Surfaces.

Terpyridine-substituted perylenes containing cyclic anhydrides in the peri position were synthesized. The anhydride group served as an anchor for assembly of the terpyridyl-crowned chromophores as monomolecular layers on metal oxide surfaces. Further coordination with Zn(2+) ions allowed for layer-by-layer formation of supramolecular assemblies of perylene imides on the solid substrates. With properly selected anchor and linker molecules it was possible to build high quality structures of greater than ten successive layers by a simple and straightforward procedure. The prepared films were stable and had a broad spectral coverage and high absorbance. To demonstrate their potential use, the synthesized dyes were employed in solid-state dye-sensitized solar cells, and electron injection from the perylene antennas to titanium dioxide was observed.

Photophysical study of a self-assembled donor-acceptor two-layer film on TiO2.

The self-assembled monolayer (SAM) technique was employed to fabricate a two-layer donor-acceptor film on the surface of TiO2. The approach is based on using donor and acceptor compounds with anchoring groups of different lengths. The acceptor, a fullerene derivative, has a carboxyl anchor attached to the fullerene moiety via a short linker that places the fullerene close to the surface. The donor, a porphyrin derivative, is equipped with a long linker that can penetrate between the fullerenes and keep porphyrin on top of the fullerene layer. The two-layer fullerene-porphyrin structures were deposited on a mesoporous film of TiO2 nanoparticles by immersing the TiO2 film sequentially into fullerene and porphyrin solutions. Transient absorption spectroscopy studies of the samples revealed that after the selective photoexcitation of porphyrin a fast (<5 ps) intermolecular electron transfer (ET) takes place from porphyrin to the fullerene layer, which confirms the formation of the interlayer donor-acceptor interface. Furthermore, in the second step of ET the fullerene anions donate electrons to the TiO2 nanoparticles. The latter reaction is relatively slow with an average time constant of 230 ps. It involves roughly half of the primary generated charges, and the second half relaxes by the interlayer charge recombination. The resulting state with a porphyrin cation and electron in TiO2 has an extremely long lifetime and recombines with an average time constant of 23 ms.

Far-red light-triggered cargo release from liposomes b ound to a photosensitizer-cellulose nanofiber hydrogel.

In our research we used the anionic nanofibrillar cellulose (ANFC) as a platform for far-red light-induced release of cargo from liposomes. In contrast to previous works, where photosensitizers are usually in the liposomal bilayers, we used a cellulose-binding dye. Our phthalocyanine derivative has been shown to bind very strongly to cellulose and cellulose nanofiber hydrogels, allowing us to place it outside of the liposomes. Both the sensitizer and cationic liposomes bind strongly to the ANFC after mixing, making the system easy to fabricate. Upon light activation, the photosensitizer generates reactive oxygen species (ROS) within the ANFC hydrogel, where the reactive oxygen species oxidize unsaturated lipids in the liposomal membrane, which makes the liposomes more permeable, resulting in on-demand cargo release. We were able to achieve ca. 70 % release of model hydrophilic cargo molecule calcein from the hydrogels with a relatively low dose of light (262 J/cm2) while employing the straightforward fabrication techniques. Our system was remarkably responsive to the far-red light (730 nm), enabling deep tissue penetration. Therefore, this very promising novel cellulose-immobilized photosensitizer liposomal platform could be used as a controlled drug delivery system, which can have applications in externally activated coatings or implants.

LASU: An efficient and stable phthalocyanine dye with tolerable safety profile for self-disinfecting anti-COVID textiles activated by ambient light.

BACKGROUND: Recent COVID crisis has demonstrated that modern society urgently needs an accessible protection against mass infections, especially viruses, as the new strains are appearing at an ever-increasing pace and cause severe harm to the population and the world economy. METHODS: We have developed an efficient phthalocyanine photosensitizer LASU, that is suitable for dyeing textiles and allows to prepare reusable self-disinfecting fabrics with strong antiviral properties. The safety profile of LASU was evaluated in accredited laboratories by several in vitro assays according to the OECD-guidelines. RESULTS: The textiles impregnated with LASU phthalocyanine showed a significant antiviral photodynamic effect even under moderate indoor and outdoor light. The dye did not show any genotoxic potential in human lymphocyte micronucleus assay. It showed a possible indication for eye irritation in human EpiOcular™ model and was phototoxic when tested in mouse BALB/c 3T3 cell test in the presence and absence of UVA-irradiation. CONCLUSION: Novel phthalocyanine-dyed textiles are suitable for general use as self-disinfecting antiviral barriers and materials in hospitals, households, and public places. The safety profile of LASU is the phototoxic effect which is related to LASU´s mode of action.

Direct evidence of significantly different chemical behavior and excited-state dynamics of 1,7- and 1,6-regioisomers of pyrrolidinyl-substituted perylene diimide.

Novel bay-functionalized perylene diimides with additional substitution sites close to the perylene core have been prepared by the reaction between 1,7(6)-dibromoperylene diimide 6 (dibromo-PDI) and 2-(benzyloxymethyl)pyrrolidine 5. Distinct differences in the chemical behaviors of the 1,7- and 1,6-regioisomers have been discerned. While the 1,6-dibromo-PDI produced the corresponding 1,6-bis-substituted derivative more efficiently, the 1,7-dibromo-PDI underwent predominant mono-debromination, yielding a mono-substituted PDI along with a small amount of the corresponding 1,7-bis-substituted compound. By varying the reaction conditions, a controlled stepwise bis-substitution of the bromo substituents was also achieved, allowing the direct synthesis of asymmetrical 1,6- and 1,7-PDIs. The compounds were isolated as individual regioisomers. Fullerene (C60) was then covalently linked at the bay region of the newly prepared PDIs. In this way, two separate sets of perylene diimide-fullerene dyads, namely single-bridged (SB-1,7-PDI-C60 and SB-1,6-PDI-C60) and double-bridged (DB-1,7-PDI-C60 and DB-1,6-PDI-C60), were synthesized. The fullerene was intentionally attached at the bay region of the PDI to achieve close proximity of the two chromophores and to ensure an efficient photoinduced electron transfer. A detailed study of the photodynamics has revealed that photoinduced electron transfer from the perylene diimide chromophore to the fullerene occurs in all four dyads in polar benzonitrile, and also occurs in the single-bridged dyads in nonpolar toluene. The process was found to be substantially faster and more efficient in the dyads containing the 1,7-regioisomer, both for the singly- and double-bridged molecules. In the case of the single-bridged dyads, SB-1,7-PDI-C60 and SB-1,6-PDI-C60, different relaxation pathways of their charge-separated states have been discovered. To the best of our knowledge, this is the first observation of photoinduced electron transfer in PDI-C60 dyads in a nonpolar medium.

Excited-state interaction of red and green perylene diimides with luminescent Ru(II) polypyridine complex.

Three new perylene diimide (PDI)-based ligands have been synthesized by the covalent attachment of dipyrido[a,c]phenazine moiety to one of the bay-positions of PDI, while the second position has been substituted with either a 4-tert-butylphenoxy or a pyrrolidinyl group to obtain two types of chromophores, Ph-PDI and Py-PDI, respectively, with distinct properties. In the case of Py-PDI, the resultant 1,7- and 1,6-regioisomers have been successfully separated by column chromatography and characterized by (1)H NMR spectroscopy. The ligands have been employed to prepare donor-acceptor-based ensembles incorporating the covalently linked PDI and Ru(II) polypyridine complex as the acting chromophores. A comprehensive study of the excited-state photodynamics of the ensembles has been performed by means of electrochemical and steady state and time-resolved spectroscopic methods. Although, in all the three ensembles, the photoexcitation of either chromophore resulted in a long-lived triplet excited state of PDI ((3)PDI) as the final excited state, the photochemical reactions leading to the triplet states were found to be essentially different for the two types of the ensembles. In the case of the Ph-PDI-based ensemble, the excitation of either chromophore leads to the electron transfer from the Ru(II) complex to Ph-PDI, whereas for the Py-PDI-based ensembles, the electron transfer is observed in the opposite direction and only when the Ru(II) complex is excited. The difference in the behavior was rationalized based on electrochemical study of the compounds, which has shown that the Ph-PDI chromophore is a better electron acceptor and the Py-PDI chromophores are relatively better electron donors. This study shows a chemical approach to control the photoreactions in PDI-based dichromophoric ensembles including the possibility to switch the direction of the photoinduced electron transfer.

Supramolecular assemblies of bay-substituted perylene diimides in solution and on a solid substrate.

Perylene diimides (PDIs) substituted with a terpyridine moiety at the bay-region have been synthesized. These building blocks were used to construct supramolecular complexes in chloroform. A dimer and a trimer were built via the bay-region complexation with zinc. The PDI compounds were further modified to have silane anchors and PDI self-assembled monolayers (SAMs) were prepared on a quartz substrate. Complexation of metal ions was also done on the surface, and this was observed clearly in the absorption spectrum. These studies on the surface show possible progress in the study of supramolecular multilayer structures.

Degradation of Structurally Modified Polylactide under the Controlled Composting of Food Waste.

The degradation of polylactide (PLA) films of different structures under conditions of controlled composting has been studied. We have demonstrated that PLA underwent degradation within one month in a substrate that simulated standard industrial composting. Regardless of the initial structure of the samples, the number-average molecular weight (Mn) decreased to 4 kDa while the degree of crystallinity increased to about 70% after 21 days of composting. Addition of an inoculant to the standard substrate resulted in the accelerated degradation of the PLA samples for one week due to an abiotic hydrolysis. These findings have confirmed that industrial composting could solve the problem of plastic disposal at least for PLA.

Azafullerene C59N-phthalocyanine dyad: synthesis, characterisation and photoinduced electron transfer.

The synthesis of a new azafullerene C(59)N-phthalocyanine (Pc) dyad is described. The key step for the synthesis of the C(59)N-Pc dyad was the formation of the C(59)N-based carboxylic acid, which was smoothly condensed with hydroxy-modified Pc. The structure of the C(59)N-Pc dyad was verified by (1)H and (13)C NMR spectroscopy, IR spectroscopy, UV/Vis spectroscopy and MS measurements. The photophysical and electrochemical properties of the C(59)N-Pc dyad were investigated in both polar and non-polar solvents by steady state and time-resolved photoluminescence and absorption spectroscopy, as well as by cyclic voltammetry. Different relaxation pathways for the photoexcited C(59)N-Pc dyad, as a result of changing the solvent polarity, were found, thus giving rise to energy-transfer phenomena in non-polar toluene and charge-transfer processes in polar benzonitrile. Finally, the detailed quenching mechanisms were evaluated and compared with that of a C(60)-Pc dyad, which revealed that the different excited-state energies and reduction potentials of the two fullerene spheres (i.e. C(59)N vs. C(60)) strongly diverged in the deactivation pathways of the excited states of the corresponding phthalocyanine dyads.

Photoinduced Electron Transfer in a Porphyrin-Fullerene Dyad at a Liquid Interface.

The excited-state properties of an amphiphilic porphyrin-fullerene dyad and of its porphyrin analogue adsorbed at the dodecane/water interface are investigated by using surface second-harmonic generation. Although the porphyrin is formally centrosymmetric, the second-harmonic spectra of both compounds are dominated by the intense Soret band of the porphyrin. Polarization-selective measurements and molecular dynamics simulations suggest an angle of about 45° between the donor-acceptor axis and the interfacial plane, with the porphyrin interacting mostly with the nonpolar phase. Time-resolved measurements reveal a marked concentration dependence of the dynamics of both compounds upon Q-band excitation, indicating the occurrence of intermolecular quenching processes. The significant differences in dynamics and spectra between the dyad and the porphyrin analogue are explained by a self-quenching of the excited dyad via an intermolecular electron transfer.

Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis.

Biological activity regulation by protein post-translational modification (PTM) is critical for cell function, development, differentiation, and survival. Dysregulation of PTM proteins is present in various pathological conditions, including rheumatoid arthritis (RA). RA is a systemic autoimmune disease that primarily affects joints, and there are three main types of protein PTMs associated with the development of this disease, namely, glycosylation, citrullination, and carbamylation. Glycosylation is important for the processing and presentation of antigen fragments on the cell surface and can modulate immunoglobulin activity. The citrullination of autoantigens is closely associated with RA, as evidenced by the presence of antibodies specific to citrullinated proteins in the serum of patients. Carbamylation and dysregulation have recently been associated with RA development in humans.In this study, we performed an overview analysis of proteins with post-translational modifications associated with the development of RA adverted in peer-reviewed scientific papers for the past 20 years. As a result of the search, a list of target proteins and corresponding amino acid sequences with PTM in RA was formed. Structural characteristics of the listed modified proteins were extracted from the Protein Data Bank. Then, molecular dynamics experiments of intact protein structures and corresponding structures with PTMs were performed regarding structures in the list announced in the ProtDB service. This study aimed to conduct a molecular dynamics study of intact proteins and proteins, including post-translational modification and protein citrullination, likely associated with RA development. We observed another exhibition of the fundamental physics concept, symmetry, at the submolecular level, unveiled as the autonomous repetitions of outside the protein structural motif performance globule corresponding to those in the whole protein molecule.

Self-assembled cellulose nanofiber-carbon nanotube nanocomposite films with anisotropic conductivity.

In this study, a nanocellulose-based material showing anisotopic conductivity is introduced. The material has up to 1000 times higher conductivity along the dry-line boundary direction than along the radial direction. In addition to the material itself, the method to produce the material is novel and is based on the alignment of cationic cellulose nanofibers (c-CNFs) along the dry-line boundary of an evaporating droplet composed of c-CNFs in two forms and conductive multi-walled carbon nanotubes (MWCNTs). On the one hand, c-CNFs are used as a dispersant of MWCNTs, and on the other hand they are used as an additional suspension element to create the desired anisotropy. When the suspended c-CNF is left out, and the nanocomposite film is manufactured using the high energy sonicated c-CNF/MWCNT dispersion only, conductive anisotropy is not present but evenly conducting nanocomposite films are obtained. Therefore, we suggest that suspending additional c-CNFs in the c-CNF/MWCNT dispersion results in nanocomposite films with anisotropic conductivity. This is a new way to obtain nanocomposite films with substantial anisotropic conductivity.

Correction: Addressing challenges in the removal of unbound dye from passively labelled extracellular vesicles.

[This corrects the article DOI: 10.1039/D1NA00755F.].