Supramolecular Self-organization Research Articles

Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes

It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin's role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.

Synthesis, Supramolecular Self-Organization, and Thermal Behavior of the Double Three-Dimensional Pseudo-Polymer Complex [Au{S2CN(CH2)6}2]4[Ag5Cl9] Comprising the New Type Silver(I) Anion

Synthesis, Supramolecular Self-Organization, and Thermal Behavior of the Double Three-Dimensional Pseudo-Polymer Complex [Au{S2CN(CH2)6}2]4[Ag5Cl9] Comprising the New Type Silver(I) Anion

Mechanisms of formation of wear-resistant dissipative structures in non-stationary lubrication conditions

The work aimed to determine the influence of the processes of supramolecular self-organization in the lubricating layer on the patterns of wear of friction pairs. The mechanisms of structural adaptability of tribocoupler elements were analyzed, and the regularities of the manifestation of a large-scale and energy jump, which characterizes the transition of the tribosystem to a metastable state, were determined. An evaluation of the tribotechnical characteristics of commercial transmission oils was carried out on a software-hardware complex that, using a roller analogy, simulates the operation of gears in conditions of rolling with slipping. It was established that the activation of contact surfaces in the mode of frequent starts and stops leads to active interaction of the lubricant's components and the metal's surface layers with the gradual formation of boundary adsorption layers. For transmission oil 'Bora B' T-Shyp, an increase in anti-friction properties has been established due to the effective lubricating ability of the oil when forming the hydro- and non-hydrodynamic components of the lubricating layer thickness. The effect of the chemical activity of the zinc dialkyl dithiophosphate antiwear additive and the hydrocarbon components of the base of transmission oils on the effectiveness of the formation of boundary films is considered. It was determined that the formation of stable boundary films of the lubricant is the leading process in manifesting their damping properties concerning the localization of elastic-plastic deformation along the depth of the metal. When boundary films are formed on 90-95% of the contact area, the change in the microstructure of the near-surface layers is fixed at a depth of up to 20 microns; when boundary films are formed on 20...50% of the surface area, the spread of elastic-plastic deformation reaches a depth of up to 50 microns. The kinetics of the formation of boundary films by the lubricant and the indicators of the specific work of friction in contact are correlated with the intensity of wear of the contact surfaces

AMMONIUM AMPHIPHILES BASED ON NATURAL COMPOUNDS: DESIGN, SYNTHESIS, PROPERTIES AND BIOMEDICAL APPLICATIONS. A REVIEW

This review analyzes and systematizes data for the last three years on the use of amphiphilic quaternary ammonium compounds (QAC) based on natural structures in the search for new antibacterial and anticancer agents. As part of the analysis, publications on the properties of QAC based on heterocyclic and pyridine alkaloids, alkylated phenols, terpenoids, and steroids were considered. Attempts have been made to reveal the relationship between the structure of ammonium salts and their supramolecular self-organization, biological activity, and cytotoxicity. From the point of view of ease of chemical modification, availability, biorelevance and effectiveness against pathogen bacterial strains and antitumor activity, prospects for the use of natural platforms for extended trials have been identified.

Double Pseudopolymeric [Au{S2CN(CH2)5}2]2[Ag2Cl4]·CH2Cl2 Complex: Preparation, Principles of Supramolecular Self-Assembly, Thermal Behavior, and Biological Activity against Mycolicibacterium smegmatis Strain

The double Au(III)–Ag(I) complex crystallizing as the solvated form of [Au{S2CN(CH2)5}2]2[Ag2Cl4]· CH2Cl2 (I) was obtained by the reaction of silver(I) N,N-pentamethylenedithiocarbamate with a solution of Na[AuCl4]/5.15 M NaCl. According to X-ray diffraction data (CIF file CCDC no. 2062810), the structural units of the compound are nonequivalent [Au{S2CN(CH2)5}2]+ cations (noncentrosymmetric A and centrosymmetric B and C in a ratio of 2 : 1 : 1), cyclic tetrachlorodiargentate(I) anions, [Ag2Cl4]2–, and solvating CH2Cl2 molecule. The latter is retained in the structure due to two nonequivalent C–H···Cl hydrogen bonds formed with the cyclic [Ag2Cl4]2– anion involving its terminal Cl(1) and bridging Cl(2) chlorine atoms. The supramolecular self-organization of I is based on a system of multiple Ag···S and Cl···S secondary interactions that сombine the ionic structural units of the complex into an intricate two-dimensional pseudopolymer layer. A study of the thermal behavior of I by simultaneous thermal analysis established the conditions for quantitative reduction of bound gold(III) and silver(I). The studied Au(III)–Ag(I) compound exhibits a high level of biological activity against the nonpathogenic M. smegmatis strain.

Preparation, Supramolecular Self-Organization (Construction of 2D Pseudopolymer Architecture), 13C and 15N CP/MAS NMR, and Thermal Behavior of the Double Au(III)–Hg(II) Complex [Au(S2CNBui2)2]2[Hg2Cl6

Preparation, Supramolecular Self-Organization (Construction of 2D Pseudopolymer Architecture), 13C and 15N CP/MAS NMR, and Thermal Behavior of the Double Au(III)–Hg(II) Complex [Au(S2CNBui2)2]2[Hg2Cl6

Bacterial Cell Wall Analogue Peptides Control the Oligomeric States and Activity of the Glycopeptide Antibiotic Eremomycin: Solution NMR and Antimicrobial Studies.

For some time, glycopeptide antibiotics have been considered the last line of defense against Methicillin-resistant Staphylococcus aureus (MRSA). However, vancomycin resistance of Gram-positive bacteria is an increasingly emerging worldwide health problem. The mode of action of glycopeptide antibiotics is essentially the binding of peptidoglycan cell-wall fragments terminating in the d-Ala-d-Ala sequence to the carboxylate anion binding pocket of the antibiotic. Dimerization of these antibiotics in aqueous solution was shown to persist and even to enhance the antibacterial effect in a co-operative manner. Some works based on solid state (ss) Nuclear Magnetic Resonance (NMR) studies questioned the presence of dimers under the conditions of ssNMR while in a few cases, higher-order oligomers associated with contiguous back-to-back and face-to-face dimers were observed in the crystal phase. However, it is not proved if such oligomers persist in aqueous solutions. With the aid of 15N-labelled eremomycin using 15N relaxation and diffusion NMR methods, we observed tetramers and octamers when the N-Ac-d-Ala-d-Ala dipeptide was added. To the contrary, the N-Ac-d-Ala or (N-Ac)2-l-Lys-d-Ala-d-Ala tripeptide did not induce higher-order oligomers. These observations are interesting examples of tailored supramolecular self-organization. New antimicrobial tests have also been carried out with these self-assemblies against MRSA and VRE (resistant) strains.

Enhanced Ordering and Efficient Photoalignment of Nanostructures in Block Copolymers Enabled by Halogen Bond

Fabrication and manipulation of macroscopically ordered nanostructures in polymer films via supramolecular self-organization are fascinating from the viewpoints of science and technology. Here, a h...

Macromolecular Effect Stabilized Color-Tunable and Room Temperature Charge-Transfer Complexes Based on Donor–Acceptor Assemblies

We report one of the first examples of room temperature stable solid-state charge transfer (CT) complexes based on a segmented π-conjugated polymer and rylene diimide donor–acceptor system having tunable optical transitions from the visible to NIR region in the solar spectrum. Semicrystalline and amorphous segmented oligo-phenylenevinylene (OPV) chromophore containing polymers were tailor-made with flexible polymethylene chains in the backbone. The electron rich segmented OPV polymers were complexed with two electron-deficient diimides based on naphthalene (NDI) and phenylene (PDI) core. The binary complexes of segmented OPV polymers and rylene diimides produced unique classes of CT complexes based on OPV-NDI and OPV-PDI chromophore diads. Electron microscope, polarizing microscope, and X-ray diffraction analyses provided direct evidence for the two-dimensional lamellar packing of D–A self-assembly in the solid state. Detailed absorption and emission photophysical studies revealed that the donor OPV polymers and acceptor chromophores exhibited a 1:1 complex with respect to the long-range order of D–A–D–A–D–A π-stacked supramolecular assemblies. The role of the macromolecular effect on the CT complexation was further investigated using structurally identical OPV monomers. The monomer OPV-NDI complexes (or PDI complexes) were found to exhibit CT complex in the solution; however, they underwent uncontrollable phase separation into their individual D and A crystalline domains and lost their CT self-assembly in the solid state. Interestingly, the macromolecular effect driven supramolecular self-organization of long chain segmented OPV polymers produced stable CT complexes both in solution and solid state under ambient conditions. Segmented OPV polymer + PDI and segmented OPV polymer + NDI complexes were produced as red and green colored CT complexes, respectively. This enabled the accomplishment of room temperature stable CT complexes in π-conjugated polymers having absorption ranging from 350 to 1100 nm. These donor–acceptor CT self-assemblies are processable into thin films under solvent free melt crystallization process; thus, the present segmented polymer design strategy opens up a platform for donor–acceptor CT complexes.

Spontaneous Resolution and Super-coiling in Xerogels of the Products of Photo-Induced Formose Reaction.

This work addresses the supramolecular self-organization in the xerogels of formose reaction products. The UV-induced formose reaction was held in over-saturated formaldehyde solutions at 70∘C without a catalyst. The solutions of the obtained carbohydrates were dried on a glass slide, and the obtained xerogels demonstrated a prominent optical activity, while the initial solutions were optically inactive. The xerogels contained highly elongated crystalline elements of a helical structure as well as the isometric ones. Thus xerogel formation was accompanied by a spontaneous resolution of enantiomers and separation of different-shaped supramolecular structures. The thick helices were twisted of thinner ones, while the latter were twisted of elementary structures having a diameter much smaller than 400 nm. Similar structural hierarchy is typical of biological macromolecules (DNA, proteins, and cellulose). Summarizing the obtained results, we proposed a hypothetical mechanism explaining the amplification of the initial enantiomeric excess, as well as chiral and chemical purification of the substances which were essential for the evolution of Life to start.

Binding of Gold(III) from Solutions with Thallium(I) Dibutyldithiocarbamate: Synthesis, Supramolecular Self-Organization, and Thermal Behavior of the Complex ([Au{S2CN(C4H9)2}2][TlCl4])n

The binding of gold(III) from solution in a 2 M HCl with thallium(I) dibutyl dithiocarbamate leads to the formation of ion-polymeric complex ([Au{S2CN(C4H9)2}2][TlCl4])n, which was studied by (13С, 15N) MAS NMR spectroscopy and X-ray diffraction analysis. In the complex comprising the nonequivalent cations [Au{S2CN(C4H9)2}2]+ (A and B) and anions [TlCl4]–, the supramolecular self-assembly is provided by secondary bonds Au···S and S···Cl. The former are involved in the formation of isomeric binuclear cations [А···А] and [В···В] that build the (···[А···А]···[В···В]···)n polymeric chain; the latter selectively combine the thallium(III) anions and the dimeric cations. Thermolysis of the complex is accompanied by gold recovery and release of TlCl.

Three-Dimensional Polymeric Thallium(I) Morpholinedithiocarbamate [Tl2{S2CN(CH2)4O}2] n and Its Capability of Binding Gold(III) from Solutions: Chemisorption Synthesis of a Heteronuclear Gold(III)–Thallium(III) Complex of the Ionic Type, ([Au{S2CN(CH2)4O}2][TlCl4]) n , the Role of Secondary Interactions Tl…O, Tl…S, and Au…S in the Supramolecular Self-Organization, 13C MAS NMR, and Thermal Behavior

Crystalline polymeric thallium(I) morpholinedithiocarbamate [Tl2{S2CN(CH2)4O}2]n (I) and the heteronuclear ion–polymeric gold(III)–thalium(III) complex ([Au{S2CN(CH2)4O}2][TlCl4])n (II) are prepara ...

Synthesis, Supramolecular Self-Organization, and Thermal Behavior of Gold(III)–Thallium(III) Heteronuclear Complexes ([Au{S2CN(CH3)2}2][TlCl4])2 and ([Au{S2CN(C2H5)2}2][TlCl4]) n

The interaction of polymeric thallium(I) dimethyl- and diethyldithiocarbamates with [AuCl4]– in 2 M HCl has been studied. Heteropolynuclear complexes ([Au{S2CN(CH3)2}2][TlCl4])2 (I) and ([Au{S2CN(C2H5)2}2][TlCl4]) n (II) have been preparatively isolated from chemisorption systems [Tl2{S2CNR2}2] n –Au3+/2 M HCl (R = CH3, C2H5). These compounds have been characterized by 13C CP/MAS NMR, and their crystal and supramolecular structures have been determined by X-ray crystallography. Basic structural units of compounds I and II are square-planar [Au{S2CNR2}2]+ cations (with S,S'- bidentate coordination of two Dtc ligands to the gold atom) and distorted tetrahedral [TlCl4]–anions. In supramolecular self-organization, the decisive role is played by relatively weak secondary interactions Au⋯S and Au⋯Cl. With the use of simultaneous thermal analysis, the thermal behavior of I and II have been studied, which enabled the elucidation of temperature-induced transformations and identification of TlCl and reduced gold among the thermolysis products.

Supramolecular Self-Organization of Fullerene Derivatives in Solutions Studied by Pulsed Field Gradient NMR Technique

Self-organization of a series of differently functionalized fullerene derivatives in solvents of different polarity was investigated by pulsed field gradient nuclear magnetic resonance on 1H, 19F and 31P nuclei. The hydrodynamic diameters were calculated for each fullerene derivative-solvent system on the basis of Stokes–Einstein model. It was shown that fullerene derivatives comprising no polar groups do not undergo any noticeable aggregation in carbon bisulfide, deutereted chloroform and toluene-d8. The particle diameters of 1.2–1.4 nm revealed for these solutions were very close to the van der Waals diameter of the fullerene derivative molecules. The fullerene derivatives comprising polar –COOH, –COOK and –P(O)(OH)2 groups appended to the carbon cage undergo self-assembling in solutions. The diameters of the formed clusters varied from 2.2 to 9.6 nm depending on the solvent and the temperature. The strongest tendency to self-assembling was revealed for water soluble fullerene derivatives in aqueous solutions where, presumably, water molecules are also incorporated in the structure of the clusters.

Computing of the Molecular Orientation State of the Lubrication Layer

The algorithm and software for computing the order parameter value describing structural sequence in the molecular model of the boundary lubrication layer have been created. It has been shown that computer estimation of a supramolecular self-organization together with a new method of polarization tribometry can enhance the efficiency of new lubrication composition creation.

Preparation, supramolecular self-organization and thermal behavior of polymeric complex of composition ([Au{S2CN(C3H7)2}2]3[Bi3Cl12]) n with unusual geometry of bismuth(III) complex anion

A reaction of freshly precipitated bismuth(III) N,N-dipropyldithiocarbamate (PDtc) with AuCl3 solution in 2 M HCl was studied. A heteropolynuclear gold(III)-bismuth complex of ionic type [Au{S2CN(C3H7)2}2]3[Bi3Cl12] (I) was isolated by crystallization of products of the heterogeneous reaction from acetone-chloroform (1: 1) solution. Crystal and supramolecular structure of compound I established by X-ray diffraction study includes structurally nonequivalent complex cations [Au{S2CN(C3H7)2}2]+ related to each other as conformers (hereinafter cations A, B, C, and D) in 1: 1: 2: 2 ratio. Due to secondary Au⋯S bonds (3.386–3.617 A), the isomeric cations form trinuclear species of two types: [C⋯A⋯C] and [D⋯B⋯D] that differ in the character of intercationic binding and Au-Au distances. Relatively weak aurophilic Au⋯Au bonds (3.4704(3) A) unite the neighboring cationic triads into zigzag polymeric chains of type (⋯[C⋯A⋯C]⋯[D⋯B⋯D]⋯)n oriented along the crystallographic axis b. The spatial isolation of neighboring chains is provided by discrete trinuclear anions [Bi3Cl12]3− where metal atoms bind four bridging (μ2 and μ3) chlorine atoms, while each bismuth atom forms distorted octahedral chromophore [BiCl6]. The complex tribismuth anion in the structure I is the first example of [Bi3Cl12]3− anion of angle rather than linear structure: Bi(1)Bi(2)Bi(3) angle is 72.358°. The thermal behavior of compound I was studied by simultaneous thermal analysis. The multistage process of thermal destruction includes the thermolysis of dithiocarbamate portion of the complex and [Bi3Cl12]3− accompanied by reduction of gold(III) to metal and release of BiCl3 (followed by its evaporation) and partial formation of Bi2S3. In the temperature range 680–760°C, bismuth sulfide undergoes oxidation to (BiO)2SO4, which decomposes above 760°C to give Bi2O3. Residue after thermolysis of compound I is gold metal and bismuth(III) oxide.

Fabrication of nanofibres with azopyridine compounds in various acids and solvents

Supramolecular self-organization behaviours of one azopyridine compound were systematically studied in a series of inorganic acids and various organic solvents.

Ostwald's rule of stages governs structural transitions and morphology of dipeptide supramolecular polymers.

The self-assembly of molecular building blocks into nano- and micro-scale supramolecular architectures has opened up new frontiers in polymer science. Such supramolecular species not only possess a rich set of dynamic features as a consequence of the non-covalent nature of their core interactions, but also afford unique structural characteristics. Although much is now known about the manner in which such structures adopt their morphologies and size distributions in response to external stimuli, the kinetic and thermodynamic driving forces that lead to their transformation from soluble monomeric species into ordered supramolecular entities have remained elusive. Here we focus on Boc-diphenylalanine, an archetypical example of a peptide with a high propensity towards supramolecular self-organization, and describe the pathway through which it forms a range of nano-assemblies with different structural characteristics. Our results reveal that the nucleation process is multi-step in nature and proceeds by Ostwald's step rule through which coalescence of soluble monomers leads to the formation of nanospheres, which then undergo ripening and structural conversions to form the final supramolecular assemblies. We characterize the structures and thermodynamics of the different phases involved in this process and reveal the intricate nature of the transitions that can occur between discrete structural states of this class of supramolecular polymers.

The role of Zundel-like ions in the supramolecular self-organization of porphyrin assemblies

Aggregates mainly consisting of mono-protonated meso-tetraphenylporphine (TPP) dimers and water self-assembled from the dimers in 0.4N aqueous HCl with 0.86molL−1 tetrahydrofuran have been investigated by means of infrared spectroscopy (IR), electronic absorption spectroscopy, and scanning electron microscopy (SEM). IR studies using deuterium labeling of small-size protonated water clusters located in the cage between TPP in the dimers allow for the assignment of a doublet at 2993, 3009cm−1 to stretching vibrations of H⋯ODH and H⋯O+DH, respectively. In the absence of heavy water in the thin film a doublet at 982, 1000cm−1 with the same energy gap of 16–18cm−1 is identified with proton sharing in the OH+⋯O moiety of the cluster. The main features of the dimers, which provide their hydration, are the protonated N groups of pyrrole rings observed in the IR near 1486cm−1 that are involved in the conjugated π-system of the porphyrin macrocycle. Stabilization of the electronic structure in the mono-protonated dimers occurs by H5O2+ ions present in the cage between TPP units and charge delocalization through hydrogen bonding. It is proposed that together with the cooperative structure of the cluster the H5O2+ ions are responsible for efficient self-assembling and self-organization of the highly ordered aggregates obtained. Based on surface studies a molecular mechanism for proton mobility is suggested to explain the origin of a slanting cross with the angle of 55°±3°, half the tetrahedral angle, on the surface of the aggregates in the solid state. Estimated proton hopping times of within 6.4–7.9ps supports this molecular mechanism.

Polymeric gold(I) diisobutyl dithiophosphate, [Au2{S2P(O-iso-C4H9)2}2]n: Synthesis, supramolecular self-organization (a role of aurophilic interaction), 13C and 31P MAS NMR spectroscopy, and thermal behavior

A new polymeric gold(I) diisobutyl dithiophosphate (Dtph), [Au2{S2P(O-iso-C4H9)2}2]n (I), was preparatively obtained and characterized by 13C and 31P MAS NMR spectroscopy and X-ray diffraction (CIF file CCDC no. 977818). Diagrams of the χ2 statistic were constructed from the complete 31P MAS NMR spectra and used to calculate the 31P chemical shift anisotropy (δaniso = δzz − δiso) and the asymmetry parameter η = (δyy − δxx)/(δzz − δiso). The main structural unit of complex I is the noncentrosymmetric dinuclear molecule [Au2{S2P(O-iso-C4H9)2}2], in which the gold atoms are linked by two bridging ligands Dtph. The central cyclic structural fragment of the dimer [Au2S4P2] is additionally stabilized by the intramolecular aurophilic interaction Au⋯Au. Further supramolecular self-organization of the complex involves intermolecular aurophilic bonds Au⋯Au that serve to unite adjacent dinuclear molecules [Au2{S2P(O-iso-C4H9)2}2] with different spatial orientations into the polymer chains ([Au2{S2P(O-iso-C4H9)2}2])n. The thermal behavior of complex I was examined by synchronous thermal analysis under argon. The character of the thermolysis of the complex to reduced metallic gold as a final product was determined.