Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry

Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.

Effect of fibers on starch structural changes during hydrothermal treatment: multiscale analyses, and evaluation of dilution effects on starch digestibility

BACKGROUND

Dietary fibers (DFs) may influence the structural, nutritional and techno-functional properties of starch within food systems. Moreover, DFs have favorable effects on the digestive system and potentially a lower glycemic index. These potential benefits may change depending on DF type. Starch processed in the presence of soluble and insoluble fibers can undergo different structural and functional changes, and the present study investigated the effects of short-chain and long-chain inulin and cellulose on the structural and digestive properties of wheat starch.

RESULTS

The combined use of differential scanning calorimetry, Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) provided insights into the structural changes in starch and inulin at different levels. Short-chain and long-chain inulin had higher water retention capacity and a potential to limit starch gelatinization. The FTIR results revealed an interaction between starch and inulin. Scanning electron microscopy analysis showed morphological changes in starch and inulin after the hydrothermal treatment. Cellulose fiber was not affected by the hydrothermal treatment and had no influence on starch behavior. The structural differences observed through XRD, FTIR and scanning electron microscopy analyses between starch with and without inulin fibers did not significantly impact starch digestibility, except for the dilution effect caused by adding DFs.

CONCLUSION

The present study highlights the importance of utilizing different analytical tools to assess changes in food samples at different scales. Although short-chain and long-chain inulin could potentially limit starch gelatinization, the duration of the heat treatment (90 °C for 10 min) was sufficient to ensure complete starch gelatinization. The dilution effect caused by adding fibers was the primary reason for the effect on starch digestibility. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Biomimetic Materials Based on Poly-3-hydroxybutyrate and Chlorophyll Derivatives

Electrospinning of biomimetic materials is of particular interest due to the possibility of producing flexible layers with highly developed surfaces from a wide range of polymers. Additionally, electrospinning is characterized by a high simplicity of implementation and the ability to modify the produced fibrous materials, which resemble structures found in living organisms. This study explores new electrospun materials based on polyhydroxyalkanoates, specifically poly-3-hydroxybutyrate, modified with chlorophyll derivatives. The research investigates the impact of chlorophyll derivatives on the morphology, supramolecular structure, and key properties of nonwoven materials. The obtained results are of interest for the development of new flexible materials with low concentrations of chlorophyll derivatives.

Testing the Performance of the Azo-Polyimide Supramolecular Systems as Substrate for Sensors Based on Platinum Electrodes

Azo-polyimide films with supramolecular structure were obtained by casting onto glass plates a mixture based on polyamidic acid and different quantities of azochromophore, followed by thermal treatment to realize the final azo-polyimide structure. The dielectric characteristics of the supramolecular structure of polymer films were investigated by broad-band dielectric spectroscopy measurements at different temperatures and frequencies. The free-standing films proved to be flexible and tough and maintained their integrity after repeated bending. The work of adhesion at the polymer/platinum interface was calculated after the evaluation of the surface energy parameters before and after plasma treatment. Atomic force microscopy was used to image the surface morphology, the evolution of the roughness parameters, and the adhesion force between the platinum-covered tip and the polymer surface, registered at the nanoscale with the quantity of the azo dye introduced in the system. The simulation of the columnar growth of a platinum layer was made to provide information about the deposition parameters that should be used for optimal results in the deposition of platinum electrodes for sensors.

Structure and Performance of All-Green Electrospun PHB-Based Membrane Fibrous Biomaterials Modified with Hemin

This work addresses the challenges concerning the development of "all-green" high-performance biodegradable membrane materials based on poly-3-hydroxybutyrate (PHB) and a natural biocompatible functional additive, iron-containing porphyrin, Hemin (Hmi) via modification and surface functionalization. A new facile and versatile approach based on electrospinning (ES) is advanced when modification of the PHB membranes is performed by the addition of low concentrations of Hmi (from 1 to 5 wt.%). Structure and performance of the resultant {HB/Hmi membranes were studied by diverse physicochemical methods, including differential scanning calorimetry, X-ray analysis, scanning electron microscopy, etc. Modification of the PHB fibrous membranes with Hmi allows control over their quality, supramolecular structure, morphology, and surface wettability. As a result of this modification, air and liquid permeability of the modified electrospun materials markedly increases. The proposed approach provides preparation of high-performance all-green membranes with tailored structure and performance for diverse practical applications, including wound healing, comfort textiles, facial protective masks, tissue engineering, water and air purification, etc.

Supramolecular Structure and Photo-Thermo-Electric Property of Hydrogen-Bonded Liquid Crystalline Polymer Containing Poly(4-vinylpridine) and Cyanostilbene Side Chains

A series of side-chain liquid crystalline polymers P4VP(CN-DBE)_x , where x is the molar ratio of cyanostilbene (CN-DBE) to poly(4-vinylpyridine) (P4VP) repeating unit, was synthesized based on the intermolecular hydrogen bonding between P4VP and CN-DBE. Their luminescent property, liquid crystalline structure and photo-thermo-electric property were elucidated using photoluminescence spectra, X-ray diffraction, thermal imaging and thermoelectric experiments. With the increase of x, the supramolecular system can be changed from lamellar structure to hexagonal columnar structure. Moreover, the P4VP(CN-DBE)_x polymer with columnar structure exhibits more efficient photothermal effect. The temperature of P4VP(CN-DBE)_0.6 can rise to 130 °C within 10 s under the irradiation of ultraviolet lamp. In addition, the supramolecular system possesses unique photo-thermo-electric conversion ability, and 25 mA current can be detected in the circuit coupled with the thermoelectric module. This work broadens the potential applications of hydrogen-bonded polymer, and provides a simple and facile strategy to prepare liquid crystalline polymers with photo-thermo-electric property.

Supramolecular Structure and Mechanical Performance of κ-Carrageenan-Gelatin Gel

In this work, by means of complex physicochemical methods the structural features of a composite κ-carrageenan–gelatin system were studied in comparison with initial protein gel. The correlation between the morphology of hydrogels and their mechanical properties was demonstrated through the example of changes in their rheological characteristics. The experiments carried out with PXRD, SAXS, AFM and rheology approaches gave new information on the structure and mechanical performance of κ-carrageenan–gelatin hydrogel. The combination of PXRD, SAXS and AFM results showed that the morphological structures of individual components were not observed in the composite protein–polysaccharide hydrogels. The results of the mechanical testing of initial gelatin and engineered κ-carrageenan–gelatin gel showed the substantially denser parking of polymer chains in the composite system due to a significant increase in intermolecular protein–polysaccharide contacts. Close results were indirectly followed from the SAXS estimations—the driving force for the formation of the common supramolecular structural arrangement of proteins and polysaccharides was the increase in the density of network of macromolecular chains entanglements; therefore, an increase in the energy costs was necessary to change the conformational rearrangements of the studied system. This increase in the macromolecular arrangement led to the growth of the supramolecular associate size and the growth of interchain physical bonds. This led to an increase in the composite gel plasticity, whereas the enlargement of scattering particles made the novel gel system not only more rigid, but also more fragile.

Domain Structure, Thermal and Mechanical Properties of Polycaprolactone-Based Multiblock Polyurethane-Ureas under Control of Hard and Soft Segment Lengths

A series of multiblock polyurethane-ureas (PUU) based on polycaprolactone diol (PCL) with a molecular mass of 530 or 2000 g/mol, as well as hard segments of different lengths and structures, were synthesized by the step-growth polymerization method. The chemical structure of the synthesized multiblock copolymers was confirmed by IR- and NMR-spectroscopy. Differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) were used to determine the relaxation and phase transition temperatures for the entire series of the obtained PUU. The X-ray diffraction (XRD) method made it possible to identify PUU compositions in which the crystallizability of soft segments (SS) is manifested due to their sufficient length for self-organization and structuring. Visualization of the crystal structure and disordering of the stacking of SS with an increase in their molecular mobility during heating are shown using optical microscopy. The change in the size of the hard phase domains and the value of the interdomain distance depending on the PCL molecular mass, as well as the length and structure of the hard block in the synthesized PUU, were analyzed using small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The evolution of the domain structure upon passing through the melting and crystallization temperatures of PUU soft blocks was studied using SANS. The studies carried out made it possible to reveal the main correlations between the chemical structure of the synthesized PUU and their supramolecular organization as well as thermal and mechanical properties.

Biodegradable Polymer Materials Based on Polyethylene and Natural Rubber: Acquiring, Investigation, Properties

The growing amount of synthetic polymeric materials is a great environmental problem that has to be solved as soon as possible. The main factor aggravating this problem is the abundance of products made from traditional synthetic polymer, such as packaging materials, cases, containers and other equipment with a short period of use, which quickly turns into polymer waste that pollutes the ecosystem for decades. In this paper, we consider the possibility of solving this problem by the development of biodegradable compositions based on polyolefins and elastomers. The addition of a natural component (natural rubber) to the matrix of the synthetic polymeric (polyethylene) leads to the significant changes in structure and properties of the material. Different aspects of mixing semicrystalline and amorphous polymers are discussed in the article. It was shown that addition of 10-50% wt. of the elastomers to the synthetic polymer increases wettability of the material, slightly reduces the mechanical properties, significantly affects the supramolecular structure of the crystalline phase of polyethylene and initiates microbiological degradation. In particular, in this work, the acquisition, structure and properties of biodegradable binary composites based on low-density polyethylene (LDPE) and natural rubber (NR) were studied. It has been shown that such compositions are biodegradable in soil under standard conditions.

Effect of the Hemin Molecular Complexes on the Structure and Properties of the Composite Electrospun Materials Based on Poly(3-hydroxybutyrate)

The creation of innovative fibrous materials based on biodegradable semicrystalline polymers and modifying additives is an urgent scientific problem. In particular, the development of biomedical materials based on molecular complexes and biopolymers with controlled properties is of great interest. The paper suggests an approach to modifying the structure and properties of the composite materials based on poly(3-hydroxybutyrate) (PHB) obtained by the electrospinning method using molecular complexes of hemin. The introduction of 1-5 wt. % of hemin has a significant effect on the supramolecular structure, morphology and properties of PHB-based fibers. Changes in the supramolecular structure intensified with the increasing hemin concentration. On the one hand, a decrease in the fraction of the crystalline phase by 8-10% was observed. At the same time, there is a decrease in the density of the amorphous phase by 15-70%. Moreover, the addition of hemin leads to an improvement in the strength characteristics of the material: the elongation at break increased by 1.5 times, and in the tensile strength, it increased by 3 times. The antimicrobial activity of the hemin-containing composite materials against Escherichia coli and Staphylococcus aureus was confirmed. The obtained materials are proposed to be used in the creation of composite systems for regenerative medicine.

Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry

Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.

Unveiling the self-association and desolvation in crystal nucleation

As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent-solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute-solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute-solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

The Investigation of the Structure and Properties of Ozone-Sterilized Nonwoven Biopolymer Materials for Medical Applications

Nowadays, the development and research of nonwoven medical fibrous materials based on biopolymers is an area of a great practical interest. One of the most promising methods for producing nonwoven materials with a highly developed surface is electrospinning (ES). In this article, the possibility of efficient sterilization of ultrathin fibers based on polyhydroxybutyrate (PHB) by ozone treatment was considered. The purpose of this work was to select the most optimal morphology of nonwoven materials for medical purposes and to establish the correlation between the supramolecular structure and the physical properties of fibrous materials while under the influence of an ozone sterilization process.

CD Imaging at High Spatial Resolution at Diamond B23 Beamline: Evolution and Applications

Circular Dichroism imaging in the 190–650 nm spectral region pionered at Diamond Light Source B23 beamline, has been made possible by the highly collimated microbeam generated at the beamline and has been used to study the homogeneity of the supramolecular structures of thin films of chiral materials deposited on fused quartz substrates. This facility has been expanded with the installation of a Mueller Matrix Polarimeter, MMP, coupled to the beamlight, of which a preliminary data will be discussed. In the solid state, the measurement of CD related to the supramolecular structure is hampered by the presence of circular birefringence, linear dichroism, and linear birefringence that can only be evaluated using the MMP technique. The ability to characterize the chiroptical property of thin chiral films prepared under a variety of conditions and protocols such as drop cast, spin coating, spray at different temperatures and concentrations will enable the determination of the critical parameters for reproducible, uniform and homogeneous specimen preparation, which is the sine qua non for any commercial application. This is of particular importance for optoelectronic materials, but it can also be extended to a broad variety of materials with applications from biosensors to biological tissues.

Peptide-Tetrapyrrole Supramolecular Self-Assemblies: State of the Art

The covalent and noncovalent association of self-assembling peptides and tetrapyrroles was explored as a way to generate systems that mimic Nature's functional supramolecular structures. Different types of peptides spontaneously assemble with porphyrins, phthalocyanines, or corroles to give long-range ordered architectures, whose structure is determined by the features of both components. The regular morphology and ordered molecular arrangement of these systems enhance the photochemical properties of embedded chromophores, allowing applications as photo-catalysts, antennas for dye-sensitized solar cells, biosensors, and agents for light-triggered therapies. Chemical modifications of peptide and tetrapyrrole structures and control over the assembly process can steer the organization and influence the properties of the resulting system. Here we provide a review of the field, focusing on the assemblies obtained from different classes of self-assembling peptides with tetrapyrroles, their morphologies and their applications as innovative functional materials.

IR Study on Cellulose with the Varied Moisture Contents: Insight into the Supramolecular Structure

The following article is the first attempt to investigate the supramolecular structure of cellulose with the varied moisture content by the means of Fourier-transform and near infrared spectroscopy techniques. Moreover, authors aimed at the detailed and precise presentation of IR spectra interpretation approach in order to create a reliable guideline for other researchers. On the basis of obtained data, factors indicating biopolymer crystallinity and development of hydrogen interactions were calculated and the peaks representing hydrogen bonding (7500-6000 cm-1, 3700-3000 cm-1, and 1750-1550 cm-1) were resolved using the Gaussian distribution function. Then, the deconvoluted signals have been assigned to the specific interactions occurring at the supramolecular level and the hydrogen bond length, as well bonding-energy were established. Furthermore, not only was the water molecules adsorption observed, but also the possibility of the 3OH⋯O5 intramolecular hydrogen bond shortening in the wet state was found-from (27,786 ± 2) 10-5 nm to (27,770 ± 5) 10-5 nm. Additionally, it was proposed that some deconvoluted signals from the region of 3000-2750 cm-1 might be assigned to the hydroxyl group-incorporated hydrogen bonding, which is, undoubtedly, a scientific novelty as the peak was not resolved before.

Nickel(II) complexes based on L-amino-acid-derived ligands: synthesis, characterization and study of the role of the supramolecular structure in carbon dioxide capture

The formation of the symmetrical μ3-carbonate-bridged self-assembled trinuclear NiII complex Na2{[Ni(LO)2(H2O)]3(μ3-CO3)} (LO is the carboxylate anion of a L-tyrosine derivative), involves atmospheric CO2 uptake. The asymmetric unit of the complex comprises an octahedral coordination for the NiII with two L-tyrosine-based ligands, a water molecule and one O atom of the carbonate bridge. The Ni3-μ3-CO3 core in this compound is the first reported of this kind according to the Cambridge Structural Database (CSD). The supramolecular structure is mainly sustained by hydrogen bonds developed by the phenolic functionality of the L-tyrosine moiety of one ligand and the carboxylate group of a neighbouring ligand. The crystal packing is then characterized by three interpenetrated supramolecular helices associated with a diastereoisomer of the type R-supP, which is essential for the assembly process. Magnetic susceptibility and magnetization data support weak ferromagnetic exchange interactions within the novel Ni3-μ3-CO3 core. The NiII complex obtained under the same synthetic conditions but using the analogous ligand derived from the amino acid L-phenylalanine instead of L-tyrosine gives rise to to a mononuclear octahedral system. The results obtained for the different complexes demonstrate the role of the supramolecular structure regarding the CO2 uptake property for these NiII-amino-acid-based systems.

Protein Supramolecular Structures: From Self-Assembly to Nanovaccine Design

Life-inspired protein supramolecular assemblies have recently attracted considerable attention for the development of next-generation vaccines to fight against infectious diseases, as well as autoimmune diseases and cancer. Protein self-assembly enables atomic scale precision over the final architecture, with a remarkable diversity of structures and functionalities. Self-assembling protein nanovaccines are associated with numerous advantages, including biocompatibility, stability, molecular specificity and multivalency. Owing to their nanoscale size, proteinaceous nature, symmetrical organization and repetitive antigen display, protein assemblies closely mimic most invading pathogens, serving as danger signals for the immune system. Elucidating how the structural and physicochemical properties of the assemblies modulate the potency and the polarization of the immune responses is critical for bottom-up design of vaccines. In this context, this review briefly covers the fundamentals of supramolecular interactions involved in protein self-assembly and presents the strategies to design and functionalize these assemblies. Examples of advanced nanovaccines are presented, and properties of protein supramolecular structures enabling modulation of the immune responses are discussed. Combining the understanding of the self-assembly process at the molecular level with knowledge regarding the activation of the innate and adaptive immune responses will support the design of safe and effective nanovaccines.

Synthesis and Characterization of Novel Nanoporous Gl-POSS-Branched Polymeric Gas Separation Membranes

Novel nanoporous Gl-POSS-branched polymers based on the macroinitiator of anionic nature, 2,4-toluene diisocyanate, and octaglycidyl polyhedral oligomeric silsesquioxane (Gl-POSS) were obtained as gas separation membranes. The synthesis of polymers was carried out using various loads of Gl-POSS. It was found that the main reaction proceeding with 2,4-toluene diisocyanate is the polyaddition, accompanied by the isocyanate groups opening of the carbonyl part. This unusual opening of isocyanate groups leads to the formation of coplanar acetal nature polyisocyanates (O-polyisocyanate). The terminal O-polyisocyanate links initiate the subsequent opening of the epoxide rings in Gl-POSS. As a result, Gl-POSS serves as a hard and bulky branching agent and creates the specific framing supramolecular structure, which leads to the formation of nanopores in the polymer, where the flexible polyether components are located inside the cavities. Thermal, mechanical, physical, and chemical properties of the obtained polymers were studied at various Gl-POSS contents in the polymer matrix. It was found that these polymers show high selectivity of gas transport properties for pure ammonia relative to nitrogen and hydrogen at ambient temperature. Measurements showed that the gas permeability coefficients and the values of ideal selectivity were in a non-additive dependence to the Gl-POSS content.

Solvent-triggered single-crystal-to-single-crystal transformation from a monomeric to polymeric copper(II) complex based on an aza macrocyclic ligand

Reversible solvent-triggered single-crystal-to-single-crystal (SCSC) transformations are observed between two copper(II) azamacrocyclic complexes: [Cu(C₁₆H₃₈N₆)(H₂O)₂](C₁₂H₆O₄) (1) and [Cu(C₁₆H₃₈N₆)(C₁₂H₆O₄)] (2). Complex (1) was prepared via self-assembly of a copper(II) azamacrocyclic complex containing butyl pendant groups, [Cu(C₁₆H₃₈N₆)(ClO₄)₂], with 2,7-naphthalenedicarboxylic acid. When monomeric compound (1) was immersed in CH₃OH, coordination polymer (2) was obtained, indicating a solvent-triggered SCSC transformation. Furthermore, when (2) was immersed in water, an reverse SCSC transformation from (2) to (1) occurred. Complex (1) presents a 3D supramolecular structure formed via intermolecular hydrogen-bonding interactions, whereas complex (2) features a 1D zigzag coordination polymer. The reversible SCSC transformation of (1) and (2) was characterized using single-crystal X-ray diffraction and in situ powder X-ray diffraction techniques. Despite its poor porosity, complex (2) displayed interesting CO₂ adsorption behaviour under CO₂ gas.

Phase Structure Recording in a Nematic Side-Chain Liquid-Crystalline Polymer

Dye-doped nematic side-chain liquid-crystalline polymers possess extraordinary large optical nonlinearity and ability to store the induced orientational deformations in a glassy state, which makes them a very promising material for photonic applications. In this study, the phase structures were generated and recorded in the bulk of a 50-μm layer of a nematic liquid-crystalline side-chain polymer, containing polyacrylate backbone, spacer having five methylene groups, and phenyl benzoate mesogenic fragment. The polymer was doped with KD-1 azodye. The director field deformations induced by the light beam close to the TEM₀₁ mode were studied for different geometries of light–polymer interaction. The phase modulation depth of 2π was obtained for the 18-μm spacing between intensity peaks. The experimental data were analyzed based on the elastic continuum theory of nematics. The possibility to induce and record positive and negative microlenses in the polymer bulk was shown experimentally.

Supramolecular insight into the substitution of sulfur by selenium, based on crystal structures, quantum-chemical calculations and biosystem recognition

Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-H...Se and C-H...S interactions (∼80%), notably less numerous are structures with Se...Se and S...S interactions (∼5%), and Se...π and S...π interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-H...Se (∼-0.8 kcal mol^-1) and C-H...S interactions are weaker than the most stable parallel interaction (∼-3.3 kcal mol^-1) and electrostatic interactions of σ/π type (∼-2.6 kcal mol^-1). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-H...Se (∼-4.4 kcal mol^-1) and N-H...Se interactions (∼-2.2 kcal mol^-1) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

The structural unit of melanin in the cell wall of the fungal pathogen Cryptococcus neoformans

Melanins are synthesized macromolecules that are found in all biological kingdoms. These pigments have a myriad of roles that range from microbial virulence to key components of the innate immune response in invertebrates. Melanins also exhibit unique properties with potential applications in physics and material sciences, ranging from electrical batteries to novel therapeutics. In the fungi, melanins, such as eumelanins, are components of the cell wall that provide protection against biotic and abiotic elements. Elucidation of the smallest fungal cell wall-associated melanin unit that serves as a building block is critical to understand the architecture of these polymers, its interaction with surrounding components, and their functional versatility. In this study, we used isopycnic gradient sedimentation, NMR, EPR, high-resolution microscopy, and proteomics to analyze the melanin in the cell wall of the human pathogenic fungus Cryptococcus neoformans We observed that melanin is assembled into the cryptococcal cell wall in spherical structures ∼200 nm in diameter, termed melanin granules, which are in turn composed of nanospheres ∼30 nm in diameter, termed fungal melanosomes. We noted that melanin granules are closely associated with proteins that may play critical roles in the fungal melanogenesis and the supramolecular structure of this polymer. Using this structural information, we propose a model for C. neoformans' melanization that is similar to the process used in animal melanization and is consistent with the phylogenetic relatedness of the fungal and animal kingdoms.

Analysis of Cellulose and Lignocellulose Materials by Raman Spectroscopy: A Review of the Current Status

This review is a summary of the Raman spectroscopy applications made over the last 10 years in the field of cellulose and lignocellulose materials. This paper functions as a status report on the kinds of information that can be generated by applying Raman spectroscopy. The information in the review is taken from the published papers and author's own research-most of which is in print. Although, at the molecular level, focus of the investigations has been on cellulose and lignin, hemicelluloses have also received some attention. The progress over the last decade in applying Raman spectroscopy is a direct consequence of the technical advances in the field of Raman spectroscopy, in particular, the application of new Raman techniques (e.g., Raman imaging and coherent anti-Stokes Raman or CARS), novel ways of spectral analysis, and quantum chemical calculations. On the basis of this analysis, it is clear that Raman spectroscopy continues to play an important role in the field of cellulose and lignocellulose research across a wide range of areas and applications, and thereby provides useful information at the molecular level.

Formation of Stable Supramolecular Structure with β-Lactoglobulin-Derived Self-Assembling Peptide f1-8 and Bovine Micellar Caseins

The development of stable macromolecular structures with tailored functional properties in the dairy industry using innovative stabilizers is of great interest. The self-assembling peptide f1-8 (Pf1-8) derived from β-lactoglobulin was found to interact with whey proteins, consequently changing their physicochemical properties. The objective of the present work was to evaluate the interaction between Pf1-8 and micellar casein (CN) and the changes in their physicochemical properties and stability at different pH values (6.6-2.6) on model solutions containing CN and Pf1-8 at various ratios (1:1, 5:1, and 10:1) using spectrofluorimetry, TEM, SEC-HPLC, and SDS-PAGE analyses. No CN precipitation occurred for the solution at the 1:1 ratio even at pH values below 4.6. In all samples, CN was completely dissociated to primary casein particles (PCP) to form stable supramolecular structures strongly bound to peptide gels via hydrophobic interactions. Thus, a novel milk-protein-derived peptide responsible for stabilizing complex structures composed of CN was discovered.

Soft-Matter Approaches for Controlling Food Protein Interactions and Assembly

Animal- and plant-based proteins are present in a wide variety of raw and processed foods. They play an important role in determining the final structure of food matrices. Food proteins are diverse in terms of their biological origin, molecular structure, and supramolecular assembly. This diversity has led to segmented experimental studies that typically focus on one or two proteins but hinder a more general understanding of food protein structuring as a whole. In this review, we propose a unified view of how soft-matter physics can be used to control food protein assembly. We discuss physical models from polymer and colloidal science that best describe and predict the phase behavior of proteins. We explore the occurrence of phase transitions along two axes: increasing protein concentration and increasing molecular attraction. This review provides new perspectives on the link between the interactions, phase transitions, and assembly of proteins that can help in designing new food products and innovative food processing operations.

Design of two series of 1:1 cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine and carboxylic acids

Two series of a total of ten cocrystals involving 4-amino-5-chloro-2,6-dimethylpyrimidine with various carboxylic acids have been prepared and characterized by single-crystal X-ray diffraction. The pyrimidine unit used for the cocrystals offers two ring N atoms (positions N1 and N3) as proton-accepting sites. Depending upon the site of protonation, two types of cations are possible [Rajam et al. (2017). Acta Cryst. C73, 862-868]. In a parallel arrangement, two series of cocrystals are possible depending upon the hydrogen bonding of the carboxyl group with position N1 or N3. In one series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine-3-bromothiophene-2-carboxylic acid (1/1), 1, 4-amino-5-chloro-2,6-dimethylpyrimidine-5-chlorothiophene-2-carboxylic acid (1/1), 2, 4-amino-5-chloro-2,6-dimethylpyrimidine-2,4-dichlorobenzoic acid (1/1), 3, and 4-amino-5-chloro-2,6-dimethylpyrimidine-2-aminobenzoic acid (1/1), 4, the carboxyl hydroxy group (-OH) is hydrogen bonded to position N1 (O-H...N1) of the corresponding pyrimidine unit (single point supramolecular synthon). The inversion-related stacked pyrimidines are doubly bridged by the carboxyl groups via N-H...O and O-H...N hydrogen bonds to form a large cage-like tetrameric unit with an R₄²(20) graph-set ring motif. These tetrameric units are further connected via base pairing through a pair of N-H...N hydrogen bonds, generating R₂²(8) motifs (supramolecular homosynthon). In the other series of cocrystals, i.e. 4-amino-5-chloro-2,6-dimethylpyrimidine-5-methylthiophene-2-carboxylic acid (1/1), 5, 4-amino-5-chloro-2,6-dimethylpyrimidine-benzoic acid (1/1), 6, 4-amino-5-chloro-2,6-dimethylpyrimidine-2-methylbenzoic acid (1/1), 7, 4-amino-5-chloro-2,6-dimethylpyrimidine-3-methylbenzoic acid (1/1), 8, 4-amino-5-chloro-2,6-dimethylpyrimidine-4-methylbenzoic acid (1/1), 9, and 4-amino-5-chloro-2,6-dimethylpyrimidine-4-aminobenzoic acid (1/1), 10, the carboxyl group interacts with position N3 and the adjacent 4-amino group of the corresponding pyrimidine ring via O-H...N and N-H...O hydrogen bonds to generate the robust R₂²(8) supramolecular heterosynthon. These heterosynthons are further connected by N-H...N hydrogen-bond interactions in a linear fashion to form a chain-like arrangement. In cocrystal 1, a Br...Br halogen bond is present, in cocrystals 2 and 3, Cl...Cl halogen bonds are present, and in cocrystals 5, 6 and 7, Cl...O halogen bonds are present. In all of the ten cocrystals, π-π stacking interactions are observed.

Supramolecular arrangement and photophysical properties of a dinuclear cyanophenylboronic acid ester

Boronic esters are useful building blocks for crystal engineering and the generation of supramolecular architectures, including macrocycles, cages and polymers (one-, two- and three-dimensional), with potential utility in diverse fields such as separation, storage and luminescent materials. The novel dinuclear cyanophenylboronic ester described herein, namely 4,4'-(2,4,8,10-tetraoxa-3,9-diboraspiro[5.5]undecane-3,9-diyl)dibenzonitrile, C₁₉H₁₆B₂N₂O₄, was prepared by condensation of 4-cyanophenylboronic acid and pentaerythritol and fully characterized by elemental analysis, IR and NMR (¹H and ¹¹B) spectroscopy, single-crystal X-ray diffraction analysis and TG-DSC (thermogravimetry-differential scanning calorimetry) studies. In addition, the photophysical properties were examined in solution and in the solid state by UV-Vis and fluorescence spectroscopies. Density functional theory (DFT) calculations with ethanol as solvent reproduced reasonably well the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) of the title compound. Hirshfeld surface and fingerprint plot analyses are presented to illustrate the supramolecular connectivity in the solid state.

Surface Adatom Mediated Structural Transformation in Bromoarene Monolayers: Precursor Phases in Surface Ullmann Reaction

Structural transformations of supramolecular systems triggered by external stimuli maintain great potential for application in the fabrication of molecular storage devices. Using combined ultrahigh vacuum scanning tunneling microscopy, X-ray photoemission spectroscopy, and density functional theory calculations, we observed the surface adatom mediated structural transformation from 4,4''-dibromo- m-terphenyl (DMTP)-based halogen-bonded networks to DMTP-Cu(Ag) coordination networks on Cu(111) and Ag(111) at low temperatures. The halogen-bonded networks, which were formed on Cu(111) at 97 K and on Ag(111) at 93 K, consist of intact DMTP molecules stabilized by triple Br···Br bonds. The DMTP-Cu(Ag) coordination networks form on Cu(111) at 113 K and on Ag(111) at 103 K. They contain alternatingly arranged intact DMTP molecules and Cu(Ag) adatoms stabilized by weak C-Br···Cu(Ag) coordination bonds. Annealing the DMTP-Ag structure to 333 K leads to the initiation of C-Br bond scission. This observation suggests that the DMTP-Ag coordination network represents the intermediate phase ready for dehalogenation, which is the first step of the surface Ullmann reaction.

Orthogonal Operation of Constitutional Dynamic Networks Consisting of DNA-Tweezer Machines

Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate the principle of the nature processes. The CDNs comprise dynamically interconvertible equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four interconvertible and mechanically triggered tweezers, AA', BB', AB' and BA', existing in closed, closed, open, and open configurations, respectively. By subjecting the CDN to auxiliary triggers, the guided stabilization of one of the network constituents dictates the dynamic reconfiguration of the structures of the tweezers constituents. The orthogonal and reversible operations of the CDN DNA tweezers are demonstrated, using T-A·T triplex or K⁺-stabilized G-quadruplex as structural motifs that control the stabilities of the constituents. The implications of the study rest on the possible applications of input-guided CDN assemblies for sensing, logic gate operations, and programmed activation of molecular machines.

On the Control of Chromophore Orientation, Supramolecular Structure, and Thermodynamic Stability of an Amphiphilic Pyridyl-Thiazol upon Lateral Compression and Spacer Length Variation

The supramolecular structure essentially determines the properties of organic thin films. Therefore, it is of utmost importance to understand the influence of molecular structure modifications on supramolecular structure formation. In this article, we demonstrate how to tune molecular orientations of amphiphilic 4-hydroxy thiazole derivatives by means of the Langmuir-Blodgett (LB) technique and how this depends on the length of an alkylic spacer between the thiazole chromophore and the polar anchor group. Therefore, we characterize their corresponding supramolecular structures, thermodynamic, absorption, and fluorescence properties. Particularly, the polarization-dependence of the fluorescence is analyzed to deduce molecular orientations and their possible changes after annealing, i.e., to characterize the thermodynamic stability of the individual solid state phases. Because the investigated thiazoles are amphiphilic, the different solid state phases can be formed and be controlled by means of the Langmuir-Blodgett (LB) technique. This technique also allows to deduce atomistic supramolecular structure motives of the individual solid phases and to characterize their thermodynamic stabilities. Utilizing the LB technique, we demonstrate that subtle molecular changes, like the variation in spacer length, can yield entirely different solid state phases with distinct supramolecular structures and properties.

Efficient resolution of venlafaxine and mechanism study via X-ray crystallography

Numbers of resolving factors were investigated to improve resolution of venlafaxine 1. An effective resolving agent, O,O'-di-p-toluoyl-(R, R)-tartaric acid 2, was screened using similar method of 'Dutch resolution' from tartaric acid derivatives. The resolution efficiency was up to 88.4%, when the ratio of rac-1 and 2 was 1:0.8 in THF with little water (10:1 v/v). Enantiomerically pure venlafaxine was prepared with 99.1% ee in 82.2% yield. The chiral resolution mechanism was first explained through X-ray crystallographic study. One diastereomeric salt with well solubility forms a columnar supramolecular structure as the acidic salt (R)-1·2, while the other diastereomeric salt with less solubility forms a multilayered sandwich supramolecular structure by enantio-differentiation self-assembly as the neutral salt 2(S)-1·2. The water molecules play a key role in the optical resolution, as indicated by the special structures of the diastereomeric salts.

Bulk Oriented UHMWPE/FMWCNT Films for Tribological Applications

Bulk oriented films based on ultrahigh molecular weight polyethylene (UHMWPE) with a drawing ratio of 35 were prepared by using a low solvent concentration. Bulk oriented films were filled with fluorinated multi-walled carbon nanotubes (FMWCNTs). The structure of bulk oriented films on UHMWPE, which were manufactured at different stages of orientation, was investigated by scanning electron microscope (SEM) and differential scanning calorimetry (DSC). The addition of FMWCNTs at a concentration of 0.05 wt % in bulk oriented UHMWPE films led to an increase in the tensile strength by 10% (up to 1020 ± 23 MPa) compared to unfilled oriented films. However, the addition of FMWCNTs at a concentration of more than 0.5 wt % led to a decrease in tensile strength due to excessive accumulation of nanotubes and hindering of self-diffusion of UHMWPE macromolecules. The multiple increase in tensile strength, doubling the hardness, the formation of fibrillar structure, and the presence of carbon nanotubes led to a significant increase in tribological properties in bulk oriented films. Bulk oriented UHMWPE/1% FMWCNT films can be operated at a maximum contact pressure that is 18 times higher and exhibit a specific wear rate more than an order of magnitude and less than the traditional UHMWPE of isotropic structure. Bulk oriented UHMWPE/1% FMWCNT films have an extremely low dry coefficient of friction (COF) of 0.075 at a contact pressure of 31 MPa. The developed bulk oriented films can be used for manufacturing frictional surfaces for sliding bearings, or for acetabular cups for knee and hip endoprostheses.

Complexes of nickel(II) and copper(II) with 1,2,4-triazole-3-carboxylic acid and of cobalt(III) with 3-amino-1,2,4-triazole-5-carboxylic acid

Because of their versatile coordination modes and strong coordination ability for metals, triazole ligands can provide a wide range of possibilities for the construction of metal-organic frameworks. Three transition-metal complexes, namely bis(μ-1,2,4-triazol-4-ide-3-carboxylato)-κ³N²,O:N¹;κ³N¹:N²,O-bis[triamminenickel(II)] tetrahydrate, [Ni₂(C₃HN₃O₂)₂(NH₃)₆]·4H₂O, (I), catena-poly[[[diamminediaquacopper(II)]-μ-1,2,4-triazol-4-ide-3-carboxylato-κ³N¹:N⁴,O-[diamminecopper(II)]-μ-1,2,4-triazol-4-ide-3-carboxylato-κ³N⁴,O:N¹] dihydrate], {[Cu₂(C₃HN₃O₂)₂(NH₃)₄(H₂O)₂]·2H₂O}_n, (II), (μ-5-amino-1,2,4-triazol-1-ide-3-carboxylato-κ²N¹:N²)di-μ-hydroxido-κ⁴O:O-bis[triamminecobalt(III)] nitrate hydroxide trihydrate, [Co₂(C₃H₂N₄O₂)(OH)₂(NH₃)₆](NO₃)(OH)·3H₂O, (III), with different structural forms have been prepared by the reaction of transition metal salts, i.e. NiCl₂, CuCl₂ and Co(NO₃)₂, with 1,2,4-triazole-3-carboxylic acid or 3-amino-1,2,4-triazole-5-carboxylic acid hemihydrate in aqueous ammonia at room temperature. Compound (I) is a dinuclear complex. Extensive O-H...O, O-H...N and N-H...O hydrogen bonds and π-π stacking interactions between the centroids of the triazole rings contribute to the formation of the three-dimensional supramolecular structure. Compound (II) exhibits a one-dimensional chain structure, with O-H...O hydrogen bonds and weak O-H...N, N-H...O and C-H...O hydrogen bonds linking anions and lattice water molecules into the three-dimensional supramolecular structure. Compared with compound (I), compound (III) is a structurally different dinuclear complex. Extensive N-H...O, N-H...N, O-H...N and O-H...O hydrogen bonding occurs in the structure, leading to the formation of the three-dimensional supramolecular structure.

Sequence-Mandated, Distinct Assembly of Giant Molecules

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collective hydrogen bonding and the sequence-mandated topology of the molecules. These results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.

The Supramolecular Buildup of Eumelanin: Structures, Mechanisms, Controllability

Research on the supramolecular buildup of eumelanin has gained high momentum in the last years. Several new aspects regarding the involved structures and mechanisms have been established, which has led to a better understanding of the entire process. This review intends to provide a clearly laid-out summary of previous and new findings regarding structures, mechanisms, and controllability. With respect to materials applications, the aspect of controllability is of supreme importance. A focus of this review is therefore set on a novel method with high potential for specific synthesis of various, isolated particle morphologies. Finally, open questions and possibilities for their elucidation are discussed.

The supramolecular structure of bone: X-ray scattering analysis and lateral structure modeling

The evolution of vertebrates required a key development in supramolecular evolution: internally mineralized collagen fibrils. In bone, collagen molecules and mineral crystals form a nanocomposite material comparable to cast iron in tensile strength, but several times lighter and more flexible. Current understanding of the internal nanoscale structure of collagen fibrils, derived from studies of rat tail tendon (RTT), does not explain how nucleation and growth of mineral crystals can occur inside a collagen fibril. Experimental obstacles encountered in studying bone have prevented a solution to this problem for several decades. This report presents a lateral packing model for collagen molecules in bone fibrils, based on the unprecedented observation of multiple resolved equatorial reflections for bone tissue using synchrotron small-angle X-ray scattering (SAXS; ∼1 nm resolution). The deduced structure for pre-mineralized bone fibrils includes features that are not present in RTT: spatially discrete microfibrils. The data are consistent with bone microfibrils similar to pentagonal Smith microfibrils, but are not consistent with the (nondiscrete) quasi-hexagonal microfibrils reported for RTT. These results indicate that collagen fibrils in bone and tendon differ in their internal structure in a manner that allows bone fibrils, but not tendon fibrils, to internally mineralize. In addition, the unique pattern of collagen cross-link types and quantities in mineralized tissues can be can be accounted for, in structural/functional terms, based on a discrete microfibril model.

Fibonacci Sequence and Supramolecular Structure of DNA

We proposed a new model of supramolecular DNA structure. Similar to the previously developed by us model of primary DNA structure [11-15], 3D structure of DNA molecule is assembled in accordance to a mathematic rule known as Fibonacci sequence. Unlike primary DNA structure, supramolecular 3D structure is assembled from complex moieties including a regular tetrahedron and a regular octahedron consisting of monomers, elements of the primary DNA structure. The moieties of the supramolecular DNA structure forming fragments of regular spatial lattice are bound via linker (joint) sequences of the DNA chain. The lattice perceives and transmits information signals over a considerable distance without acoustic aberrations. Linker sequences expand conformational space between lattice segments allowing their sliding relative to each other under the action of external forces. In this case, sliding is provided by stretching of the stacked linker sequences.

Two novel ferrocenyl dipeptide-like compounds generated via the Ugi four-component reaction

The Ugi four-component reaction, a powerful method for the synthesis of diverse dipeptide-like derivatives in combinatorial chemistry, was used to synthesize (S)-1'-{N-[1-(anthracen-9-yl)-2-(tert-butylamino)-2-oxoethyl]-N-(4-methoxyphenyl)carbamoyl}ferrocene-1-carboxylic acid dichloromethane disolvate, [Fe(C6H5O2)(C33H31N2O3)]·2CH2Cl2, (I), and (S)-2-(anthracen-9-yl)-N-tert-butyl-2-[N-(4-methylphenyl)ferrocenylformamido]acetamide, [Fe(C5H5)(C33H31N2O2)], (II). They adopt broadly similar molecular conformations, with near-eclipsed cyclopentadienyl rings and near-perpendicular amide planes in their dipeptide-like chains, one of which is almost coplanar with its attached cyclopentadienyl ring but perpendicular to the aromatic ring bound to the N atom. In the supramolecular structure of (I), a two-dimensional network is constructed based on molecular dimers and a combination of intermolecular O-H···O, N-H···O and C-H···O hydrogen bonds, forming R2(2)(11), R2(2)(16), R2(2)(22) and C(9) motifs. These two-dimensional networks are connected by C-H···O and C-H···Cl contacts to create a three-dimensional framework, where one dichloromethane solvent molecule acts as a bridge between two neighbouring networks. In the packing of (II), classical hydrogen bonds are absent and an infinite one-dimensional chain is generated via a combination of C-H···O hydrogen bonds and C-H···π interactions, producing a C(7) motif. This work describes a simple synthesis and the supramolecuar structures of ferrocenyl dipeptide-like compounds and is significant in the development of redox-active receptors.

Synthesis and crystal structures of two coordination polymers and a binuclear cadmium(II) complex containing 3- and 4-aminobenzoate ligands

Due to their wide range of coordination modes and versatile conformations when binding to metal atoms, multicarboxylate ligands are of interest in the design of metal-organic frameworks (MOFs). Three Cd(II) complexes, namely catena-poly[diammonium [[chloridocadmium(II)]-di-μ-chlorido-[chloridocadmium(II)]-bis(μ-3-aminobenzoato)-κ(3)N:O,O';κ(3)O,O':N]], {(NH4)[CdCl2(C7H6NO2)]}n, (I), catena-poly[[[aquacadmium(II)]-bis(μ-4-aminobenzoato)-κ(3)N:O,O';κ(3)O,O':N] monohydrate], {[Cd(C7H6NO2)2(H2O)]·H2O}n, (II), and di-μ-acetato-κ(4)O:O'-bis[(4-aminobenzoato-κ(2)O,O')(2,2'-bipyridine-κ(2)N,N')cadmium(II)], [Cd2(CH3COO)2(C7H6NO2)2(C10H8N2)2], (III), with different stuctural forms are reported. Complex (I) has a one-dimensional ladder structure, with strong N-H···O and weak N-H···Cl hydrogen bonds linking the cations and anions in the three-dimensional supramolecular structure. Complex (II) has a one-dimensional chain structure. Extensive O-H···O and N-H···O hydrogen bonds between the anionic ligands and the solvent water molecules and π-π stacking interactions between the centroids of the benzene rings lead to the three-dimensional supramolecular structure. Complex (III) is a binuclear molecule which is extended into a three-dimensional supramolecular structure via strong N-H···O and weak C-H···O hydrogen bonds.

A new three-dimensional CdII supramolecular framework constructed from the 1-[(1H-tetrazol-5-yl)methyl]-1,4-diazoniabicyclo[2.2.2]octane ligand

A new tetrazole-metal supramolecular compound, di-μ-chlorido-bis(trichlorido{1-[(1H-tetrazol-5-yl-κN(2))methyl]-1,4-diazoniabicyclo[2.2.2]octane}cadmium(II)), [Cd2(C8H16N6)2Cl8], has been synthesized and structurally characterized by single-crystal X-ray diffraction. In the structure, each Cd(II) cation is coordinated by five Cl atoms (two bridging and three terminal) and by one N atom from the 1-[(1H-tetrazol-5-yl)methyl]-1,4-diazoniabicyclo[2.2.2]octane ligand, adopting a slightly distorted octahedral coordination geometry. The bridging bicyclo[2.2.2]octane and chloride ligands link the Cd(II) cations into one-dimensional ribbon-like N-H...Cl hydrogen-bonded chains along the b axis. An extensive hydrogen-bonding network formed by N-H...Cl and C-H...Cl hydrogen bonds, and interchain π-π stacking interactions between adjacent tetrazole rings, consolidate the crystal packing, linking the poymeric chains into a three-dimensional supramolecular network.

Packing forces in dichloridobis(3,5-diphenyl-1H-pyrazole-κN(2))cobalt(II) dichloromethane hemisolvate

The title compound, [CoCl2(C15H12N2)2]·0.5CH2Cl2, was crystallized from a binary mixture of dichloromethane and hexane and a dimeric supramolecular structure was isolated. The Co(II) centre exhibits a distorted tetrahedral geometry, with two independent pyrazole-based ligands occupying two coordination sites and two chloride ligands occupying the third and fourth coordination sites. The supramolecular structure is supported by complementary hydrogen bonding between the pyrazole NH group and the chloride ligand of an adjacent molecule. This hydrogen-bonding motif yields a ten-membered hydrogen-bonded ring. Density functional theory (DFT) simulations at the PBE/6-311G level of theory were used to probe the solid-state structure. These simulations suggest that the chelate undergoes a degree of conformational distortion from the lowest-energy geometry to allow for optimal hydrogen bonding in the solid state.

[2,5-Bis(2,2'-bipyridyl-6-yl)-3,4-diazahexa-2,4-diene]dichloridomanganese(II): from a mononuclear compound to a three-dimensional supramolecular framework through C-H···Cl hydrogen bonds and π-π stacking interactions

The title compound, [MnCl2(C24H20N6)], has been synthesized and characterized based on the multifunctional ligand 2,5-bis(2,2'-bipyridyl-6-yl)-3,4-diazahexa-2,4-diene (L). The Mn(II) centre is five-coordinate with an approximately square-pyramidal geometry. The L ligand acts as a tridendate chelating ligand. The mononuclear molecules are bridged into a one-dimensional chain by two C-H···Cl hydrogen bonds. These chains are assembled into a two-dimensional layer through π-π stacking interactions between adjacent uncoordinated bipyridyl groups. Furthermore, a three-dimensional supramolecular framework is attained through π-π stacking interactions between adjacent coordinated bipyridyl groups.

Supramolecular structures in three thiouracil derivatives: 5,6-trimethylene-2-sulfanylidene-1,2-dihydropyrimidin-4(3H)-one, 2-(4-fluorobenzylsulfanyl)-5,6-trimethylenepyrimidin-4(3H)-one and methyl 2-{[2-(4-fluorobenzylsulfanyl)-5,6-trimethylenepyrimidin-4-yl]oxy}acetate

The molecules of the title compounds, C7H8N2OS, (1), C14H13FN2OS, (2), and C17H17FN2O3S, (3), crystallize in the space groups C2/m, C2/c and Ia, respectively. Compounds (1) and (2), an S-alkylated derivative of (1), consist of only one symmetry-independent molecule, while (3), an O-alkylated derivative of (2), contains two independent molecules in the asymmetric unit. The molecules of (1) sit on crystallographic mirror planes. In the supramolecular structure of (1), a combination of N-H···O and N-H···S hydrogen bonds creates a molecular strap with C(6) and R2(2)(8) motifs, which is further stabilized by an S···S contact. In the packing of (2), a one-dimensional molecular column is made up of two kinds of dimers. One dimer, with an R2(2)(18) motif, is formed by a pair of C-H···O soft hydrogen bonds and the other, with an R2(2)(8) motif, is produced via a pair of N-H···O hard hydrogen bonds. In the packing of (3), molecules A and B form two different types of one-dimensional chain by intermolecular C-H···N hydrogen bonds, and by C···N and O···S contacts, respectively. Two such kinds of chain are connected alternately via interchain C-H···O hydrogen bonds, giving a two-dimensional sheet. Finally, a three-dimensional supramolecular structure is formed through weak intersheet C-H···F hydrogen bonds. The study of the molecular and supramolecular structures of thiouracil derivatives is significant in the development of lipoprotein-associated phospholipase A2 inhibitors.

Chlorido(2,3,7,8,12,13,17,18-octaethylporphyrinato)iron(III): a new triclinic polymorph of Fe(OEP)Cl

The previous structure determination of the title compound, [Fe(C36H44N4)Cl], was of a monoclinic polymorph [Senge (2005). Acta Cryst. E61, m399-m400]. The crystal structure of a new triclinic polymorph has been determined based on single-crystal X-ray diffraction data collected at 100 K. The asymmetric unit contains one molecule of the high-spin square-pyramidal iron(III) porphyrinate. The structure exhibits distinct nonstatistical alternative positions for most atoms and was consequently modeled as a whole-molecule disorder. The compound is characterized by an average Fe-N bond length of 2.065 (2) Å, an Fe-Cl bond length of 2.225 (4) Å, and the iron(III) cation displaced by 0.494 (4) Å from the plane of the 24-atom porphyrinate core, essentially the same as in the previously determined polymorph. Common features of the porphyrin plane-plane stacking involve two types of synthons, each of which can be further stabilized with additional H···Cl interactions to the axial chloride ligand, exhibiting concerted interactions of H atoms from the ethyl groups with the π-cloud electron density of adjacent molecules; the shortest methylene H-atom contacts are in the range 2.75-2.91 Å, resulting in plane-plane separations of 3.407 (4) and 3.416 (4) Å, and the shortest methyl H-atom contacts are 2.56-2.95 Å, resulting in plane-plane separations of 4.900 (5) and 4.909 (5) Å in the monoclinic polymorph. The plane-to-plane stacking synthons in the triclinic polymorph are similar, but at greater distances; the shortest methylene H-atom contacts are 2.86-2.94 Å, resulting in plane-plane separations of 3.45 (2) and 3.45 (3) Å, and the shortest methyl H-atom contacts are 2.89-3.20 Å, resulting in plane-plane separations of 5.081 (13) and 5.134 (13) Å, consistent with the density of the triclinic polymorph being 1.5% lower, suggesting lesser packing efficiency and lower stability in the triclinic polymorph. The major molecular differences found in the polymorphs is in three different orientations of the ethyl-group side chains on the periphery of the porphyrin core.

Comparison of N-(3,4,5-trimethoxybenzylidene)naphthalen-1-amine and its reduction product N-(3,4,5-trimethoxybenzyl)naphthalen-1-amine

The molecules in (E)-N-(3,4,5-trimethoxybenzylidene)naphthalen-1-amine, C20H19NO3, (I), and its reduction product N-(3,4,5-trimethoxybenzyl)naphthalen-1-amine, C20H21NO3, (II), are both conformationally chiral, but (I) crystallizes in a centrosymmetric space group, while (II) crystallizes with just one conformational enantiomer in each crystal. A combination of two C-H···O hydrogen bonds links the molecules of (I) into sheets containing a single type of R(6)(6)(44) ring, and these sheets are linked into a continuous three-dimensional array by a single π-π stacking interaction. The molecules of (II) are linked into complex sheets by a combination of N-H···O, C-H···O and C-H···π(arene) hydrogen bonds.

4-Oxo-N-phenyl-4H-chromene-2-carboxamide and of a new polymorph of 7-methoxy-4-oxo-N-p-tolyl-4H-chromene-2-carboxamide and its hemihydrate

4-Oxo-N-phenyl-4H-chromene-2-carboxamide, C16H11NO3, crystallizes in the space group P2(1)/n and its derivative 7-methoxy-4-oxo-N-p-tolyl-4H-chromene-2-carboxamide, C18H15NO4, forms two polymorphs which crystallize in the space groups P2(1)/c and P1. The structures have an anti-rotamer conformation about the C-N bond; however, the amide O atom can be either trans- or cis-related to the O atom of the pyran ring. The latter compound also crystallizes as a hemihydrate, C18H15NO4·0.5H2O, in the space group C2/c. This compound has a similar structure to that of the unsolvated compound.

The supramolecular structure of a cadmium complex with the new functionalized terpyridine ligand 4'-[4-(pyrimidin-5-yl)phenyl]-2,2':6',2''-terpyridine (L1): aqua(L1-κ³N,N',N'')(nitrato-κ²O,O')(nitrato-κO)cadmium(II) dihydrate

The monomeric title compound, aqua(nitrato-κ²O,O')(nitrato-κO){4'-[4-(pyrimidin-5-yl)phenyl]-2,2':6',2''-terpyridine-κ³N,N',N''}cadmium(II) dihydrate, [Cd(NO₃)₂(C₂₅H₁₇N₅)(H₂O)]·2H₂O, consists of a seven-coordinated CdII centre bound to the novel 4'-[4-(pyrimidin-5-yl)phenyl]-2,2':6',2''-terpyridine (L1) ligand (behaving as a tridentate chelate), two nitrate anions (as chelating-bidentate and monodentate ligands) and a water O atom. Both chelating groups define the base of a slightly deformed pentagonal bipyramid, while the monocoordinated ligands occupy the apices. The four heterocycles in L1 form a planar skeleton, while the central benzene ring is rotated from this planar geometry by more than 30°, probably because of packing effects. Noncovalent interactions lead to the formation of columnar arrays parallel to [100].

Intermolecular vs molecule-substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

The competition between intermolecular interactions and long-range lateral variations in the substrate-adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results.

Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil

Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 A resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35 degrees and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35 degrees instead of 18 degrees in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers.