Self-organization Of Molecules Research Articles

Modelling structure and ionic diffusion in a class of ionic liquid crystal-based solid electrolytes.

Next-generation high-efficiency Li-ion batteries require an electrolyte that is both safe and thermally stable. A possible choice for high performance all-solid-state Li-ion batteries is a liquid crystal, which possesses properties in-between crystalline solids and isotropic liquids. By employing molecular dynamics simulations together with various experimental techniques, we have designed and analyzed a novel liquid crystal electrolyte composed of rigid naphthalene-based moieties as mesogenic units, grafted to flexible alkyl chains of different lengths. We have synthesized novel highly ordered lamellar phase liquid crystal electrolytes at 99% purity and have evaluated the effect of alkyl chain length variation on ionic conduction. We find that the conductivity of the liquid crystal electrolytes is directly dependent on the extent of the nanochannels formed by molecule self-organization, which itself depends non-monotonously on the size of the alkyl chains. In addition, we show that the ion pair interaction between the anionic center of the liquid crystal molecules and the Li+ ions plays a crucial role in the overall conductivity. Based on our results, we suggest that further improvement of the ionic conductivity performance is possible, making this novel family of liquid crystal electrolytes a promising option for the design of entirely solid-state Li+ ion batteries.

Качественный и количественный анализ морфологии поверхности порфириновых пленок

The surface morphology of tetraphenylporphyrin thin polycrystalline films – H2TPP and ZnTPP obtained by vacuum condensation under quasi-equilibrium conditions is analyzed by sc. The use of analytical methods for processing images of the organic films surface obtained by standard methods, allows to identify not only qualitative, but also quantitative characteristics of the polycrystalline films structure: the average grain size, grain size distribution, the presence of texture and characteristic of crystallites orientations. It is shown that free based H2TPP tetraphenylporphyrin films have a more pronounced texture and a larger crystallite size than ZnTPP, which is due to the peculiarities of self-organization of molecules, if condensation occurs under the same conditions. The applicability of this method of image analysis for obtaining information about the structure and morphology of the surface of thin organic films during vacuum condensation is shown.

Carbazole-functionalized polyfluorenes: synthesis and conformational properties in chloroform solution and β-phase formation in copolyfluorene films

Novel copolyfluorenes (CPFs) containing 2.5 or 10 mol% of carbazole-2,7-diyl (2,7-Cz) or carbazole-3,6-diyl (3,6-Cz) derivatives in the backbone have been synthesized by means of palladium-catalyzed Suzuki polymerization under microwave irradiation. The structure of the CPF polymers was also modified by insertion of additional 2-ethylhexyl or carbazole, diaryloxadiazole, or triphenylamine units via 3,6-Cz or 2,7-Cz comonomer units in the side chains of polymers. The self-organization of molecules in chloroform solutions was investigated using light scattering and within a wide concentration interval. Analysis of the behavior of the CPFs showed that the synthesized copolymers have an increased equilibrium rigidity of molecules with a Kuhn segment length A = (10–15) nm. The A value decreases with the introduction of Cz-units into the macromolecule in the meta-position. It is shown that chemical structure of the CPFs and thermal treatment in the temperature range 60–150 °C have a dominant effect on the optoelectronic properties as well as on microstructures of their films.

Phenyl Ring: A Steric Hindrance or a Source of Different Hydrogen Bonding Patterns in Self-Organizing Systems?

A series of five alcohols (3-methyl-2-butanol, 1-cyclopropylethanol, 1-cyclopentylethanol, 1-cyclohexylethanol, and 1-phenylethanol) was used to study the impact of the size of steric hindrance and its aromaticity on self-assembling phenomena in the liquid phase. In this Letter, we have explicitly shown that the phenyl ring exerts a much stronger effect on the self-organization of molecules via the O–H···O scheme than any other type of steric hindrance, leading to a significant decline in the size and concentration of the H-bonded clusters. Given the combination of calorimetric, dielectric, infrared, and diffraction studies, this phenomenon was ascribed to its additional proton-acceptor function for the competitive intermolecular O–H···π interactions. The consequence of this is a different packing of molecules on the short- and medium-range scale.

Pyrene Associates As a New Highly Sensitive Sensor for Monitoring the Content of Silver Nanoparticles in Aqueous Media

A study is performed of the luminescence of pyrene molecules solubilized in a supramolecular ordered structure formed as a result of the self-organization of molecules of cationic surfactant cetyltrimethylammonium bromide (CTAB) in the presence of trace amounts of aggregated silver nanoparticles (NPs). The study is performed using dilute aqueous solutions of CTAB and at CTAB concentrations that exceed the critical micelle concentration. The formation of a number of pyrene associates (high-energy excimers) that glow in the short-wavelength region of the optical spectrum is observed, relative to the glow of a low-energy dimer (470 nm), and the intensity of the glow of the resulting associates depends on the concentration of silver aquasol introduced into the considered solution. The phenomenon is explained by the location of pyrene molecules near the surfaces of aggregated silver nanoparticles, which have high-density electromagnetic fields caused by surface plasmon resonance. It is found that pyrene associates can be used as sensors for determining trace amounts of silver NPs in aqueous media.

Исследование природы водородных связей в 3,5-диметилпиразоле

Compounds containing a pyrazole fragment in their structure are part of many medicines and have a wide range of bioactivity (for example, antimicrobial, anti-tuberculosis, etc.), and are also successfully used for the development of various synthetic anti-tumor agents. Interest in them is also caused by the presence of hydrogen bonds, which are the main motive for self-organization of molecules. A theoretical study of the nature of hydrogen bonds in various hydrogen-bound motifs in 3,5-dimethylpyrazole was performed using the DFT/B3LYP/6-31G(d,p) method. The results obtained indicate the possible existence of dimeric, trimeric, and tetrameric cyclic forms. Geometric and energy parameters of hydrogen bonds N-H...N are determined and the energies of donor-acceptor interaction in possible forms of self-organization of the molecules of the studied compound are calculated. It has been established that the hydrogen bond (H-bond) is the result of the interaction of a hybrid unshielded pair of a nitrogen atom of one molecule and a loosening natural orbital between the nitrogen atoms of one molecule and the hydrogen of another molecule (σ* N-H). The formation of the binding σ-orbital of the H-bond indicates the predominance of covalent interaction in the hydrogen bond. The study and analysis of the results showed that the formation of supramolecular systems of 3,5-dimethylpyrazole most likely structures are trimers and tetramers.

Thermosensitive star-shaped poly-2-ethyl-2-oxazine. Synthesis, structure characterization, conformation, and self-organization in aqueous solutions

Star-shaped four-arm poly-2-ethyl-2-oxazine with calix[4]arene core was synthesized. Molar masses of the polymer star and its arms were 7100 and 1300 g·mol−1, respectively. The self-organization of molecules in aqueous solutions was investigated using light scattering and turbidity within a wide concentration interval. At room temperature, in solutions of synthesized polymer, in addition to macromolecules, a small fraction of aggregates is observed, which result from the interactions of hydrophobic branching centers. Phase separation temperatures decrease with increase in concentration. Low critical solution temperature for the investigated star-shaped poly-2-ethyl-2-oxazine is lower than LCST for aqueous solutions of linear and star-shaped poly-2-ethyl-oxazoline and higher than that for star-shaped poly-2-isopropyl-2-oxazine with calix[4]arene core and similar molar mass.

Vinyl and phenyl terminated octasilsesquioxane thin films: Evidence for π-stacking induced self-organization of the spherically symmetrical molecules

Organosilicon compounds are surprising in the diversity of their applications as a result of the enormous diversity in their structure. Of particular interest are the self-assembling possibilities of silsesquioxane molecules leading to the formation of thin films with thicknesses not exceeding tens of nanometers. To date, only cases of self-organization of molecules with a strongly asymmetrical shape have been known. This study is aimed at obtaining confirmation of self-organization of silsesquioxane molecules in which the π-stacking interaction between arranged spherically symmetrical aromatic rings leads to the formation of a new smectic phase not observed for bulk material. For this purpose, the morphology of growth and the structure of thin octasilsesquioxane layers substituted either with vinyl or phenyl groups was compared. Due to the use of molecular beam technique for thin-film deposition under ultra-high vacuum conditions, any undesirable external influences as well as those associated with the solvent were avoided. The main measurement techniques were the X-Ray Reflectometry and Atomic Force Microscopy, which provided the final proof of the key role of aromatic rings in the self-assembly of these spherically symmetrical molecules.

Aggregation in Biocompatible Linear Block Copolymers: Computer Simulation Study

The self-organization of molecules of linear diblock copolymer poly(ethylene oxide)–polylactide and triblock copolymer polylactide–poly(ethylene oxide)–polylactide in aqueous solution is studied by the dissipative particle dynamics method, and quantitative comparison with the experimental data is performed. It is shown that the diblock copolymers are aggregated to spherical micelles, their average aggregation number increases with increasing both polymer concentration and hydrophobic block length. For the given type of molecules, the simulation results agree well with the experiment. For the case of triblock copolymers it is predicted that stable supramolecular aggregates of various morphologies exist in solution even at low concentrations.

Construction of Supramolecular Nanostructures from V-Shaped Amphiphilic Rod-Coil Molecules Incorporating Phenazine Units.

A series of bent-shaped molecules, consisting of dibenzo[a,c]phenazine and phenyl groups connected together as a rod segment, and poly(ethylene oxide) (PEO) with a degree of polymerization (DP) of 6 as the coil segment, were synthesized. The self-assembling behavior of these molecules by differential scanning calorimetry (DSC), thermal optical polarized microscopy (POM), small-angle X-ray scattering spectroscopy (SAXS), atomic force microscopy (AFM), and transmission electron microscopy (TEM), revealed that carboxyl or butoxy carbonyl groups at the 11 position of dibenzo[a,c]phenazine noticeably influence self-organization of molecules into supramolecular aggregates in bulk and aqueous solutions. Molecules 1 and 2 with chiral or non-chiral PEO coil chains and the carboxyl group at the rod segments self-organize into a hexagonal perforated lamellar structure and a hexagonal columnar structure in the solid state. In aqueous solution, molecules 1 and 2 self-assemble into diverse lengths of nanofibers, whereas molecules 3 and 4 with butoxy carbonyl groups exhibit a self-organizing capacity to form diverse sizes of spherical aggregates.

Characteristics of Intramolecular Charge Transfer by J-Aggregates in Merocyanine Dye LB Films.

In this study, for the development of future molecular electronic devices, we have investigated the characteristics of the aggregates of Langmuir-Blodgett films. The characteristics of intramolecular charge transfer by J-aggregates in merocyanine dye LB films have been studied experimentally by using UV irradiation and heat treatment. In addition to intramolecular charge transfer, we also studied the conjugation and energy changes of the molecules. In case a dye is thinned by LB method, the alkyl chain is often displaced in order to form a mono-molecular film with ease. Since the molecular association form is often made by self-organization of molecules themselves, in case the dye and the alkyl chain are strongly bonded by the covalent bond, it may be said that the properties of the LB film to be built up are almost determined at the time of synthesis of film-forming molecules. Meanwhile, since, in case LB film is fabricated by the diffusion absorption method, the cohesive force between the water-soluble dye and the surface-active mono-molecular film is electrostatic, the dye molecule can move relatively freely on the air/water interface, which may be regarded as a two-dimensional crystal growth process.

Hydrogel control of water uptake by pectins during in vitro pollen hydration of Eucalyptus globulus.

Upon pollination, dehydrated pollen grains take water out of the stigma surface, an event that constitutes the first functional checkpoint of sexual reproduction in higher plants. Little is known about possible functional connections between rehydration speed and further steps of fertilization. Here we addressed the mechanisms of water uptake control by dehydrated pollen grains. Because dehydrated cells have no energy-driven active mechanism such as membrane-based osmoregulation for controlling water movement, we tested the hypothesis that another mechanism might exist, namely, the use of hydrogel-behaving molecules. We developed an imaging protocol to visualize and quantify the rate of water entry into pollen grains of Eucalyptus globulus and tested the influence of different treatments linked to hydrogel-behaving molecules. We complemented these analyses by immunostaining pectins in the pollen grain with monoclonal antibodies JIM5 and JIM7. Water entry seemed to proceed exclusively through the germination apertures of the pollen grain, and the changes observed in different hydration media are compatible with hydrogel behavior. When JIM5 and JIM7 were used to characterize pectins on the germination apertures during hydration, pectin localization and esterification changed during hydration and were affected by the hydration solutions. These results suggest that chemical modification of the pectins may change their hydrogel behavior, thus modifying the hydration speed. The hydrogel behavior of pectins and pectin localization on apertures strongly suggest that pectins act like "valves" for water entry, enabling a regulated process of water uptake into the dehydrated pollen grain. We propose that this regulation evolved in terms of achieving the correct self-organization of molecules and cellular components to resume metabolism and pollen tube growth, especially in species that are subject to demanding environmental water stress.

Dependence of the solubility of natural flavonoids in water on the concentration of miramistin, polyvinylpyrrolidone, and human serum albumin

In organized media of the cationic surfactant miramistin and the polymers polyvinylpyrrolidone and human serum albumin, the solubility of natural flavonoids quercetin and rutin increased by one or two orders of magnitude. The increase was more significant for hydrophobic quercetin than for hydrophilic rutin. The solubility also depended on the structure and self-organization of molecules in organized media and the site of flavonoids in them. The calculated binding constants increased in the series polyvinylpyrrolidone < miramistin < human serum albumin.

A Fractal Space-Time Structure of Nonequilibrium Living Systems Is Essential Property and Fractal Property of Dynamics Systems on Cosmic Scales Is Foundation for the Origin of the Living Systems

The experimental data represented in the bibliography are theoretically analyzed to construct an adequate model for dynamics of an open nonequilibrium living system. It is shown that the viable microorganisms are capable of forming the fractal structure, whose dimensionality is certainly non-integral. In addition, we have attempted to provide a generalized description of the properties of living and nonliving matter (in the addition to that described in work [1]). Relevant published data were used to demonstrate a fractal structure of the space in the vicinity of centrally gravitating bodies with satellites revolving around them along closed trajectories and serving as a kind of testers of the neighboring space. A local violation of its discontinuity is likely to be a necessary (yet not sufficient!) dynamic characteristic of the spatiotemporal continuum for self-organization of molecules into a living, i.e., self-replicating, system.

Self-organized optical device driven by motor proteins

Protein molecules produce diverse functions according to their combination and arrangement as is evident in a living cell. Therefore, they have a great potential for application in future devices. However, it is currently very difficult to construct systems in which a large number of different protein molecules work cooperatively. As an approach to this challenge, we arranged protein molecules in artificial microstructures and assembled an optical device inspired by a molecular system of a fish melanophore. We prepared arrays of cell-like microchambers, each of which contained a scaffold of microtubule seeds at the center. By polymerizing tubulin from the fixed microtubule seeds, we obtained radially arranged microtubules in the chambers. We subsequently prepared pigment granules associated with dynein motors and attached them to the radial microtubule arrays, which made a melanophore-like system. When ATP was added to the system, the color patterns of the chamber successfully changed, due to active transportation of pigments. Furthermore, as an application of the system, image formation on the array of the optical units was performed. This study demonstrates that a properly designed microstructure facilitates arrangement and self-organization of molecules and enables assembly of functional molecular systems.

Physical Computation as Dynamics of Form that Glues Everything Together

The framework is proposed where matter can be seen as related to energy in a way structure relates to process and information relates to computation. In this scheme matter corresponds to a structure, which corresponds to information. Energy corresponds to the ability to carry out a process, which corresponds to computation. The relationship between each two complementary parts of each dichotomous pair (matter/energy, structure/process, information/computation) are analogous to the relationship between being and becoming, where being is the persistence of an existing structure while becoming is the emergence of a new structure through the process of interactions. This approach presents a unified view built on two fundamental ontological categories: Information and computation. Conceptualizing the physical world as an intricate tapestry of protoinformation networks evolving through processes of natural computation helps to make more coherent models of nature, connecting non-living and living worlds. It presents a suitable basis for incorporating current developments in understanding of biological/cognitive/social systems as generated by complexification of physicochemical processes through self-organization of molecules into dynamic adaptive complex systems by morphogenesis, adaptation and learning—all of which are understood as information processing.

Distinctive H-(RLDL)4-OH peptide complexes potentiate nanostructure self-assembling in water

thatspatial network of filaments is formed during the ionicpeptide selfassembling. The fibril structure wasshown to consist of the peptide molecules in theβsheet conformation oriented perpendicularly to thelongitudinal axis of the filament body [2]. Identification of the factors which may influence peptide molecule selforganization is a highly demanded task interms of search for new approaches to develop bothpreventative and medical treatments for amyloidosisand the diseases accompanied by accumulating theamylome and amyloid deposits in tissues and cells [1]and for designing new biomimetics for medicine, sincethey have advantages for tissue engineering [2]. Itshould be noted the crucial details of the peptide molecule selfassembling, especially the initial stages ofprotofilament formation, are not clarified yet. Thegoal of this work was to examine the conformationalcharacteristics of H⎯(RLDL)

Molecular Materials Meeting (M3@Singapore)

Organized by the Singapore A*STAR Institute of Materials Research and Engineering (IMRE), in partnership with other A*STAR institutes, the inaugural Molecular Materials Meeting (M3) held on the 10th and 11th of January 2011 in Singapore was a resounding success.Withmore than 60 talks by prominent scientists from across the globe and almost 90 poster presentations, this was an ambitious first meeting in many regards (Fig. 1). The conference also marked the inauguration of the International Year of Chemistry 2011 in Singapore. This conference was strategically named to cover a broad spectrum of materials research. The term ‘molecular materials’ puts emphasis on creating materials with new applications by studying, designing, and engineering their basic building blocks, i.e. their molecules, using chemical methods and processing techniques. By bringing together top minds from diverse fields, M3@Singapore aimed to foster new connections among scientists to discuss ideas targeted at the major technological challenges in selected application domains, i.e. health, urban lifestyle, high-value manufacturing, and sustainability. The theme of the meeting was ‘Big Ideas in Molecular Materials’. This theme set the expectation for the 2-day meeting during which there were candid discussions. This special issue of M3@Singapore comprises a selection of papers that epitomizes the current sentiments in molecular materials research, a sampling of which is mentioned in the following. In the focus article by J.M. MacLeod and F. Rosei (Universite du Quebec, Canada), the self-organization of molecules at solution/solid interfaces was investigated as a function of temperature. A related paper on self-organization, i.e. the self-assembly of block copolymer molecules in aqueous solutions is presented by A. M. H. Leung et al. (University of Waterloo, Canada). On a sustainability-related topic, K. J. Young et al. (Yale University, USA) contribute a paper on a photocatalytic cell for water splitting that was inspired by molecular studies of the photosystem II protein complex, and W. Zhang et al. (National University of Singapore) contribute a paper on TiO2 nanorod photoelectrodes for dyesensitized solar cells. In the area of health technology, a paper on functionalized polymers for the detection of cells is presented by U. Latif et al. (University of Vienna, Austria), together with two papers by X. D. Su et al. (Institute of Materials Research and Engineering, Singapore) on metallic nanoparticle interactions with DNA. In addition, the readers will find several other stimulating papers in this issue. In this molecular age, if we can creatively design, synthesize, process, and applymaterials usingmolecular techniques, we can certainly expect quantum leaps in advances in materials research. We believe that the solution to the hard problems in science and technologywill be found in the scrutiny of materials from the molecular level to the nano-scale. The advances of the likes of carbon-materials such as fullerenes and graphene and hybrid materials like nano composites and hetero-structures are just some successful examples. If chemistry can energize the biology field to the extent that it could create a new field called ‘chemical biology’, there is every reason to be enthusiastic

ChemInform Abstract: Self-Organization of Molecules by Covalent Bonds: Selective Tetramerization of a p-Quinodimethane.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Influence of structural features on the self-assembly of short ionic oligopeptides

We investigated the self-aggregation of 12 short ionic oligopeptides constituted by 4-7 amino acid residues to establish useful structure-property relationships that might be exploited in the biomedical field by using the concept of molecular Lego. We show that the critical aggregation concentration (CAC) of tetrapeptides decreases with increasing hydrophobicity of neutral residues. Additionally, the dependence of the CAC of isomeric oligopeptides on the distribution of amino acid residues confirms the high tendency to self-organization of molecules with alternating ionic and neutral residues. Indeed, atomic force microscopy (AFM) images recorded on oligopeptide solutions above the CAC show the presence of either fibrillar or spherical aggregates depending on oligopeptide structure and concentration, steric hindrance, solution pH, and time. The potential of the investigated oligopeptides in tissue engineering applications is supported by their in vitro cytocompatibility.