Spherical Motifs Research Articles

Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0.

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.

Diverse superlattices constructed via perylene bisimide type of giant shape amphiphiles: Assisted with unimolecular nanoparticles

Complex superlattices formed by spherical motifs in soft matter have attracted more interest in the last two decades. Herein, we report the supramolecular assembly behaviors of four types of giant shape amphiphiles composed of perylene bisimide and isooctyl-polyhedral oligomeric silsesquioxane (OPOSS) with different linkages. The glass forming temperatures of these giant shape amphiphiles decrease from 10.3 °C to -14.3 °C with increasing of the linker length. These giant molecules can self-assemble into well-ordered Frank-Kasper (FK) A15 phases. Furthermore, blending with unimolecular nanoparticles, diverse superlattices including FK (such as Laves C15, also called MgCu2) and quasi-FK (such as NaZn13) phases are found. This work could provide a basic understanding towards the phase behaviors of spherical motifs constructed by giant molecules, as well as supports our previous findings about binary blending in complex superlattices formation.

Soft Alloys Constructed with Distinct Mesoatoms via Self-Sorting Assembly of Giant Shape Amphiphiles.

The packing structures of spherical motifs affect the properties of resultant condensed materials such as in metal alloys. Inspired by the classic metallurgy, developing complex alloy-like packing phases in soft matter (also called "soft alloys") is promising for the next-generation superlattice engineering. Nevertheless, the formation of many alloy-like phases in single-component soft matter is usually thermodynamically unfavourable and technically challenging. Here, we utilize a novel self-sorting assembly approach to tackle this challenge in binary blends of soft matter. Two types of giant shape amphiphiles self-sort to form their discrete spherical motifs, which further simultaneously pack into alloy-like phases. Three unconventional spherical packing phases have been observed in these binary systems, including MgZn2 , NaZn13 , and CaCu5 phases. It's the first time that the CaCu5 phase is experimentally observed in soft matter. This work demonstrates a general approach to constructing unconventional spherical packing phases and other complex superlattices in soft matter.

Soft Alloys Constructed with Distinct Mesoatoms via Self‐Sorting Assembly of Giant Shape Amphiphiles

AbstractThe packing structures of spherical motifs affect the properties of resultant condensed materials such as in metal alloys. Inspired by the classic metallurgy, developing complex alloy‐like packing phases in soft matter (also called “soft alloys”) is promising for the next‐generation superlattice engineering. Nevertheless, the formation of many alloy‐like phases in single‐component soft matter is usually thermodynamically unfavourable and technically challenging. Here, we utilize a novel self‐sorting assembly approach to tackle this challenge in binary blends of soft matter. Two types of giant shape amphiphiles self‐sort to form their discrete spherical motifs, which further simultaneously pack into alloy‐like phases. Three unconventional spherical packing phases have been observed in these binary systems, including MgZn2, NaZn13, and CaCu5 phases. It's the first time that the CaCu5 phase is experimentally observed in soft matter. This work demonstrates a general approach to constructing unconventional spherical packing phases and other complex superlattices in soft matter.

Superlattice Engineering with Chemically Precise Molecular Building Blocks.

Correlating nanoscale building blocks with mesoscale superlattices, mimicking metal alloys, a rational engineering strategy becomes critical to generate designed periodicity with emergent properties. For molecule-based superlattices, nevertheless, nonrigid molecular features and multistep self-assembly make the molecule-to-superlattice correlation less straightforward. In addition, single component systems possess intrinsically limited volume asymmetry of self-assembled spherical motifs (also known as "mesoatoms"), further hampering novel superlattices' emergence. In the current work, we demonstrate that properly designed molecular systems could generate a spectrum of unconventional superlattices. Four categories of giant molecules are presented. We systematically explore the lattice-forming principles in unary and binary systems, unveiling how molecular stoichiometry, topology, and size differences impact the mesoatoms and further toward their superlattices. The presence of novel superlattices helps to correlate with Frank-Kasper phases previously discovered in soft matter. We envision the present work offers new insights about how complex superlattices could be rationally fabricated by scalable-preparation and easy-to-process materials.

Surfactant-Free Synthesis of Three-Dimensional Perovskite Titania-Based Micron-Scale Motifs Used as Catalytic Supports for the Methanol Oxidation Reaction.

We synthesized and subsequently rationalized the formation of a series of 3D hierarchical metal oxide spherical motifs. Specifically, we varied the chemical composition within a family of ATiO3 (wherein “A” = Ca, Sr, and Ba) perovskites, using a two-step, surfactant-free synthesis procedure to generate structures with average diameters of ~3 microns. In terms of demonstrating the practicality of these perovskite materials, we have explored their use as supports for the methanol oxidation reaction (MOR) as a function of their size, morphology, and chemical composition. The MOR activity of our target systems was found to increase with decreasing ionic radius of the “A” site cation, in order of Pt/CaTiO3 (CTO) > Pt/SrTiO3 (STO) > Pt/BaTiO3 (BTO). With respect to morphology, we observed an MOR enhancement of our 3D spherical motifs, as compared with either ultra-small or cubic control samples. Moreover, the Pt/CTO sample yielded not only improved mass and specific activity values but also a greater stability and durability, as compared with both commercial TiO2 nanoparticle standards and precursor TiO2 templates.

Screw dislocation-induced pyramidal crystallization of dendron-like macromolecules featuring asymmetric geometry.

We report herein that dendron-shaped macromolecules ABn crystallize into well-ordered pyramid-like structures from mixed solvents, instead of spherical motifs with curved structures, as found in the bulk. The design of the asymmetric molecular architecture and the choice of mixed solvents are applied as strategies to manipulate the crystallization process. In mixed solvents, the solvent selection for the Janus macromolecule and the existence of dominant crystalline clusters contribute to the formation of flat nanosheets. Whereas during solvent evaporation, the bulkiness of the asymmetric macromolecules easily creates defects within 2D nanosheets which lead to their spiral growth through screw dislocation. The size of the nanosheets and the growth into 2D nanosheets or 3D pyramidal structures can be regulated by the solvent ratio and solvent compositions. Moreover, macromolecules of higher asymmetry generate polycrystals of lower orderliness, probably due to higher localized stress.

Constituent Isomerism-Induced Quasicrystal and Frank–Kasper σ Superlattices Based on Nanosized Shape Amphiphiles

Naturally, subtle variations in the chemical structures of constituent molecules may significantly affect their multiscale spatial arrangements, properties, and functions. Deceptively simple spheri...

Identification of a Frank-Kasper Z phase from shape amphiphile self-assembly.

Frank-Kasper phases, a family of ordered structures formed from particles with spherical motifs, are found in a host of materials, such as metal alloys, inorganic colloids and various types of soft matter. All the experimentally observed Frank-Kasper phases can be constructed from the basic units of three fundamental structures called the A15, C15 and Z phases. The Z phase, typically observed in metal alloys, is associated with a relatively large volume ratio between its constituents, and this constraint inhibits its formation in most self-assembled single-component soft-matter systems. We have assembled a series of nanosized shape amphiphiles that comprise a triphenylene core and six polyhedral oligomeric silsesquioxane cages grafted onto it through linkers to give a variety of unconventional structures, which include the Z phase. This structure was obtained through fine tuning of the linker lengths between the core and the peripheral polyhedral oligomeric silsesquioxane cages, and exhibits a relatively large volume asymmetry between its constituent polyhedral particle motifs.

Breaking Parallel Orientation of Rods via a Dendritic Architecture toward Diverse Supramolecular Structures

AbstractSelf‐assembled nanostructures of rod‐like molecules are commonly limited to nematic or layered smectic structures dominated by the parallel arrangement of the rod‐like components. Distinct self‐assembly behavior of four categories of dendritic rods constructed by placing a tri(hydroxy) group at the apex of dendritic oligo‐fluorenes is observed. Designed hydrogen bonding and dendritic architecture break the parallel arrangement of the rods, resulting in molecules with specific (fan‐like or cone‐like) shapes. While the fan‐shaped molecules tend to form hexagonal packing cylindrical phases, the cone‐shaped molecules could form spherical motifs to pack into various ordered structures, including the Frank–Kasper A15 phase and dodecagonal quasicrystal. This study provides a model system to engineer diverse supramolecular structures by rod‐like molecules and sheds new light into the mechanisms of the formation of unconventional spherical packing structures in soft matter.

Breaking Parallel Orientation of Rods via a Dendritic Architecture toward Diverse Supramolecular Structures.

Self-assembled nanostructures of rod-like molecules are commonly limited to nematic or layered smectic structures dominated by the parallel arrangement of the rod-like components. Distinct self-assembly behavior of four categories of dendritic rods constructed by placing a tri(hydroxy) group at the apex of dendritic oligo-fluorenes is observed. Designed hydrogen bonding and dendritic architecture break the parallel arrangement of the rods, resulting in molecules with specific (fan-like or cone-like) shapes. While the fan-shaped molecules tend to form hexagonal packing cylindrical phases, the cone-shaped molecules could form spherical motifs to pack into various ordered structures, including the Frank-Kasper A15 phase and dodecagonal quasicrystal. This study provides a model system to engineer diverse supramolecular structures by rod-like molecules and sheds new light into the mechanisms of the formation of unconventional spherical packing structures in soft matter.

Structural evolution and electronic properties of Cu-Zn alloy clusters

Brass (Cu-Zn) is one of the typical Hume-Rothery alloys, which is extensively used in material science and industry. Earlier studies revealed that the structures of Cu-Zn alloys correlate with the average number of valence electrons or the electron-per-atom (e/a) ratio, but structural evolution rule still remains unclear. In this work, the Cu-Zn nanoalloy clusters (elementary cells of bulk brass) are studied to reveal the evolutional rule of their structures with sizes. Systematic unbiased global search is performed for structural prediction of CuxZny nanoalloys in a size range (x + y = 3–10) by using genetic algorithm with density functional theory. The global minimum and low-lying isomers of the series of nanoalloy clusters are obtained, and the structural phase diagrams are plotted depending on the relative energy. The results show that geometric structures of Cu-Zn nanoalloys are also determined by the total number of valence electrons (n*), just as in bulk brass. Cu-Zn nanoalloys with same n* have similar geometric motifs. When n* = 6, the clusters adopt planar motif, which have σ-aromaticity following the (4n+2) rule. When n* = 8, 18 and 20, the clusters keep spherical motifs, which satisfy the magic numbers of Jellium model and could be viewed as stable superatoms. In most of cases for n* = 10, 12 and 14, the clusters adopt prolate motifs, which have similar electronic structures to N2, O2, and F2 molecules, respectively, based on the super valence bond model. Moreover, in some cases for n* = 10 and 12, the clusters can be seen as an 8e-superatom combined with one (8e+2e) or two (8e+2e+2e) separate Zn atoms.

Hierarchical Self-Organization of AB n Dendron-like Molecules into a Supramolecular Lattice Sequence.

To understand the hierarchical self-organization behaviors of soft materials as well as their dependence on molecular geometry, a series of ABn dendron-like molecules based on polyhedral oligomeric silsesquioxane (POSS) nanoparticles were designed and synthesized. The apex of these molecules is a hydrophilic POSS cage with 14 hydroxyl groups (denoted DPOSS). At its periphery, there are different numbers (n = 1–8) of hydrophobic POSS cages with seven isobutyl groups (denoted BPOSS), connected to the apical DPOSS via flexible dendron type linker(s). By varying the BPOSS number from one to seven, a supramolecular lattice formation sequence ranging from lamella (DPOSS-BPOSS), double gyroid (space group of Ia3̅d, DPOSS-BPOSS2), hexagonal cylinder (plane group of P6mm, DPOSS-BPOSS3), Frank–Kasper A15 (space group of Pm3̅n, DPOSS-BPOSS4, DPOSS-BPOSS5, and DPOSS-BPOSS6), to Frank–Kasper sigma (space group of P42/mnm, DPOSS-BPOSS7) phases can be observed. The nanostructure formations in this series of ABn dendron-like molecules are mainly directed by the molecular geometric shapes. Furthermore, within each spherical motif, the spherical core consists hydrophilic DPOSS cages with flexible linkages, while the hydrophobic BPOSS cages form the relative rigid shell, and contact with neighbors to provide decreased interfaces among the spherical motifs for constructing final polyhedral motifs in these Frank–Kasper lattices. This study provides the design principle of molecules with specific geometric shapes and functional groups to achieve anticipated structures and macroscopic properties.

Revisit of Sin (n = 21–29) Clusters by Ab Initio Global Search

Using our improved genetic algorithm combined with density functional theory calculations, we perform unbiased global search for the most stable structures of Sin clusters with n = 21–29. A new principal direction crossover operation is introduced to search the prolate structures on the potential energy surface. We confirmed previous results for most sized Sin clusters and find more stable structure at n = 23 and 26. In particular, we find a new endohedral cage structure at Si23, which is 0.4 eV lower in energy than previously reported prolate structure and exhibit a distinct peak on the second order difference of total cluster energy. We discuss the competition between prolate and spherical motifs in the medium-sized Sin clusters in light of binding energy and HOMO–LUMO gap. The transition of structural motif from prolate to near spherical in Sin clusters occurs at n = 26. The outer cages are composed of pentagon, hexagon, quadrangle and heptagon, with one to three interior atoms filled inside the cage. These results establish a more complete picture for the structural evolution of the medium-sized silicon clusters. Average bond lengths and Mayer bond order are also discussed.

Self-assembly studies on triazolepolycarbodiimide-g-polystyrene copolymers

We report here the formation of polycarbodiimide-g-polystyrene copolymer secondary structures, i.e. nano-rings, “craters”, and spherical particles, resulted from dewetting phenomena that have been corroborated by combination of tapping mode AFM, SEM, DLS, and powder XRD techniques. These morphological findings represent certain interest in the area of novel functional materials. Well-defined ring-like aggregates are believed to be the transition motifs arising due to the concentration changes and, therefore, mainly seen when diluted CHCl3 stock solutions were used for AFM specimen preparation. Applying more polar THF or THF/EtOH (25% by volume) solvent systems influenced aggregation of grafted copolymers into spherical motifs with a particle size dependent on concentration that was also confirmed by dynamic light scattering (DLS) studies in solution. Characterization performed by electron microscopy techniques (SEM and TEM) provides evidence that AFM-observed morphologies do exist beyond the thin film phase and XRD findings are suggestive that non-covalent interactions of macromolecules play an important role in their self-organization in solid state.

Appearance of bulk-like motifs in Si, Ge, and Al clusters

Using a genetic algorithm method to search for low-energy structures, we studied the evolution of structural motifs in Si, Ge, and Al clusters. We were able to observe how bulk-like structural motifs occur in these clusters as the size of the system increases, replacing structural motifs characteristic of clusters at smaller sizes. Si and Ge clusters adopt prolate structures at small sizes. While Si clusters switch to a spherical motif around the size of 30 atoms, Ge clusters exhibit plate-like motifs at the size of 40-atom clusters before transforming into more spherical shapes. For Al clusters, an ordered layered structural motif begins to appear at a relatively small cluster size around 25-27 atoms.

A new nano-scale ferrocene assembly supported by a supercubane framework

Six ferrocenedicarboxylate units were supported by a supercubane framework to create a new nano-scale ferrocene assembly with a spherical motif, whose structure and redox properties were characterized.

More spherical large fullerenes and multi-layer fullerene cages

According to the experimental investigation, the carbon nano-particles have spherical multi-layer structure (also called onion-like carbon structure). Theoretically, the optimum structures of these large fullerenes contain highly faceted shapes with icosahedral symmetry. This discrepancy in structure may be attributed to the formation mechanism. Thus, a method is devised to construct spherical large fullerenes (C240, C540, C960, C2160, C2940, C3840, C4860) by using the triangular motif. The 5–7–5–7 shape defect is applied in this method for assembling the large spherical fullerenes which could transform the graphene sheet to a spherical motif via SW rearrangement. The geometry-optimized structures of large spherical fullerenes have been generated by molecular mechanics calculation. Then, the average radius and standard deviation of these large fullerenes were obtained to verify the spherical shape. The multi-layer fullerene with spherical shape was confirmed by the TEM observation. According to the structure analysis, the distance between two neighboring encapsulating carbons is about 3.5Å, which approximately coincides with the distance between two layers of graphite. The van der Waals force per carbon atom and of multi-layer fullerene with the spherical shape generated by force field calculation, predict their relative stability.

Do you know where your group is? development of a group-as-a-whole compass. Part I

A therapist's ability to locate the essential dimensions of a group is a critical skill. The literature on group-as-a-whole theory and practice is a rich body of work that reveals a variety of discrete models and approaches with little coordination between them. This paper is an attempt at theory binding. A group-as-a-whole compass is introduced as a spherical motif to integrate varied conceptual understandings of whole-group functioning. The compass, by providing a metapsychological framework, is designed to orient the therapist and theoretician to the myriad ways that group-centered configurations come to life and can be known.