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H2 is Cyanogen Chloride-derived structured and crystallizes in the triclinic P-1 space group. The structure is zero-dimensional and consists of four hydrogen molecules and four molecular hydrogen molecules.
Analysis of C-alpha atom positions from cysteines involved in disulphide bridges in protein crystals shows that their geometric characteristics are unique with respect to other Cys-Cys, non-bridging pairs. They may be used for predicting disulphide connections in incompletely determined protein structures, such as low resolution crystallography or theoretical folding experiments. The basic unit for analysis and prediction is the 3 x 3 distance matrix for Cx positions of residues (i - 1), Cys(i), (i +1) with (j - 1), Cys(j), (j + 1). In each of its columns, row and diagonal vector--outer distances are larger than the central distance. This analysis is compared with some analytical models.
Abstract Humankind has been obsessed with knots in religion, culture and daily life for millennia, while physicists like Gauss, Kelvin and Maxwell already involved them in models centuries ago. Nowadays, colloidal particles can be fabricated to have shapes of knots and links with arbitrary complexity. In liquid crystals, closed loops of singular vortex lines can be knotted by using colloidal particles and laser tweezers, as well as by confining nematic fluids into micrometer-sized droplets with complex topology. Knotted and linked colloidal particles induce knots and links of singular defects, which can be interlinked (or not) with colloidal particle knots, revealing the diversity of interactions between topologies of knotted fields and topologically nontrivial surfaces of colloidal objects. Even more diverse knotted structures emerge in nonsingular molecular alignment and magnetization fields in liquid crystals and colloidal ferromagnets. The topological solitons include hopfions, skyrmions, heliknotons, torons and other spatially localized continuous structures, which are classified based on homotopy theory, characterized by integer-valued topological invariants and often contain knotted or linked preimages, nonsingular regions of space corresponding to single points of the order parameter space. A zoo of topological solitons in liquid crystals, colloids and ferromagnets promises new breeds of information displays and a plethora of data storage, electro-optic and photonic applications. Their particle-like collective dynamics echoes coherent motions in active matter, ranging from crowds of people to schools of fish. This review discusses the state of the art in the field, as well as highlights recent developments and open questions in physics of knotted soft matter. We systematically overview knotted field configurations, the allowed transformations between them, their physical stability and how one can use one form of knotted fields to model, create and imprint other forms. The large variety of symmetries accessible to liquid crystals and colloids offer insights into stability, transformation and emergent dynamics of fully nonsingular and singular knotted fields of fundamental and applied importance. The common thread of this review is the ability to experimentally visualize these knots in real space. The review concludes with a discussion of how the studies of knots in liquid crystals and colloids can offer insights into topologically related structures in other branches of physics, with answers to many open questions, as well as how these experimentally observable knots hold a strong potential for providing new inspirations to the mathematical knot theory.
The significant differences in scattering cross sections between deuterium and protium are unique to neutron scattering techniques and have been a long-standing area of interest within the neutron scattering community. Researchers have explored selective deuteration to manipulate scattering contrast in soft matter systems, leading to the widespread use of deuterium labeling in materials development. As deuteration changes the atomic mass, it alters physical properties such as molecular volume, polarizability, and polarity, which in turn may affect noncovalent interactions and crystal ordering. Despite previous studies, there remains a limited understanding of how deuteration impacts donor–acceptor (DA) conjugated polymers. To address this, we synthesized deuterated DPP polymers and systematically investigated the effects of side-chain deuteration on their thermal stability, crystal packing, morphology, and optoelectronic properties. We found that deuteration increased the melting and crystallization temperatures of DPP polymers, although it did not significantly alter their morphology, molecular packing, or charge mobility. These properties were assessed by using atomic force microscopy (AFM), X-ray scattering, and thin-film transistor device measurements, respectively, for DPP polymers. Our work shows that deuterium labeling could be a powerful method for controlling scattering length density, enabling neutrons to study the structure and dynamics of conjugated polymers without impacting their electronic performance.
Cesium-based quasi-2D halide perovskites (HPs) offer promising functionalities and low-temperature manufacturability, suited to stable tandem photovoltaics. However, the chemical interplays between the molecular spacers and the inorganic building blocks during crystallization cause substantial phase complexities in the resulting matrices. To successfully optimize and implement the quasi-2D HP functionalities, a systematic understanding of spacer chemistry, along with the seamless navigation of the inherently discrete molecular space, is necessary. Herein, by utilizing high-throughput automated experimentation, the phase complexities in the molecular space of quasi-2D HPs are explored, thus identifying the chemical roles of the spacer cations on the synthesis and functionalities of the complex materials. Furthermore, a novel active machine learning algorithm leveraging a two-stage decision-making process, called gated Gaussian process Bayesian optimization is introduced, to navigate the discrete ternary chemical space defined with two distinctive spacer molecules. Through simultaneous optimization of photoluminescence intensity and stability that “tailors” the chemistry in the molecular space, a ternary-compositional quasi-2D HP film realizing excellent optoelectronic functionalities is demonstrated. Finally, this work not only provides a pathway for the rational and bespoke design of complex HP materials but also sets the stage for accelerated materials discovery in other multifunctional systems.
Recent experimental developments in hydrogen-rich materials at high pressures have put this class of materials above others in the race toward room-temperature superconductivity. As it is the basis of all the materials in this class, the efforts to determine the properties of pure solid hydrogen at high pressures remain intense. Most notably, a recent experimental study of the metallization of hydrogen identified the crystal phase of the solid as the C2/c-24 molecular phase up to ~425 GPa [Loubeyre et al., Nature (London) 577, 631 (2020)10.1038/s41586-019-1927-3]. It is possible that the observed metallization is caused by band structure effects and not a structural phase transition, and the material remains in this crystal phase up to higher pressures [Dogan et al., J. Phys.: Condens. Matter 33, 03LT01 (2020)10.1088/1361-648X/abba8a]. Therefore, it is of crucial importance to determine the superconducting properties of the C2/c-24 phase. Here, we employ a Wannier function-based dense k-point and q-point sampling to compute the electron-phonon coupling and superconducting properties of molecular hydrogen in the C2/c-24 phase. We find that the material has a high superconducting transition temperature of 242 K at 500 GPa. We also find that the transition temperature rapidly increases with pressure in the 400-500-GPa range.
The evolution of crystallinity resulting from stress imposed on a melt, known as flow-induced crystallinity, can strongly influence the mechanical and physical properties of semicrystalline polymers. This study investigates shear-induced crystallization by applying an ultrasonic field to the melt flow as it passes through dies with various geometries. A custom-built sonication die is employed for controlling the dynamic temperature and shear environment, resulting in molecular alignment and potential for flow-induced crystallization. Application of both conventional and ultrasonic shear rates at the equilibrium melt temperature of high-density polyethylene (HDPE) was investigated to accelerate crystallinity and manipulate the crystal morphology across the film in pursuit of improved mechanical and gas barrier properties without the need for additives or other polymer layers. The relationships among ultrasonic-assisted extrusion processing, polymer structure, and performance were analyzed using wide- and small-angle X-ray scattering (WAXS and SAXS), tensile testing, and oxygen transmission rate (OTR) analysis. Multiple linear regression models were implemented to predict the correlation among HDPE structure, process, and properties. Structural analysis revealed that both conventional and ultrasonic shear rates had the most significant influence on lamellar spacing and redistribution of rigid and soft amorphous fractions within the crystalline domains, ultimately dictating the mechanical and physical properties of the films. The goal is to explore the potential of the ultrasonic-assisted high crystallinity monolayer that can replace some of the functionality of complex, heterogeneous multilayer packaging with a single-material film having enhanced oxygen barrier properties.
An unusually large and structurally complex charge-neutral polynuclear cluster, hexa-μ 2 -azido-di-μ 3 -chlorido-hexa-μ 2 -hydroxido-di-μ 3 -oxido-hexakis(pentamethylcyclopentadienyl)hexathorium–diethyl ether–tetrahydrofuran (1/0.56/1.44), [Th 3 (C 10 H 15 ) 6 Cl 3 (N 3 ) 6 (OH) 6 O 2 ]·0.56C 4 H 10 O·1.44C 4 H 8 O or [Th 3 (Cp*) 3 (O)(OH) 3 ] 2 Cl 2 (N 3 ) 6 ·0.56C 4 H 10 O·1.44C 4 H 8 O (Cp* = [pentamethylcyclopentadienyl]) − , has been crystallized as a mixed tetrahydrofuran/diethyl ether solvate and structurally characterized. The molecule contains a number of unusual features, the most notable being a finite yet exceptionally long cyclic metal-azido chain. These rare features are the consequence of both sterically protecting Cp* ligands and highly bridging oxide and hydroxide ligands in the same system and illustrate the interesting new possibilities that can arise from combining organometallic and solvothermal f -block element chemistry.
A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.
Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.
Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.
Shock wave interactions with perturbations on a free surface can lead to the inversion and growth of the perturbation and eventual ejection of a jet of material, referred to as an ejecta microjet, from shocked surfaces. Here, this study carries out large-scale molecular dynamics (MD) simulations using single-crystal Cu and Sn systems with a pre-existing groove to characterize the localized gradients in temperatures and pressures generated that render the microjet formation. MD simulations are carried out for three loading orientations (along the [001], [011], and [111] directions) and shock pressures ranging from 16 GPa to 100 GPa to understand the role of temperatures generated at the groove vertex on the formation of ejecta. The simulations suggest that the interaction of the shock wave with the groove results in a localized increase in temperatures, leading to localized softening at the groove vertex and the generation of an ejecta microjet. For Cu systems, the simulations suggest that the orientation effects on shock wave structures, velocities, and localized softening affect the ejecta formation at low pressures. Jetting is only observed when temperatures at the groove vertex are high enough to induce localized softening (close to melting temperature), and the jet velocity increases with shock pressure. In contrast, the loading orientation is rendered inconsequential for Sn systems due to the melting of the material during shock compression at the pressures chosen. The jet velocities are similar, regardless of crystal orientation in Sn systems.
Doping a luminescent tris(2,4,6-trichlorophenyl)methyl diradical m (TTM) 2 into a host crystal of its diamagnetic precursor m (HTTM) 2 creates a molecular color center with enhanced optical-spin interface properties important for quantum sensing. Optical polarization of the |T 0 ⟩ sublevel of the diradical triplet ground state is achieved by spin-selective intersystem crossing from the |T + ⟩ and |T – ⟩ sublevels of the triplet excited state at ambient and cryogenic temperatures. Coherent spin control of m (TTM) 2 doped into m (HTTM) 2 using pulsed optically detected magnetic resonance (ODMR) spectroscopy results in a 10-fold improvement in ODMR contrast over that observed for randomly oriented m (TTM)2 using continuous-wave ODMR. The diradical doped crystal powders achieve spin coherence times of 2.8, 3.4, and 7.4 μs at 294, 85, and 5 K, respectively. The diradical photoluminescence is sensitive to weak applied magnetic fields independent of temperature, excitation wavelength, and dopant concentration, providing a promising pathway toward robust quantum sensing of anisotropic magnetic fields under ambient conditions.
A partial charge empirical potential for the Nb-O pair has been developed based on existing parameters of other pairs in a Teter potential to enable molecular dynamics simulations of both lithium niobate crystal and lithium niobosilicate glasses. The developed potential is capable of describing structural features of lithium niobosilicate glasses in a wide composition range, including niobium coordination number and bond length, density, bond angle distribution, polyhedral distribution and fraction of bridging oxygen. Furthermore, the results obtained using this new potential show good agreement with experimental data of density and structure from Raman spectroscopy of lithium niobosilicate glasses and X-ray absorption spectroscopy near Nb K-edge.
Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life, is referred to as organic synthesis on mineral surfaces. Furthermore, it is suggested that the interaction between mineral surfaces and simple organic molecules resulted in the formation of amino acids, RNA, and perhaps other more complex molecules such as proteins. On the other hand, in natural systems, it is recognized that functional groups on cell walls or membranes of microorganisms serve as sites of nucleation and crystallization. The precise replication of biominerals with controlled structure, morphology, size and texture is not confined to higher organisms as it also occurs in primitive prokaryotic cells such as magnetotactic bacteria and cyanobacteria. This suggests that the principal strategies of biomineralization were established early on in the evolutionary history of organisms. It is critical, therefore, to search for common mechanisms within diverse biological systems. One such common factor is the capability for organization and self-assembly. Organic macromolecules such as proteins and lipids can aggregate and polymerize forming membranes or extracellular matrix. At the organic-inorganic interface, several factors such as lattice geometry, polarity, stereochemistry and topography may act in concert to control nucleation and growth of crystals. Although several models have been proposed that discuss the significance of these factors for biomineralization, no comprehensive experimental data are available. In contrast to crystallization in exclusively inorganic systems, the kinetics of reaction and structural relationships between organic and inorganic phases in biominerals or biomimetic material is poorly understood. For example, it is not clear if the concept of epitactic growth (geometrical matching of unit cells at the interface of a secondary crystal growing on a primary crystal) applies to organic-inorganic systems. In contrast to inorganic templates that often have a smooth and rigid surface that promotes epitactic growth, biological substrates are usually rough and result in a large degree of mismatch. It is apparent that factors controlling the reaction at the crystal-matrix interface are strongly dependent upon the nature of the substrate. Therefore, characterization of the assembled organic surface and surface structure of the inorganic phase is crucial to understanding the processes of biomineralization. The focus of our research is the investigation of the processes leading to the nucleation and growth of crystals on both natural and synthetic systems through an interdisciplinary approach that integrates molecular biology, morphology and mineralogy using advanced preparation and analytical techniques. We have studied run-products, particularly magnetite, siderite and other carbonates, that resulted from extracellular biomineralization by extremophiles isolated from a variety of extreme environments ranging from permafrost to hydrothermal vent systems. The results of this study are critical to recognizing biomarkers in terrestrial and extraterrestrial environments.
The efficient preparation of single-crystalline ionic polymers and fundamental understanding of their structure–property relationships at the molecular level remains a challenge in chemistry and materials science. Herein, we observe the single-crystal structure of a highly ordered polycationic polymer (polyelectrolyte) and its proton conductivity. The polyelectrolyte single crystals can be prepared on a gram-scale in quantitative yield, by taking advantage of an ultraviolet/sunlight-induced topochemical polymerization, from a tricationic monomer—a self-complementary building block possessing a preorganized conformation. A single-crystal-to-single-crystal photopolymerization was revealed unambiguously by in situ single-crystal X-ray diffraction analysis, which was also employed to follow the progression of molecular structure from the monomer, to a partially polymerized intermediate, and, finally, to the polymer itself. Collinear polymer chains are held together tightly by multiple Coulombic interactions involving counterions to form two-dimensional lamellar sheets (1 nm in height) with sub-nanometer pores (5 Å). The polymer is extremely stable under 254 nm light irradiation and high temperature (above 500 K). The extraordinary mechanical strength and environmental stability—in combination with its impressive proton conductivity (~3 × 10 –4 S cm –1 )—endow the polymer with potential applications as a robust proton-conducting material. By marrying supramolecular chemistry with macromolecular science, the outcome represents a major step toward the controlled synthesis of single-crystalline polyelectrolyte materials with perfect tacticity.
Abstract The advent of two-dimensional (2D) crystals has led to numerous scientific breakthroughs. Conventional 2D systems have in-plane covalent bonds and a weak out-of-plane van-der-Waals bond. Here we report a new type of 2D material composed of discrete magnetic molecules, where anisotropic van-der-Waals interactions bond the molecules into a 2D packing. Through mechanical exfoliation, we can obtain single-crystalline molecular monolayers, which can be readily integrated into other 2D systems. Optical spectroscopy suggests the few-layered molecules preserve the temperature-induced spin-crossover switching observed in the bulk form but show a drastic increase in thermal hysteresis unique to these thin 2D molecule assemblies. The trapping of spin bistability with decreasing layer number can arise from domain wall dynamics in reduced dimensions. Our results establish molecular solids with strong anisotropy of intermolecular interactions as precursors to a new class of 2D materials, affording possibilities to control molecular functionalities through substrate and interlayer interactions.