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Design of Chiral Domains by Surface Confinement of Liquid Crystals
Chirality, or absence of mirror symmetry, is a fascinating attribute of inanimate and living objects, which inspires artists and fascinates scientists in various disciplines, from physics to mathematics, biology to chemistry and crystallography. Producing and controlling the sense of handedness in systems formed by mirror-symmetric elements or containing an equal amount of left- and right-twisted elements is usually a nontrivial task. In this issue of ACS Central Science, Geonhyeong Park et al [1] demonstrate that a slab of a lyotropic chromonic liquid crystal (LCLC), formed by achiral molecules dispersed in water, can produce a periodic array of domains with left- and right-handed twists of the orientation of molecular aggregates. The twist develops over macroscopic regions of tens of microns in size and is caused by a balance of two facets of the orientational order pertinent to liquid crystals: the elastic response to deformations of orientation and anisotropy of surface interactions at confining boundaries.
Antiferro- and metamagnetism in the S = 7 / 2 hollandite analog Eu Ga 2 Sb 2
Recent work analyzing the impact of nonsymmorphic symmetries on electronic states has given rise to the discovery of multiple types of topological matter. Here we report the single-crystal synthesis and magnetic properties of Eu Ga 2 Sb 2 , a Eu-based antiferromagnet structurally consisting of pseudo-1D chains of Eu ions related by a nonsymmorphic glide plane. Here we find the onset of antiferromagnetic order at T N = 8K. Above T N the magnetic susceptibility is isotropic. Curie-Weiss analysis suggests competing ferromagnetic and antiferromagnetic interactions, with p eff = 8.1 μ B as expected for 4f 7 J = S = 7/2 Eu 2+ ions. Below T N and at low applied magnetic fields, an anisotropy develops linearly, reaching χ ⊥ /χ ∥ = 6 at T = 2K. There is concomitant metamagnetic behavior along χ ∥ , with a magnetic field of μ 0 H ≈ 0.5 T sufficient to suppress the anisotropy. Independent of crystal orientation, there is a continuous evolution to a field-polarized paramagnetic state with M = 7μ B /Eu 2+ at μ 0 H = 2 T as T → 0 K. Specific-heat measurements show a recovered magnetic entropy of ΔS mag ≈ 16.4 Jmol –1 K –1 from T ~ 0 K to T = T N , close to the expected value of R ln(8) for an S = 7/2 ion, indicating negligible low-dimensional spin fluctuations above T N . We find no evidence of unusual behaviors arising either from the dimensionality or the presence of the nonsymmorphic symmetries.
Crystallization and initial X-ray diffraction analysis of human pyruvate dehydrogenase
Human pyruvate dehydrogenase (E1) is a component enzyme of the pyruvate dehydrogenase complex. The enzyme catalyzes the irreversible decarboxylation of pyruvic acid and the rate-limiting reductive acetylation of the lipoyl moiety linked to the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex. E1 is an alpha(2)beta(2) tetramer ( approximately 154 kDa). Crystals of this recombinant enzyme have been grown in polyethylene glycol 3350 using a vapor-diffusion method at 295 K. The crystals are characterized as orthorhombic, space group P2(1)2(1)2(1), with unit-cell parameters a = 64.2, b = 126.9, c = 190.2 A. Crystals diffracted to a minimum d spacing of 2.5 A. The asymmetric unit contains one alpha(2)beta(2) tetrameric E1 assembly; self-rotation function analysis showed a pseudo-twofold symmetry relating the two alphabeta dimers.
Kramers nodal line in the charge density wave state of YTe 3 and the influence of twin domains
Recent studies have focused on the relationship between charge density wave (CDW) collective electronic ground states and nontrivial topological states. YTe 3 , a nonmagnetic quasi-two-dimensional chalcogenide, has been reported to exhibit a CDW state below 334 K. Using angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT), we establish that YTe 3 is a CDW-induced Kramers nodal line (KNL) metal, a recently proposed topological state of matter. Scanning tunneling microscopy and low energy electron diffraction reveal two orthogonal domains, each with a unidirectional CDW and a similar wave vector (𝐪 CDW ). When the influence of twin domains is considered, the effective band structure (EBS) computations that utilize DFT-calculated bands using a noncentrosymmetric structure determined by x-ray crystallography, show excellent agreement with ARPES. The noncentrosymmetry of YTe 3 is established by Raman spectroscopy. The Fermi surface and ARPES intensity plots show weak shadow bands displaced by 𝐪 CDW from the main bands. Furthermore, these are linked to CDW modulation, as the EBS calculation confirms. Bilayer split main and shadow bands suggest the existence of crossings, according to theory and experiment. DFT bands, including spin-orbit coupling, indicate existence of a KNL along the Σ direction from multiple crossings of bands dispersing perpendicular to it. Additionally, doubly degenerate bands are only found along the KNL at all energies, with some bands dispersing through the Fermi level.
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly
The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.
S -matrix positivity without Lorentz invariance: a case study
We investigate the analytic structure of scattering amplitudes in theories in which Lorentz invariance is spontaneously broken. We do so by computing and studying the S-matrix for a simple example: a superfluid described by a complex scalar with quartic interactions. The computation is confined to tree-level, for there are no absolutely stable single-particle states, though the lifetime can be made long by lowering the chemical potential. For the 2 → 2 amplitude in center-of-mass configurations, not only is crossing symmetry violated, there appears a tree level branch cut for unphysical kinematics. Its appearance is a consequence of non-analyticity in the dispersion relation. The branch point defines a new scale in the problem, which scales inversely with the chemical potential. In this example, even derivatives of the forward amplitude are positive while odd derivatives are negative. This pattern can be understood in a general way in the limit of a small chemical potential, or weak Lorentz breaking.
Chemistry, Structure, and Function of Lone Pairs in Extended Solids
The lone pair has been a known feature of the electronic structure of molecules for over 100 years. Beginning with the pioneering work of Lewis and others that was later developed into useful guidelines for predicting molecular structure, lone pairs and their steric consequences are now taught at the very earliest stages of a chemistry education. In the crystalline solid state, lone pairs have perhaps had a less visible yet equally consequential role, with a significant impact on a range of properties and functionalities. Important properties associated with s 2 electron-derived lone pairs include their role in creating conditions favorable for ion transport, in the formation and correlation of local dipoles and the resulting polar behavior leading to ferroics and multiferroics, in increasing the refractive index of glass, in reducing the thermal conductivity of thermoelectric materials, and in breaking local symmetry permitting second-harmonic light generation.. In recent years, the role of the lone pair in developing the electronic structure of some topological quantum materials has also been recognized. While structural distortions due to lone pairs have traditionally been characterized through their crystallography, recent advances in scattering and spectroscopy have revealed the presence of local lone pair-driven distortions that do not correlate over long length scales. The role of these crystallographically “hidden” lone pairs, their detection, and their impact on properties have become a growing body of work in the literature. Hidden lone pairs are an effective argument for considering a role for lone pairs that goes beyond their being objects that occupy space in the coordination polyhedra of cations. This Account introduces the chemistry of lone pairs in extended crystalline solids, including a discussion of when they are stereochemically active, how they manifest in the structure, and how their chemistry can be tuned by the chemical environment around them. Eventually, all of these factors work in unison to help develop and tune properties of interest. Certain specific examples of structure–property relationships in materials that are driven by lone pair behavior are described here, including the potential impact of lone pairs on the optical and electronic properties of hybrid halide perovskite compounds that are relevant to their photovoltaic applications. Here, we highlight the role of lone pairs in the dielectric behavior of geometrically frustrated pyrochlores, the temperature-dependent optoelectronic behavior of halide perovskites, the polar phase transitions in lead-free ferroelectric perovskites, and the compositional insulator-to-metal transition in ruthenium pyrochlores. The theme underpinning this Account is that the lone pair can be considered to be a powerful design element for a broad range of material function.
Revisiting the structures and phase transitions of Ba 2 NaNb 5 O 15
The room-temperature and low-temperature structure(s) of Ba 2 NaNb 5 O 15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.
Supramolecular Support of Cuprophilic Network Bonding in 2-D Copper n -Alkanethiolates
Here, the development of heterogeneous materials, catalysts, and semiconductors is often reliant on precise control of self-assembly and crystal packing. Many new materials are initially synthesized as microcrystalline powders, making them incompatible with typical methods of structure determination, such as single-crystal X-ray diffraction. This resultant lack of structural information has made thorough investigation into the effect of metal substitution on crystal structure in metal-organic chalcogenolates (MOChas) challenging. Here, we use small molecule serial femtosecond crystallography (smSFX) to present the structures of four copper n-alkanethiolates: CuSC4, CuSC5, CuSC6, and CuSC7. Divergent patterns of alkyl chain packing are identified from microcrystalline powders via smSFX. An odd-even effect in crystal packing has been identified and attributed to different orientations of symmetry elements in the even- and odd-numbered chains. This results in minute changes in the azimuthal organization of the even-numbered chains and the network of cuprophilic interactions. Additionally, we present a synthesis of crystalline gold n-alkanethiolates to provide the first comparison between three d 10 coinage metals (Cu, Ag, and Au) and their resultant n-alkanethiolates.
X-ray Crystallographic Study of Preferred Spacing by the NF-κB p50 Homodimer on κB DNA
Though originally characterized as an inactive or transcriptionally repressive factor, the NF-κB p50 homodimer has become appreciated as a physiologically relevant driver of specific target gene expression. By virtue of its low affinity for cytoplasmic IκB protein inhibitors, p50 accumulates in the nucleus of resting cells, where it is a binding target for the transcriptional co-activator IκBζ. In this study, we employed X-ray crystallography to analyze the structure of the p50 homodimer on κB DNA from the promoters of human interleukin-6 (IL-6) and neutrophil-gelatinase-associated lipocalin (NGAL) genes, both of which respond to IκBζ. The NF-κB p50 homodimer binds 11-bp on IL-6 κB DNA, while, on NGAL κB DNA, the spacing is 12-bp. This begs the question: what DNA binding mode is preferred by NF-κB p50 homodimer? To address this, we engineered a “Test” κB-like DNA containing the core sequence 5'-GGGGAATTCCCC-3' and determined its X-ray crystal structure in complex with p50. This revealed that, when presented with multiple options, NF-κB p50 homodimer prefers to bind 11-bp, which necessarily imposes asymmetry on the complex despite the symmetry inherent in both the protein and its target DNA, and that the p50 dimerization domain can contact DNA via distinct modes.
The Anisotropic Adsorption of De Novo Allosteric Two‐Component Protein Fibers on Mica Surfaces
Protein adsorption at solid–liquid interfaces underlies many biomedical and materials applications, yet the mechanisms governing adsorption of proteins and their assemblies remain poorly understood. Here we investigate de novo–designed proteins that self-assemble into three fibrillar morphologies — small (S), large (L), and helical (H)—on muscovite mica. S-fibers are metastable, forming first but diminishing as L- and H-fibers develop and deposit. Adsorption of both fibers and monomers depends on fiber morphology and solvent environment, which is modulated by the substrate. The anisotropic surface features of the fiber types—long axis of S- and L-fibers and helical grooves of H-fibers—correlate with specific crystallographic directions on mica (001). S- and L-fibers align along the unique lattice axis, while the substrate-facing groove of H-fibers preferentially aligns along the remaining symmetry-related directions. Increasing potassium chloride (KCl) concentrations to molar levels alters adsorption, decreasing monomer coverage relative to fibers. These observations, interpreted through the effect of interfacial interface, indicate that ion-mediated modulation of hydration layers governs electrostatic interactions and alignment. This study reveals how coupling between protein topography, substrate crystallography, and hydration structure dictates selective adsorption and orientation of protein assemblies, offering insights for rational biomolecular material design.
C–H Bond Activation via U(II) in the Reduction of Heteroleptic Bis(trimethylsilyl)amide U(III) Complexes
Reduction of (C 5 Me 5 ) 2 U III (NR 2 ) and (C 5 Me 5 )U III (NR 2 ) 2 (R = SiMe 3 ) with potassium graphite in the presence of 2.2.2-cryptand (crypt) generates dark solutions that have UV-visible spectra consistent with time-dependent density functional theory (TDDFT) calculations on the U(II) products, [(C 5 Me 5 ) 2 U II (NR 2 )] - and [(C 5 Me 5 )U II (NR 2 ) 2 ] - . However, the solutions quickly change color and form the U(III) C–H bond activation products [K(crypt)][(C 5 Me 5 ) 2 U III (CH 2 SiMe 2 NSiMe 3 –κC,κN)], 1, and [K(crypt)][(C 5 Me 5 )U III (NR 2 )(CH 2 SiMe 2 NSiMe 3 –κC,κN)], 2, that were identified by X-ray crystallography. DFT calculations on the putative [(C 5 Me 5 ) 2 U II (NR 2 )] - and [(C 5 Me 5 )U II (NR 2 ) 2 ] - complexes revealed 5f 3 6d 1 ground state electron configurations as previously found in isolable [(C 5 H 4 SiMe 3 ) 3 U II ] - , which indicated that these low symmetry heteroleptic complexes are reasonable precursors for new U(II) complexes.
Homoleptic 1,2-benzenedithiolate complexes of thorium and uranium
Reaction of 4 equiv. of [Li(TMEDA)] 2 [1,2-S 2 C 6 H 4 ] with [ThCl 4 (DME) 2 ] or [UCl 4 (THF) 3 ] in THF results in formation of [Li(THF) 2 ] 4 [An(1,2-S 2 C 6 H 4 ) 4 ] (An = Th, 1; An = U, 2), whereas reaction of 4 equiv. of [Li(TMEDA)] 2 [1,2-S 2 C 6 H 4 ] with UCl 4 in Et 2 O results in formation of [Li(TMEDA)] 4 [U(1,2-S 2 C 6 H 4 ) 4 ] (3). Complexes 1–3 represent the first reported benzenedithiolate complexes of the actinides. Here, they were characterized by NMR spectroscopy and X-ray crystallography. In the solid state, complexes 1–3 exhibit triangular dodecahedral geometries about their actinide centers. Additionally, their Li + cations are bound by two sulfur atoms of adjacent [1,2-S 2 C 6 H 4 ] 2− ligands, in addition to two solvent donor atoms. In solution, complexes 2 and 3 exhibit spectral data consistent with S 4 symmetry (and non-exchanging Li + sites), whereas complex 1 exhibits spectral properties consistent with labile Li + cations.
Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism
Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.
Deep Bayesian local crystallography
Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.
Crystallography of Reactive Intermediates
Metal–ligand (M–L) multiply bonded complexes hold a central place in inorganic chemistry and catalysis: From fundamental and historical perspectives, these species have played a critical role in the articulation of important bonding principles (i.e. the vanadyl ion in the development of molecular orbital theory); from a practical perspective, these species are critical intermediates in a variety of chemical reactions (i.e. N 2 and O 2 reduction, H 2 O oxidation, and C–H functionalization). For many high-valent, early metal complexes, overlap of ligand-based electrons with vacant π-symmetry orbitals leads to strong M–L multiple bonds. The stability of these species enables straightforward characterization with a suite of standard spectroscopic and diffraction-based experiments. Mid- and late-transition metal complexes, with attendant higher d-electron counts, often support more reactive M–L multiply bonded fragments. The reactivity of these species simultaneously renders them attractive intermediates for catalysis but challenging synthetic targets to observe and characterize. A number of important strategies have been advanced to enable experimental characterization of mid- to late-metal–ligand multiply bonded species. Synthetic manipulation of the coordination geometry and ligand donicity, as well as introduction of sterically encumbering ligands, have each emerged as powerful methods to tame the inherent reactivity of kinetically labile M–L multiple bonds. While these efforts have resulted in families of well-characterized complexes and provided critical insights regarding structure and bonding, the synthetic derivatization required to stabilize M–L fragments of interest often obviates the substrate functionalization activity relevant to catalysis. Photochemical synthesis of reactive species provides a conceptually attractive strategy to generate reactive M–L fragments under conditions compatible with time-resolved or cryogenic steady-state characterization, and photogeneration has enabled observation of a number of reactive M–L fragments. The suite of tools available to characterize photogenerated reactive species is often more limited than typical for kinetically stabilized complexes and structural characterization is typically not possible. Recently, photocrystallographic experiments, in which reactive M–L multiply bonded intermediates are generated within single-crystal matrices, have been advanced as a strategy to interrogate the structures of reactive intermediates in C–H functionalization. Lastly, this Comment describes the historical antecedents to these experiments, highlights examples of photocrystallographic characterization of reactive intermediates, and discusses future opportunities.
A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries
An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase α/β titanium alloy. The data were recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3 nm step size. The results show the expected Burgers orientation relationships between the α laths and β matrix, as well as the expected misorientations between α laths. A minor issue was found that one area was affected by 180° ambiguities in indexing occur due to this area being aligned too close to a zone axis of the α with twofold projection symmetry (not present in 3D) in the zero-order Laue Zone, and this should be avoided in data acquisition in the future. Nevertheless, this study demonstrates a good workflow for the analysis of nanocrystalline two- or multi-phase materials, which will be of widespread use in analysing two-phase titanium and other systems and how they evolve as a function of thermomechanical treatments.