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The surface structure of silver-coated gold nanocrystals and its influence on shape control
Abstract not provided
Topologically guided tuning of Zr-MOF pore structures for highly selective separation of C6 alkane isomers
Effective separation of alkane isomers is a critical step in the petroleum refining process to produce gasoline with high octane rating. Current technology relies on energy intensive distillation method. Adsorptive separation using porous solids offers an alternative route that is more cost effective, lower energy and higher efficiency. Guided by topology-directed design and synthesis, we have developed a series of zirconium-based metal-organic frameworks with optimized pore structure for efficient separation of C6 alkane isomers, Zr-bptc adsorbs a large amount of n-hexane while excluding branched isomers. The n-hexane uptake is ~70% higher than that of a benchmark adsorbent, zeolite-5A. A derivative structure, Zr-abtc, is capable of discriminating all three C6 isomers with a high separation factor for 3-methylpentane over 2,3-dimethylbutane. This property is important for producing gasoline with further improved quality.
Structural water and disordered structure promote aqueous sodium-ion energy storage in sodium-birnessite
Abstract Birnessite is a low-cost and environmentally friendly layered material for aqueous electrochemical energy storage; however, its storage capacity is poor due to its narrow potential window in aqueous electrolyte and low redox activity. Herein we report a sodium rich disordered birnessite (Na 0.27 MnO 2 ) for aqueous sodium-ion electrochemical storage with a much-enhanced capacity and cycling life (83 mAh g −1 after 5000 cycles in full-cell). Neutron total scattering and in situ X-ray diffraction measurements show that both structural water and the Na-rich disordered structure contribute to the improved electrochemical performance of current cathode material. Particularly, the co-deintercalation of the hydrated water and sodium-ion during the high potential charging process results in the shrinkage of interlayer distance and thus stabilizes the layered structure. Our results provide a genuine insight into how structural disordering and structural water improve sodium-ion storage in a layered electrode and open up an exciting direction for improving aqueous batteries.
Crystal structure of misoprostol bound to the labor inducer prostaglandin E 2 receptor
Abstract not provided
Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states
Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. Here we introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, which calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.
X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus
Abstract not provided
High-pressure X-ray diffraction, Raman, and computational studies of MgCl 2 up to 1 Mbar: Extensive pressure stability of the β-MgCl 2 layered structure
We studied magnesium chloride (MgCl 2 ) with the rhombohedral layered CdCl 2 -type structure (α-MgCl 2 ), experimentally, using synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy using a diamond-anvil cell up to 100 GPa at room temperature and theoretically using first-principles density functional calculations. Our results reveal a pressure-induced second-order structural phase transition to a hexagonal layered CdI 2 -type structure (β-MgCl 2 ) at 0.7 GPa: the stacking sequence of the Cl anions are altered resulting in a reduction of the c-axis length. Theoretical calculations confirm this phase transition sequence and the calculated transition pressure is in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phase. According to our experimental results MgCl 2 remains in a 2D layered phase up to 100 GPa and further, the 6-fold coordination of Mg cations is retained. Theoretical calculations of relative enthalpy suggest that this extensive pressure stability is due to a low enthalpy of the layered structure ruling out kinetic barrier effects. Our observation is unusual, as it contradicts with the general structural behavior of highly compressed AB 2 compounds.
Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose
The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose, the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.
Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin]
Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction, respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.
Structural characterization of framework–gas interactions in the metal–organic framework Co 2 (dobdc) by in situ single-crystal X-ray diffraction
The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH 4 , N 2 , O 2 , Ar, and P 4 adsorption in Co2(dobdc) (dobdc 4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(II) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(II) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH 4 and Co–Ar interactions observed in Co 2 (dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH 4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(II) sites in Co 2 (dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol –1 (for Ar). Moreover, the structures of Co 2 (dobdc)·3.8N 2 , Co 2 (dobdc)·5.9O 2 , and Co 2 (dobdc)·2.0Ar reveal the location of secondary (N 2 , O 2 , and Ar) and tertiary (O 2 ) binding sites in Co 2 (dobdc), while high-pressure CO 2 , CO, CH 4 , N 2 , and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures.
Pressure-induced structural transformations and new polymorphs in BiVO[subscript 4]
Abstract not provided
Synthesis and structural characterization of the new Zintl phases Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12
Two new ternary compounds, Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12 , were synthesized and structurally characterized. The synthesis was achieved either through reactions in sealed niobium tubes or in alumina crucibles by combining the elements in excess molten Sb. Their structures were elucidated using single-crystal X-ray diffraction, and they were determined to crystallize in the orthorhombic space group Cmmm (no. 65) with the Eu 10 Cd 6 Bi 12 structure type. Akin to the archetype phase, both Mn and Zn sites contain about 25% of vacancies. Furthermore, the anionic substructure of the title phases can be described as [M 6 Pn 12 ] (M = Zn, Mn; Pn = Sb, Bi) double layers composed of the corner and edge-sharing [MPn 4 ] tetrahedra, linked by [Pn 2 ] 4– dumbbells. Eu 2+ /Yb 2+ cations fill the space between the layers, with the valence electron counts adhering closely to the Zintl–Klemm rules, i.e., both Eu 10 Mn 6 Bi 12 and Yb 10 Zn 6 Sb 12 are expected to be valence-precise compounds. Analysis of the electronic structure and transport properties of Yb 10 Zn 6 Sb 12 indicate semimetallic behavior with relatively low Seebeck coefficient and resistivity that slightly decreases as a function of temperature.
Toward epitaxially grown two-dimensional crystal hetero-structures: Single and double MoS{sub 2}/graphene hetero-structures by chemical vapor depositions
Uniform large-size MoS{sub 2}/graphene hetero-structures fabricated directly on sapphire substrates are demonstrated with layer-number controllability by chemical vapor deposition (CVD). The cross-sectional high-resolution transmission electron microscopy (HRTEM) images provide the direct evidences of layer numbers of MoS{sub 2}/graphene hetero-structures. Photo-excited electron induced Fermi level shift of the graphene channel are observed on the single MoS{sub 2}/graphene hetero-structure transistors. Furthermore, double hetero-structures of graphene/MoS{sub 2}/graphene are achieved by CVD fabrication of graphene layers on top of the MoS{sub 2}, as confirmed by the cross-sectional HRTEM. These results have paved the possibility of epitaxially grown multi-hetero-structures for practical applications.
Structural transitions of 4:1 methanol–ethanol mixture and silicone oil under high pressure
A 4:1 (volume ratio) methanol–ethanol (ME) mixture and silicone oil are two of the most widely used liquid pressure-transmitting media (PTM) in high-pressure studies. Their hydrostatic limits have been extensively studied using various methods; however, the evolution of the atomic structures associated with their emerging nonhydrostaticity remains unclear. Here, we monitor their structures as functions of pressure up to ∼30 GPa at room temperature using in situ high-pressure synchrotron x-ray diffraction (XRD), optical micro-Raman spectroscopy, and ruby fluorescence spectroscopy in a diamond anvil cell. No crystallization is observed for either PTM. The pressure dependence of the principal diffraction peak position and width indicates the existence of a glass transition in the 4:1 ME mixture at ∼12 GPa and in the silicone oil at ∼3 GPa, beyond which a pressure gradient emerges and grows quickly with pressure. There may be another liquid-to-liquid transition in the 4:1 ME mixture at ∼5 GPa and two more glass-to-glass transitions in the silicone oil at ∼10 GPa and ∼16 GPa. By contrast, Raman signals only show peak weakening and broadening for typical structural disordering, and Raman spectroscopy seems to be less sensitive than XRD in catching these structural transitions related to hydrostaticity variations in both PTM. These results uncover rich pressure-induced transitions in the two PTM and clarify their effects on hydrostaticity with direct structural evidence. The high-pressure XRD and Raman data on the two PTM obtained in this work could also be helpful in distinguishing between signals from samples and those from PTM in future high-pressure experiments.
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription
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Effects of fluorinated solvents on electrolyte solvation structures and electrode/electrolyte interphases for lithium metal batteries
Electrolyte is very critical to the performance of the high-voltage lithium (Li) metal battery (LMB), which is one of the most attractive candidates for the next generation high-density energy storage systems. Electrolyte formulation and structure determine the physical properties of the electrolytes and their interfacial chemistries on the electrode surfaces. Localized high-concentration electrolytes (LHCEs) outperform state-of-the-art carbonate electrolytes in many aspects in LMBs due to their unique solvation structure. Types of fluorinated co-solvents used in LHCEs are investigated here in searching for the most suitable diluent for high concentration electrolytes (HCEs). Non-solvating solvents (including fluorinated ethers, fluorinated borate and fluorinated orthoformate) added in HCEs enable the formation of LHCEs with high-concentration solvation structures. However, low solvating fluorinated carbonate will coordinate with Li+ ions and form a second solvation shell or a pseudo-LHCE which diminishes the benefits of LHCE. In addition, it is evident that the diluent has significant influence on the electrode/electrolyte interphases (EEIs) beyond retaining the high-concentration solvation structures. Diluent molecules surrounding the high-concentration clusters could accelerate or decelerate the anion decomposition through co-participation of diluent decomposition in the EEI formation. The varied interphase features lead to significantly different battery-performance. This study points out the importance of diluents and their synergetic effects with the conductive salt and the solvating solvent in designing LHCEs. These systematic comparisons and fundamental insights into LHCEs using different types of fluorinated solvents can guide further development of advanced electrolytes for high-voltage LMBs.