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The final steps of cell-wall biosynthesis in bacteria are carried out by penicillin-binding proteins (PBPs), whose transpeptidase domains form the cross-links in peptidoglycan chains that define the bacterial cell wall. These enzymes are the targets of β-lactam antibiotics, as their inhibition reduces the structural integrity of the cell wall. Bacterial resistance to antibiotics is a rapidly growing concern; however, the structural underpinnings of PBP-derived antibiotic resistance are poorly understood. PBP4 and PBP5 are low-affinity, class B transpeptidases that confer antibiotic resistance to Enterococcus faecalis and Enterococcus faecium, respectively. We report the crystal structures of PBP4 (1.8 Å) and PBP5 (2.7 Å) in their apo and acyl-enzyme complexes with the β-lactams benzylpenicillin, imipenem, and ceftaroline. We found that, although these three β-lactams adopt geometries similar to those observed in other class B PBP structures, there are small, but significant, differences that likely decrease antibiotic efficacy. Further, we also discovered that the N-terminal domain extensions in this class of PBPs undergo large rigid-body rotations without impacting the structure of the catalytic transpeptidase domain. Together, our findings are defining the subtle functional and structural differences in the Enterococcus PBPs that allow them to support transpeptidase activity while also conferring bacterial resistance to antibiotics that function as substrate mimics.
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The hydration and ion pair structure of Cl- ion in aqueous cesium chloride solutions at 0.5, 6 and 11 mol/kg (H2O) has been studied using Extended X-ray Absorption Fine Structure (EXAFS) at the Cl K-edge. The co-refinement of multiple EXAFS datasets shows the hydration structure of the free Cl- ion is consistent with previously reported studies. In concentrated solution the Cl- ion is strongly associated with the cation forming contact ion pairs with 1.6 and 2.8 Cs ions in 6 and 11 mol/kg aqueous CsCl, respectively. The fact that the degree of ion pairing of Cs-Cl is higher than that of both aqueous RbCl and RbBr at the same concentration is an interesting result as it deviates from the Collins’s law of matching water affinities. The reported Cs-Cl ion-pair structure provides a basis for the development and testing of improved interaction potentials leading to more realistic structures from molecular dynamics (MD) simulations. ACKNOWLEDGEMENT VTP was supported by the Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 103.99-2013.19. Work by JLF was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The PNC/XSD facilities at the Advanced Photon Source, and research at these facilities, are supported by DOE/BES, the Canadian Light Source and its funding partners, the University of Washington, and the Advanced Photon Source. Use of the Advanced Photon Source, an Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory, was supported by the DOE under Contract No. DE-AC02-06CH11357.
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Using neutron spin-echo spectroscopy, we studied the microscopic structural relaxation of a prototypical network ionic liquid ZnCl 2 at the structure factor primary peak and pre-peak. The results show that the relaxation at the primary peak is faster than the pre-peak and the activation energy is ≈33% higher. Stretched exponential relaxation is observed even at temperatures well above the melting point T m . Surprisingly, the stretching exponent shows a rapid increase upon cooling, especially at the primary peak, where it changes from stretched exponential to simple exponential on approaching T m . Furthermore, these results suggest that the appearance of glassy dynamics typical of the supercooled state even in the equilibrium liquid state of ZnCl 2 as well as the difference of activation energy at the two investigated length scales are related to the formation of network structure on cooling.
There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH 4 ) 2 and Mg(TFSI) 2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH 4 ) 2 /Mg(TFSI) 2 were investigated using a combination of natural abundance 25 Mg NMR, quantum chemistry calculations of 25 Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg 2+ and BH 4 – anions. A small increase is observed in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg 2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI) 2 in DGM electrolyte at dilute concentrations the TFSI - is fully dissociated from Mg 2+ . At higher concentrations, Mg 2+ and TFSI - are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH 4 ) 2 (saturated concentration) in DGM, the first solvation shell of a Mg 2+ ion contains two BH 4 - anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH 4 ) 2 and Mg(TFSI) 2 in DGM was found to result in the observation of a single 25 Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.
The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.
Abstract not provided
Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal–metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. Here, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.
The new uranyl aqua sulfate compound [({CH_3}{sub 3}N{sub 2}C{sub 3}H{sub 3}{CH_2COOH})(H{sub 3}O)] [(UO{sub 2}){sub 2}(SO{sub 4}){sub 3}(H{sub 2}O)]·1.5H{sub 2}O was synthesized and the crystal structure determined. The two-dimensional uranyl-aqua sulfate compound exhibits a previously reported anionic structural unit topology, but features an interstitial complex incorporating hydronium in the form of a disorder Zundel cation and the cation moiety from the ionic liquid 1-carboxymethyl 3-methylimidazolium bistriflimide [HBetMIm][Tf{sub 2}N], which forms hydrogen bonding dimer pairs. An analysis of similar uranyl sulfate complexes from the literature is conducted to explore the relative importance and role of structure directing factors in alkylammonium charge-balanced two-dimensional uranyl sulfates. A correlation is observed between structural unit charge density and interlayer spacing, with a concomitant direction of structural and orientational geometric isomerism of the anionic structural unit. We discuss the role of synthetic conditions and molecular cation properties in directing structural unit formation through charge density matching and hydrogen bonding.
The energy levels and γ-ray decay scheme of the positive-parity states in the Tz=12 nucleus 67As have been studied by using the 40Ca(36Ar,2αp)67As reaction at a beam energy of 145 MeV. Two new band structures have been identified which can be connected to the previously known levels. The results for these bands are compared with configuration-dependent cranked Nilsson–Strutinsky calculations. The good level of agreement between theory and experiment suggests that these structures can be interpreted in terms of configurations that involve three g92 particles and that both possess noncollective terminating states.
Abstract not provided
The properties of amorphous calcium carbonate provide the foundation for understanding mineralization of calcified skeletons but inconsistencies between studies suggest the physical picture is incomplete. This study quantifies the metastable solubility and structure of ACC produced under a series of chemical conditions. Using complementary in situ methods that quantify ACC structure (in situ PDF analysis) in parallel with chemical composition (TGA, ICP-OES), we find two short-range structures are produced that also show distinct morphological differences. Conditions with high carbonate ion concentrations stabilize a Ca-rich ACC with short-range order that is independent of Mg content. In contrast, low carbonate solutions favor Mg-rich ACC with mixed Ca- and Mg-short range order. Measurements of solubility product determined from supersaturated and undersaturated conditions find the distinctive structures are related to solution carbonate activity while solubility is primarily determined by the magnesium content of the solid. Bulk solubility is a composite that concurs with established values. The findings demonstrate the type of ACC that forms is tuned by Mg2+ and CO3-2- concentration and suggest ACC structure, not bulk composition, is a reliable indicator of intermediate phase. This chemical framework also provides a basis for interpreting apparent differences between observations of ACC in synthetic and natural systems that reconciles previous structural studies.