Dynamic Structural Transformations in a Series of Zero-Strain Lithium-Ion Battery Materials: Almost Simultaneous Operando X-ray Diffraction and X-ray Absorption Spectroscopy on Li2ZnTi3O8 and Related Compounds.

A series of Li4/3-2x/3ZnxTi5/3-x/3O4 (LZTO) with 0 ≤ x ≤ 0.5 have received considerable interest as a negative electrode material for long-cycle-life lithium-ion batteries. However, their dynamic structural transformations under operating conditions have remained unknown, making an in-depth understanding essential for further improving the electrochemical performance. We, thus, performed almost simultaneous operando X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) studies on x = 0.125, 0.375, and 0.5. The x = 0.5 sample, Li2ZnTi3O8, indicated differences in the cubic lattice parameter between the discharge and charge reactions (δacs), corresponding to the reversible movement of Zn2+ ions between the tetrahedral and octahedral sites. δac was also observed for x = 0.125 and 0.375, although the capacity region exhibiting δac decreased with a decrease in x. For all of the samples, there is no significant difference in the nearest-neighbor distance of the Ti-O bond (dTi-O) between the discharge and charge reactions. We also demonstrated different structural transformations between the micro- (XRD) and atomic (XAS) scales. In the case for x = 0.5, for instance, the maximum microscale change in ac was within +0.29(3)%, whereas at the atomic scale, dTi-O changed by up to +4.8(3)%. Combined with our previous results for ex situ XRD and operando XRD/XAS measurements on other x compositions, the whole structural nature of LZTO, such as correspondence between ac and dTi-O, origins for voltage hysteresis, and zero-strain reaction mechanisms, has been unveiled.

Operando X-ray Diffraction and Double-Edge X-ray Absorption Spectroscopy Studies on a Perfect Zero-Strain Material.

"Zero-strain" insertion materials are essential for high-performance Li-ion batteries, but the experimental determination of changes in their local structures remains challenging. In this study, we successfully visualized the reaction scheme of a perfect zero-strain material, (Li0.75Zn0.25)[Li0.417Ti1.583]O4 with a spinel framework, using operando X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS). The operando XRD/XAS technique, which provided a series of XRD, Ti K-edge XAS, and Zn K-edge XAS data, can be employed owing to a recently developed tapered undulator and monochromator system. Although previous ex situ XRD measurements indicated the immutable cubic lattice parameter (ac) during the discharge process, these studies unveiled drastic structural variations occurring on the atomic scale between the charge and discharge reactions, such as differences in the ac, bond distances, and occupancies of the Zn2+ ions. This dynamic information obtained under operating conditions could be useful not only for understanding the zero-strain reaction scheme but also for designing advanced zero-strain insertion materials with enhanced energy density.

Revisiting LiCoO2 Using a State-of-the-Art In Operando Technique.

Lithium overstoichiometric cobalt oxide, Li(LiδCo1-δ)O2-δ, still occupies a privileged position as a positive electrode material for lithium-ion batteries. However, despite its widespread applications in commercial lithium-ion batteries, little is known about its reaction mechanisms and the effects of δ on cyclability at deep charge. We herein revisited this material through a recently developed in operando technique, i.e., rapid, alternating measurements of X-ray diffraction and X-ray absorption spectroscopy. The cyclability degraded when the charge cutoff voltage was >4.4 V versus Li+/Li, which corresponds to the Li composition exhibiting a minimum (maximum) lattice parameter along the ah (ch) axis. Differences in the structural parameters such as lattice parameters and bond distances clearly appeared between the charge and discharge reactions at a capacity below ∼220 mAh g-1. These changes occurred because deep charge and/or increasing the amount of δ induced a local distortion in the CoO6 octahedra. We found a critical Li extraction content that satisfied the need for both high capacity and cyclability for Li(LiδCo1-δ)O2-δ, which can be applied to other layered materials.

Charge Trapping Process in Photoexcited Nitrogen-Doped Titanium Oxides.

We present a first-principles study on the structural changes induced by charge trapping that occurs after photoexcitation in nitrogen-doped titanium oxide (N-TiO2). The charge trapping site and the corresponding K edge EXAFS spectra of Ti atoms were predicted and compared with those obtained by an experiment under ultraviolet (UV) light excitation. The results indicate that charge trapping occurs in the neighborhood of the oxygen vacancy (O-vac) sites. Furthermore, our calculations show that the O-vac site significantly affects the EXAFS spectra, while substitutional nitrogen doping for an oxygen site in the vicinity of the O-vac site is insensitive in the EXAFS spectra. Based on this observation combined with the knowledge from previous experiments, we propose a charge trapping process where the UV light-excited electron migrates at the O-vac site in bulk (∼300 ps) while the visible light-excited electron (N 2p → Ti 3d) is immediately trapped at the O-vac site neighboring the N site (∼1 ps).

Fe2+ Ions Alleviate the Symptom of Citrus Greening Disease.

Citrus greening (CG) is among the most devastating citrus diseases worldwide. CG-infected trees exhibit interveinal chlorotic leaves due to iron (Fe) deficiency derived from CG; thus, Fe content is lower in infected leaves than in healthy leaves. In this study, we demonstrated that the foliar application of Fe2+ relieves the symptom of CG infection in citrus trees. We applied Fe2+ and citrate to the leaves of infected rough lemon plants. Following this treatment, a reduction in the number of yellow symptomatic leaves was observed, and their growth was restored. Using chlorophyll content as an index, we screened for effective Fe complexes and found that a high ratio of citrate to Fe2+ in the applied solution led to effects against CG in Shikuwasa trees. A high proportion of Fe2+ to total Fe was another key factor explaining the effectiveness of the solution in CG infection, indicating the importance of Fe2+ absorption into plant cells. We confirmed the proportion of Fe2+ to total Fe through the high correlation of reflectometry data via a triazine reaction and X-ray absorption fine structure analysis. These results demonstrate that the foliar application of a high-Fe2+ citrate solution can restore the growth of CG diseased trees.

Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen, Fusobacterium nucleatum.

Hydrogen sulfide (H2S) plays important roles in the pathogenesis of periodontitis. Oral pathogens typically produce H2S from l-cysteine in addition to pyruvate and [Formula: see text] However, fn1055 from Fusobacterium nucleatum subsp. nucleatum ATCC 25586 encodes a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the production of H2S and l-serine from l-cysteine and H2O, an unusual cysteine (hydroxyl) lyase reaction (ß-replacement reaction). To reveal the reaction mechanism, the crystal structure of substrate-free Fn1055 was determined. Based on this structure, a model of the l-cysteine-PLP Schiff base suggested that the thiol group forms hydrogen bonds with Asp232 and Ser74, and the substrate α-carboxylate interacts with Thr73 and Gln147 Asp232 is a unique residue to Fn1055 and its substitution to asparagine (D232N) resulted in almost complete loss of ß-replacement activity. The D232N structure obtained in the presence of l-cysteine contained the α-aminoacrylate-PLP Schiff base in the active site, indicating that Asp232 is essential for the addition of water to the α-aminoacrylate to produce the l-serine-PLP Schiff base. Rapid-scan stopped-flow kinetic analyses showed an accumulation of the α-aminoacrylate intermediate during the reaction cycle, suggesting that water addition mediated by Asp232 is the rate-limiting step. In contrast, mutants containing substitutions of other active-site residues (Ser74, Thr73, and Gln147) exhibited reduced ß-replacement activity by more than 100-fold. Finally, based on the structural and biochemical analyses, we propose a mechanism of the cysteine (hydroxyl) lyase reaction by Fn1055. The present study leads to elucidation of the H2S-producing mechanism in F. nucleatum.

Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1.

The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.

A new EXAFS method for the local structure analysis of low-Z elements.

A unique analytical method is proposed for local structure analysis via extended X-ray absorption fine structure (EXAFS) spectroscopy. The measurement of electron energy distribution curves at various excitation photon energies using an electron energy analyzer is applied to determine a specific elemental Auger spectrum. To demonstrate the method, the N K-edge EXAFS spectra for a silicon nitride film were obtained via simultaneous measurement of the N KLL Auger and background spectra using dual-energy windows. The background spectrum was then used to remove the photoelectrons and secondary electron mixing in the energy distribution curves. The spectrum obtained following this subtraction procedure represents the `true' N K-edge EXAFS spectrum without the other absorptions that are observed in total electron yield N K-edge EXAFS spectra. The first nearest-neighbor distance (N-Si) derived from the extracted N K-edge EXAFS oscillation was in good agreement with the value derived from Si K-edge analysis. This result confirmed that the present method, referred to as differential electron yield (DEY)-EXAFS, is valid for deriving local surface structure information for low-Z elements.

Fungal type III polyketide synthases.

This article covers the literature on fungal type III polyketide synthases (PKSs) published from 2005 to 2014. Since the first discovery of fungal type III PKS genes in Aspergillus oryzae, reported in 2005, putative genes for type III PKSs have been discovered in fungal genomes. Compared with type I PKSs, type III PKSs are much less abundant in fungi. However, type III PKSs could have some critical roles in fungi. This article summarizes the studies on fungal type III PKS functional analysis, including Neurospora crassa ORAS, Aspergillus niger AnPKS, Botrytis cinerea BPKS and Aspergillus oryzae CsyA and CsyB. It is mostly in vitro analysis using their recombinant enzymes that has revealed their starter and product specificities. Of these, CsyB was found to be a new kind of type III PKS that catalyses the coupling of two ß-keto fatty acyl CoAs. Homology modelling reported in this article supports the importance of the capacity of the acyl binding tunnel and active site cavity in fungal type III PKSs.

Crystallization and preliminary X-ray crystallographic analysis of the inhibitory domain of the tomato mosaic virus resistance protein Tm-1.

Tm-1, an inhibitor protein of Tomato mosaic virus RNA replication, contains two conserved domains: an uncharacterized domain at its N-terminus and a TIM-barrel-like domain at its C-terminus. The N-terminal domain of Tm-1 has an inhibitory activity and its three-dimensional structure has not been determined. Here, the crystallization and preliminary X-ray diffraction of the N-terminal domain of Tm-1 are reported. A three-wavelength MAD data set was collected from a selenomethionine-labelled crystal and processed to 2.7 Å resolution. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 77.97, b = 105.28, c = 110.62 Å, α = 94.6, ß = 109.3, γ = 108.0°.

Toward Improving the Thermal Stability of Negative Electrode Materials: Differential Scanning Calorimetry and In Situ High-Temperature X-ray Diffraction/X-ray Absorption Spectroscopy Studies of Li2ZnTi3O8 and Related Compounds.

Negative electrode materials with high thermal stability are a key strategy for improving the safety of lithium-ion batteries for electric vehicles without requiring built-in safety devices. To search for crucial clues into increasing the thermal stability of these materials, we performed differential scanning calorimetry (DSC) and in situ high-temperature (HT)-X-ray diffraction (XRD)/X-ray absorption (XAS) up to 450 °C with respect to a solid-solution compound of Li4/3-2x/3ZnxTi5/3-x/3O4 with 0 ≤ x ≤ 0.5. The DSC profile of fully discharged x = 0.5 (Li2ZnTi3O8) with a LiPF6-based electrolyte could be divided into three temperature (T) regions: (i) T ≤ 250 °C for ΔHaccumi, (ii) 250 °C < T ≤ 350 °C for ΔHaccumii, and (iii) T > 350 °C for ΔHaccumiii, where ΔHaccumn is the accumulated change in enthalpy in region n. The HT-XRD/XAS analyses clarified that ΔHaccumi and ΔHaccumii originated from the decomposition of solid electrolyte interphase (SEI) films and the formation of a LiF phase, respectively. Comparison of the DSC profiles with x = 0 (Li[Li1/3Ti5/3]O4) and graphite revealed the operating voltage, i.e., amount of SEI films, and stability of the crystal lattice play significant roles in the thermal stability of negative electrode materials. Indeed, the highest thermal stability was attained at x = 0.25 using this approach.

Reversible CO2 Fixation and Release by a Trinuclear Zn(II) Cryptate Complex and Operando Analysis of the Complex Structure.

Metal complexes inspired by carbonic anhydrase (CA), which is a metalloenzyme containing Zn(II), have been investigated as alternatives for CO2 fixation systems operating under ambient temperature and pressure conditions. In this study, we designed a trinuclear Zn(II) cryptate complex (Zn3 L) and demonstrated rapid CO2 fixation with carbonation of CO2 using Zn3 L. The CO2 fixation performance of Zn3 L surpassed that of a standard CO2 absorbent, KOH(aq) solution, under conditions of the same solute concentration. In addition, the reaction achieved operation without support addition of base, which has been often required in systems of CA-inspired complexes. Fixed CO2 was released by protonating polyazacryptate ligand (L) and breaking the complex structure, and deprotonation of L induced the reconstruction of Zn3 L, allowing it to refix CO2 . This reaction mechanism was proposed based on the analysis of operando extended X-ray absorption fine structure spectroscopy. Zn3 L also demonstrated the ability to capture dilute CO2 from air, and the volume of CO2 captured by Zn3 L was approximately 2.6 times that captured by the KOH(aq) solution. Our Zn3 L exhibited three valuable properties: rapid CO2 fixation without a base, reversibility, and ability to capture dilute CO2 ; thus Zn3 L is a promising candidate as CO2 fixatives.

Highly selective CO2 electrolysis in aqueous media by a water-soluble cobalt dimethyl-bipyridine complex.

A water-soluble Co complex with dimethyl-bipyridine ligands reduced CO2 to CO electrochemically with almost 100% selectivity at -0.80 V vs. NHE in an aqueous medium (pH 6.8) without an organic solvent. The reaction overpotential was 270 mV. A possible CO formation mechanism was discussed based on experiments and calculations.

Surface loops of extracellular phospholipase A(1) determine both substrate specificity and preference for lysophospholipids.

Members of the pancreatic lipase family exhibit both lipase activity toward triacylglycerol and/or phospholipase A(1) (PLA(1)) activity toward certain phospholipids. Some members of the pancreatic lipase family exhibit lysophospholipase activity in addition to their lipase and PLA(1) activities. Two such enzymes, phosphatidylserine (PS)-specific PLA(1) (PS-PLA(1)) and phosphatidic acid (PA)-selective PLA(1)α (PA-PLA(1)α, also known as LIPH) specifically hydrolyze PS and PA, respectively. However, little is known about the mechanisms that determine their substrate specificities. Crystal structures of lipases and mutagenesis studies have suggested that three surface loops, namely, ß5, ß9, and lid, have roles in determining substrate specificity. To determine roles of these loop structures in the substrate recognition of these PLA(1) enzymes, we constructed a number of PS-PLA(1) mutants in which the three surface loops are replaced with those of PA-PLA(1)α. The results indicate that the surface loops, especially the ß5 loop, of PA-PLA(1)α play important roles in the recognition of PA, whereas other structure(s) in PS-PLA(1) is responsible for PS preference. In addition, ß5 loop of PS-PLA(1) has a crucial role in lysophospholipase activity toward lysophosphatidylserine. The present study revealed the critical role of lipase surface loops, especially the ß5 loop, in determining substrate specificities of PLA(1) enzymes.

Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans.

Galectin-8 has much higher affinity for 3'-O-sulfated or 3'-O-sialylated glycoconjugates and a Lewis X-containing glycan than for oligosaccharides terminating in Galß1→3/4GlcNAc, and this specificity is mainly attributed to the N-terminal carbohydrate recognition domain (N-domain, CRD) (Ideo, H., Seko, A., Ishizuka, I., and Yamashita, K. (2003) Glycobiology 13, 713-723). In this study, we elucidated the crystal structures of the human galectin-8-N-domain (-8N) in the absence or presence of 4 ligands. The apo molecule forms a dimer, which is different from the canonical 2-fold symmetric dimer observed for galectin-1 and -2. In a galectin-8N-lactose complex, the lactose-recognizing amino acids are highly conserved among the galectins. However, Arg(45), Gln(47), Arg(59), and the long loop region between the S3 and S4 ß-strands are unique to galectin-8N. These amino acids directly or indirectly interact with the sulfate or sialic acid moieties of 3'-sialyl- and 3'-sulfolactose complexed with galectin-8N. Furthermore, in the LNF-III-galectin-8N complex, van der Waals interactions occur between the α1-3-branched fucose and galactose and between galactose and Tyr(141), and these interactions increase the affinity toward galectin-8N. Based on the findings of these x-ray crystallographic analyses, a mutagenesis study using surface plasmon resonance showed that Arg(45), Gln(47), and Arg(59) of galectin-8N are indispensable and coordinately contribute to the strong binding of galectins-8N to sialylated and sulfated oligosaccharides. Arg(59) is the most critical amino acid for binding in the S3-S4 loop region.

Structural insights into catalysis by ßC-S lyase from Streptococcus anginosus.

Hydrogen sulfide (H(2)S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H(2)S production is associated with ßC-S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the α,ß-elimination of sulfur-containing amino acids. When Lcd acts on L-cysteine, H(2)S is produced along with pyruvate and ammonia. To understand the H(2)S-producing mechanism of Lcd in detail, we determined the crystal structures of substrate-free Lcd (internal aldimine form) and two reaction intermediate complexes (external aldimine and α-aminoacrylate forms). The formation of intermediates induced little changes in the overall structure of the enzyme and in the active site residues, with the exception of Lys234, a PLP-binding residue. Structural and mutational analyses highlighted the importance of the active site residues Tyr60, Tyr119, and Arg365. In particular, Tyr119 forms a hydrogen bond with the side chain oxygen atom of L-serine, a substrate analog, in the external aldimine form suggesting its role in the recognition of the sulfur atom of the true substrate (L-cysteine). Tyr119 also plays a role in fixing the PLP cofactor at the proper position during catalysis through binding with its side chain. Finally, we partly modified the catalytic mechanism known for cystalysin, a ßC-S lyase from Treponema denticola, and proposed an improved mechanism, which seems to be common to the ßC-S lyases from oral bacteria.

Purification, crystallization and preliminary X-ray analysis of two hydrogen sulfide-producing enzymes from Fusobacterium nucleatum.

Hydrogen sulfide produced by oral bacteria is responsible for oral malodour. Two homologous hydrogen sulfide-producing enzymes, Fn1220 and Cdl, from Fusobacterium nucleatum (which actively produces hydrogen sulfide) were overproduced, purified and crystallized. X-ray diffraction data were collected from the crystals using a synchrotron-radiation source. The Fn1220 crystal belonged to tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 (unit-cell parameters a=b=116.8, c=99.2 Å) and the Cdl crystal belonged to monoclinic space group P2(1) (unit-cell parameters a=84.9, b=70.9, c=87.6 Å, ß=90.3°).

How Fluorine Introduction Solves the Spinel Transition, a Fundamental Problem of Mn-Based Positive Electrodes.

In pursuit of high-capacity Mn-based oxides as positive electrode materials for lithium-ion batteries, the changes in the charge-discharge curve due to the spinel transition still stand in the way of the cycling stability. We found in this study that Li1.12Mn0.74O1.60F0.40 (LMOF05) positive electrodes with a loose-crystalline rock salt structure (LCRS), in which F is placed near Mn, show a stable and high capacity (300 mA h g-1, 952 W h kg-1) with little change in the charge-discharge curve. We demonstrated by F K-edge soft X-ray absorption spectroscopy and X-ray diffraction (XRD) that a part of F in the LCRS positive electrode forms F-Mn bonds. Operando XRD/X-ray absorption fine structure measurements revealed the lattice size and Mn surrounding environment during charge/discharge of F-containing LCRS positive electrodes (LMOF05), LCRS-LiMnO2 (LMO), and a spinel-like Li1.1Al0.1Mn1.8O4 positive electrode (SPINEL). Micro- and macroscopic structural changes indicate how the introduction of F suppresses the local spinel transition in Mn-based positive electrodes. These findings should be an effective tool for applying Co-free positive electrode materials for lithium-ion batteries.

Hidden function of catalytic domain in 6-methylsalicylic acid synthase for product release.

Functional investigation of the proposed dehydratase domain of ATX, a 6-methylsalicylic acid synthase from Aspergillus terreus, revealed that the domain is not involved in dehydration of the beta-hydroxytriketide intermediate tethered on the acyl carrier protein but catalyzes thioester hydrolysis to release the product from the acyl carrier protein. Thus, we renamed this domain the thioester hydrolase (TH) domain. The intermediate bound to the TH domain of mutant H972A formed in the presence of NADPH was released as 6-methylsalicylic acid by both the intact ATX and by THID (a 541-amino acid region containing TH domain and its downstream) protein, in trans. Furthermore, THID showed a catalytic activity to hydrolyze a model substrate, 6-methylsalicylic acid-N-acetylcysteamine. The TH domain is the first example of a product-releasing domain that is located in the middle of a multidomain iterative type I polyketide synthase. Moreover, it is functionally different from serine protease-type thioesterase domains of iterative type I polyketide synthases.

Thermodynamic characterization of OsGID1-gibberellin binding using calorimetry and docking simulations.

Gibberellins (GAs) are phytohormones regulating various developmental processes in plants. In rice, the initial GA-signaling events involve the binding of a GA to the soluble GA receptor protein, GID1. Although X-ray structures for certain GID1/GA complexes have recently been determined, an examination of the complexes does not fully clarify how GID1s discriminate among different GAs. Herein, we present a study aimed at defining the types of forces important to binding via a combination of isothermal titration calorimetry (ITC) and computational docking studies that employed rice GID1 (OsGID1), OsGID1 mutants, which were designed to have a decreased possible number of hydrogen bonds with bound GA, and GA variants. We find that, in general, GA binding is enthalpically driven and that a hydrogen bond between the phenolic hydroxyl of OsGID1 Tyr134 and the C-3 hydroxyl of a GA is a defining structural element. A hydrogen-bond network that involves the C-6 carboxyl of a GA that directly hydrogen bonds the hydroxyl of Ser198 and indirectly, via a two-water-molecule network, the phenolic hydroxyl of Tyr329 and the NH of the amide side-chain of Asn255 is also important for GA binding. The binding of OsGID1 by GA(1) is the most enthalpically driven association found for the biologically active GAs evaluated in this study. This observation might be a consequence of a hydrogen bond formed between the hydroxyl at the C-13 position of GA(1) and the main chain carbonyl of OsGID1 Phe245. Our results demonstrate that by combining ITC experiments and computational methods much can be learned about the thermodynamics of ligand/protein binding.