A Combination of X‐Ray Tomography and Carbon Binder Modeling: Reconstructing the Three Phases of LiCoO2 Li‐Ion Battery Cathodes

X‐ray tomography allows the active‐material domain (LiCoO₂) of Li‐ion battery cathodes to be imaged, but it is unable to resolve the carbon‐binder domain (CBD). Here, a new method for creating a complete 3D representation (virtual design) of all three phases of a cathode is provided; this includes the active‐material domain, the CBD, and the electrolyte‐filled pore space. It combines X‐ray tomographic data of active material with a statistically modeled CBD. Two different statistical CBD morphology models are compared as examples: i) a random cluster model representing a standard mixture of carbon black and polyvenylidene fluoride (PVDF) and ii) a fiber model. The transport parameters are compared in a charged and a discharged cathode. The results demonstrate that the CBD content and morphology changes the ionic and electronic transport parameters dramatically and thus cannot be neglected. Calculations yield that the fiber model shows up to three times higher electrical conductivity at the same CBD content (discharged case) and better ionic diffusion conditions for all CBD contents. In the charged case, the morphology impact on electrical conduction is small. This effective method to generate transport parameters for different CBDs can be transferred to other CBD morphologies and electrodes.     

Three‐Phase Multiscale Modeling of a LiCoO2 Cathode: Combining the Advantages of FIB–SEM Imaging and X‐Ray Tomography

LiCoO₂ electrodes contain three phases, or domains, each having specific‐intended functions: ion‐conducting pore space, lithium‐ion‐reacting active material, and electron conducting carbon‐binder domain (CBD). Transport processes take place in all domains on different characteristic length scales: from the micrometer scale in the active material grains through to the nanopores in the carbon‐binder phase. Consequently, more than one imaging approach must be utilized to obtain a hierarchical geometric representation of the electrode. An approach incorporating information from the micro‐ and nanoscale to calculate 3D transport‐relevant properties in a large‐reconstructed active domain is presented. Advantages of focused ion beam/scanning electron microscopy imaging and X‐ray tomography combined by a spatial stochastic model, validated with an artificially produced reference structure are used. This novel approach leads to significantly different transport relevant properties compared with previous tomographic approaches: nanoporosity of the CBD leads to up to 42% additional contact area between active material and pore space and increases ionic conduction by a factor of up to 3.6. The results show that nanoporosity within the CBD cannot be neglected.     

Silicon Composite Electrodes with Dynamic Ionic Bonding

Silicon (Si) composite electrodes are developed with increased cycle lifetimes and reliability through dynamic ionic bonding between active Si nanoparticles and a polymer binder. Amine groups are covalently attached to Si nanoparticles via surface functionalization. Si composite electrodes are fabricated by combining the Si nanoparticles with a poly(acrylic acid) (PAA) binder. The formation of ionic bonds between amine groups on Si particles and carboxylic acid groups on the PAA binder is characterized by X‐ray photoelectron spectroscopy and Raman spectroscopy. Si composite anodes with ionic bonding demonstrate long term cycling stability with capacity retention of 80% at 400 cycles at a current density of 2.1 A g^?1 and good rate capability. The dynamic ionic bonds effectively mitigate the deterioration of electrical interfaces in the composite anodes as suggested by stable impedance over 300 cycles.     

Quantification of Heterogeneous Degradation in Li‐Ion Batteries

The multiscale chemomechanical interplay in lithium‐ion batteries builds up mechanical stress, provokes morphological breakdown, and leads to state of charge heterogeneity. Quantifying the interplay in complex composite electrodes with multiscale resolution constitutes a frontier challenge in precisely diagnosing the fading mechanism of batteries. In this study, hard X‐ray phase contrast tomography, capable of nanoprobing thousands of active particles at once, enables an unprecedented statistical analysis of the chemomechanical transformation of composite electrodes under fast charging conditions. The damage heterogeneity is demonstrated to prevail at all length scales, which stems from the unbalanced electron conduction and ionic diffusion, and collectively leads to the nonuniform utilization of active particles spatially and temporally. This study highlights that the statistical mapping of the chemomechanical transformation offers a diagnostic method for the particles utilization and fading, hence could improve electrode formulation for fast‐charging batteries.     

Thick Binder‐Free Electrodes for Li–Ion Battery Fabricated Using Templating Approach and Spark Plasma Sintering Reveals High Areal Capacity

The templating approach is a powerful method for preparing porous electrodes with interconnected well‐controlled pore sizes and morphologies. The optimization of the pore architecture design facilitates electrolyte penetration and provides a rapid diffusion path for lithium ions, which becomes even more crucial for thick porous electrodes. Here, NaCl microsize particles are used as a templating agent for the fabrication of 1 mm thick porous LiFePO₄ and Li₄Ti₅O₁₂ composite electrodes using spark plasma sintering technique. These sintered binder‐free electrodes are self‐supported and present a large porosity (40%) with relatively uniform pores. The electrochemical performances of half and full batteries reveal a remarkable specific areal capacity (20 mA h cm^?2), which is 4 times higher than those of 100 µm thick electrodes present in conventional tape‐casted Li–ion batteries (5 mA h cm^?2). The 3D morphological study is carried out using full field transmission X‐ray microscopy in microcomputed tomography mode to obtain tortuosity values and pore size distributions leading to a strong correlation with their electrochemical properties. These results also demonstrate that the coupling between the salt templating method and the spark plasma sintering technique turns out to be a promising way to fabricate thick electrodes with high energy density.     

Electron tomography reveals diverse conformations of integrin alphaIIbbeta3 in the active state

We used electron tomography to determine the three-dimensional (3D) structure of integrin alphaIIbbeta3 in the active state. We found that we obtained better density maps when we reconstructed a 3D volume for each individual particle in the tilt series rather than to extract the particle-containing subvolumes from a 3D reconstruction of the entire specimen area. The 3D tomographic reconstructions of 100 particles revealed that activated alphaIIbbeta3 adopts many different conformations. An average of all the individual 3D reconstructions nicely accommodated the crystal structure of the alphaVbeta3 headpiece, confirming the locations assigned to the alpha- and beta-subunit in the density map. The most striking finding of our study is the structural flexibility of the lower leg of the beta-subunit as opposed to the conformational stability of the leg of the alpha-subunit. The good fit of the atomic structure of the betaI domain and the hybrid domain in the active state showed that the hybrid domain swings out, and most particles used for tomography are in the active state. Multivariate statistical analysis and classification applied to the set of 3D reconstructions revealed that more than 90% reconstructions are grouped into the classes that show the active state. Our results demonstrate that electron tomography can be used to classify complexes with a flexible structure such as integrins.     

Carbon Coated ZnFe2O4 Nanoparticles for Advanced Lithium‐Ion Anodes

The preparation and electrochemical characterization of a new material consisting of carbon coated ZnFe₂O₄ nanoparticles is presented. This material, which offers an interesting combination of alloying and conversion mechanisms, is capable of hosting up to nine equivalents of lithium per unit formula, corresponding to an exceptional specific capacity, higher than 1000 mAh g^?1. Composite electrodes of such a material, prepared using environmentally friendly sodium carboxymethyl cellulose as binder, showed the highest, ever reported, specific capacity and high rate performance upon long‐term testing. Furthermore, in situ X‐ray diffraction analysis allowed identifying the reduction process occurring upon initial lithiation.     

Nanosilicon‐Based Thick Negative Composite Electrodes for Lithium Batteries with Graphene as Conductive Additive

Reduced graphene oxide (rGO) is used as a conductive additive for nanosilicon‐based lithium battery anodes with the high active‐mass loading typically required for industrial applications. In contrast to conventional Si electrodes that use acetylene black (AcB) as an additive, the rGO system shows pronounced improvement of electrochemical performance, irrespective of the cycling conditions. With capacity limitation, the rGO system results in improved coulombic efficiency (99.9%) and longer cycle life than conventional electrodes. Upon cycling without capacity limitation, much higher discharge capacity is maintained (2000 mAh g^?1 after 100 cycles for 2.5 mg of Si cm^?2). Used in conjunction with the bridging carboxymethyl cellulose binder, the crumpled and resilient rGO allows highly reversible functioning of the electrode in which the Si particles repeatedly inflate and deflate upon alloying and dealloying with lithium.     

Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose

D ‐Tetronitrose is a nitro‐containing tetradeoxysugar found attached to the antitumor and antibacterial agent tetrocarcin A. The biosynthesis of this highly unusual sugar in Micromonospora chalcea requires 10 enzymes. The fifth step in the pathway involves the transfer of a methyl group from S‐adenosyl‐L ‐methionine (SAM) to the C‐3′ carbon of dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐D ‐glucose. The enzyme responsible for this transformation is referred to as TcaB9. It is a monomeric enzyme with a molecular architecture based around three domains. The N‐terminal motif contains a binding site for a structural zinc ion. The middle‐ and C‐terminal domains serve to anchor the SAM and dTDP–sugar ligands, respectively, to the protein, and the active site of TcaB9 is wedged between these two regions. For this investigation, the roles of Tyr 76, His 181, Tyr 222, Glu 224, and His 225, which form the active site of TcaB9, were probed by site‐directed mutagenesis, kinetic analyses, and X‐ray structural studies. In addition, two ternary complexes of the enzyme with bound S‐adenosyl‐L ‐homocysteine and either dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐D ‐glucose or dTDP‐3‐amino‐2,3,6‐trideoxy‐D ‐galactose were determined to 1.5 or 1.6 Å resolution, respectively. Taken together, these investigations highlight the important role of His 225 in methyl transfer. In addition, the structural data suggest that the methylation reaction occurs via retention of configuration about the C‐3′ carbon of the sugar.     

Rational Design of Holey 2D Nonlayered Transition Metal Carbide/Nitride Heterostructure Nanosheets for Highly Efficient Water Oxidation

Due to integrated advantages in electrochemical functionalities for energy conversion, 2D nonlayered heterostructure nanosheets offer new and fascinating opportunities for electrocatalysis but their fabrication is challenging when compared with the widely studied 2D layered heterostructure. Herein, a bottom‐up approach is established for facile synthesis of holey 2D transition metal carbide/nitride heterostructure nanosheets (h‐TMCN) with regulated hole sizes by controlled thermal annealing of the Mo/Zn bimetallic imidazolate frameworks (Mo/Zn BIFs). Ex situ phase and structural identifications disclose that the Mo/Zn BIFs precursor experiences interconnected three steps of transformation to produce h‐TMCN. Especially, the slow successive solid‐state diffusion of nitrogen and carbon into immediate noncrystalline molybdenum oxides allows the intergrowth of Mo₂C and Mo₂N into the 2D nonlayered heterostructure. X‐ray fine structure analysis coupled with high resolution X‐ray photoelectron spectroscopy demonstrate that Mo₂C and Mo₂N in the microdomains can chemically bond with each other, producing the abundant active N–Mo–C interfaces toward water splitting. Consequently, h‐TMCN affords low overpotentials, high turnover frequencies, rapid charge transfer, and superior long‐term stability toward electrocatalytic water oxidation. The present work demonstrates the feasibility of developing a broad range of 2D nonlayered heterostructures for high efficiency chemical energy conversion.     

A comparative structure‐function analysis of active‐site inhibitors of Vibrio cholerae cholix toxin

Cholix toxin from Vibrio cholerae is a novel mono‐ADP‐ribosyltransferase (mART) toxin that shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin. Herein, we have used the high‐resolution X‐ray structure of full‐length cholix toxin in the apo form, NAD⁺ bound, and 10 structures of the cholix catalytic domain (C‐domain) complexed with several strong inhibitors of toxin enzyme activity (NAP, PJ34, and the P‐series) to study the binding mode of the ligands. A pharmacophore model based on the active pose of NAD⁺ was compared with the active conformation of the inhibitors, which revealed a cationic feature in the side chain of the inhibitors that may determine the active pose. Moreover, a conformational search was conducted for the missing coordinates of one of the main active‐site loops (R‐loop). The resulting structural models were used to evaluate the interaction energies and for 3D‐QSAR modeling. Implications for a rational drug design approach for mART toxins were derived. Copyright © 2015 John Wiley & Sons, Ltd.     

Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase

The GTPase aIF5B is a universally conserved initiation factor that assists ribosome assembly. Crystal structures of its nucleotide complexes, X‐ray(GTP) and X‐ray(GDP), are similar in the nucleotide vicinity, but differ in the orientation of a distant domain IV. This has led to two, contradictory, mechanistic models. One postulates that X‐ray(GTP) and X‐ray(GDP) are, respectively, the active, “ON” and the inactive, “OFF” states; the other postulates that both structures are OFF, whereas the ON state is still uncharacterized. We study GTP/GDP binding using molecular dynamics and a continuum electrostatic free energy method. We predict that X‐ray(GTP) has a ≈ 3 kcal/mol preference to bind GDP, apparently contradicting its assignment as ON. However, the preference arises mainly from a single, nearby residue from the switch 2 motif: Glu81, which becomes protonated upon GTP binding, with a free energy cost of about 4 kcal/mol. We then propose a different model, where Glu81 protonation/deprotonation defines the ON/OFF states. With this model, the X‐ray(GTP):GTP complex, with its protonated Glu81, is ON, whereas X‐ray(GTP):GDP is OFF. The model postulates that distant conformational changes such as domain IV rotation are “uncoupled” from GTP/GDP exchange and do not affect the relative GTP/GDP binding affinities. We analyze the model using a general thermodynamic framework for GTPases. It yields rather precise predictions for the nucleotide specificities of each state, and the state specificities of each nucleotide, which are roughly comparable to the homologues IF2 and aIF2, despite the lack of any conformational switching in the model. © 2012 Wiley Periodicals, Inc.     

A Novel Strategy to Suppress Capacity and Voltage Fading of Li‐ and Mn‐Rich Layered Oxide Cathode Material for Lithium‐Ion Batteries

Poor cycling stability is one of the key scientific issues needing to be solved for Li‐ and Mn‐rich layered oxide cathode. In this paper, sodium carboxymethyl cellulose (CMC) is first used as a novel binder in Li_1.2Ni_0.13Co_0.13Mn_0.54O₂ cathode to enhance its cycling stability. Electrochemical performance is conducted by galvanostatic charge and discharge. Structure and morphology are characterized by X‐ray diffraction, scanning electronic microscopy, high‐resolution transmission electron microscopy, and X‐ray photoelectron spectroscopy. Results reveal that the CMC as binder can not only stabilize the electrode structure by preventing the electrode materials to detach from the current collector but also suppress the voltage fading of the Li_1.2Ni_0.13Co_0.13Mn_0.54O₂ cathode due to Na⁺ ions doping. Most importantly, the dissolution of metal elements from the cathode materials into the electrolyte is also inhibited.     

3D Hierarchical Porous α‐Fe2O3 Nanosheets for High‐Performance Lithium‐Ion Batteries

To develop a long cycle life and good rate capability electrode, 3D hierarchical porous α‐Fe₂O₃ nanosheets are fabricated on copper foil and directly used as binder‐free anode for lithium‐ion batteries. This electrode exhibits a high reversible capacity and excellent rate capability. A reversible capacity up to 877.7 mAh g^?1 is maintained at 2 C (2.01 A g^?1) after 1000 cycles, and even when the current is increased to 20 C (20.1 A g^?1), a capacity of 433 mA h g^?1 is retained. The unique porous 3D hierarchical nanostructure improves electronic–ionic transport, mitigates the internal mechanical stress induced by the volume variations of the electrode upon cycling, and forms a 3D conductive network during cycling. No addition of any electrochemically inactive conductive agents or polymer binders is required. Therefore, binder‐free electrodes further avoid the uneven distribution of conductive carbon on the current collector due to physical mixing and the addition of an insulator (binder), which has benefits leading to outstanding electrochemical performance.     

X‐ray vs. NMR structures as templates for computational protein design

Certain protein‐design calculations involve using an experimentally determined high‐resolution structure as a template to identify new sequences that can adopt the same fold. This approach has led to the successful design of many novel, well‐folded, native‐like proteins. Although any atomic‐resolution structure can serve as a template in such calculations, most successful designs have used high‐resolution crystal structures. Because there are many proteins for which crystal structures are not available, it is of interest whether nuclear magnetic resonance (NMR) templates are also appropriate. We have analyzed differences between using X‐ray and NMR templates in side‐chain repacking and design calculations. We assembled a database of 29 proteins for which both a high‐resolution X‐ray structure and an ensemble of NMR structures are available. Using these pairs, we compared the rotamericity, χ₁‐angle recovery, and native‐sequence recovery of X‐ray and NMR templates. We carried out design using RosettaDesign on both types of templates, and compared the energies and packing qualities of the resulting structures. Overall, the X‐ray structures were better templates for use with Rosetta. However, for ～20% of proteins, a member of the reported NMR ensemble gave rise to designs with similar properties. Re‐evaluating RosettaDesign structures with other energy functions indicated much smaller differences between the two types of templates. Ultimately, experiments are required to confirm the utility of particular X‐ray and NMR templates. But our data suggest that the lack of a high‐resolution X‐ray structure should not preclude attempts at computational design if an NMR ensemble is available. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Highly Stable Carbon‐Free Ag/Co3O4‐Cathodes for Lithium‐Air Batteries: Electrochemical and Structural Investigations

Lithium‐air batteries with an aqueous alkaline electrolyte promise a much higher practical energy density and capacity than conventional lithium‐ion batteries. However, high cathode overpotentials are some of the main problems during cycling. In our previous work, a catalyst combination of Ag and Co₃O₄ is found that reduces overpotential significantly, and is highly active and also long‐term stable. In the present investigations, X‐ray diffraction and X‐ray photoelectron spectroscopy are applied to study the structure and composition of the cathode material during oxygen reduction reaction and oxygen evolution reaction. Changes of the oxidation states during cycling are responsible for an enhanced oxygen evolution reaction current density but also for losses due to a lower electronic conductivity of the electrodes. The presence and formation of a mixed oxidation state for silver oxide (Ag^IAg^IIIO₂) at high potentials is identified. In contradiction to literature, time dependent X‐ray diffraction measurements evidence that this phase is not stable under dry conditions and progressively decays to Ag₂O. Electrode mappings show a highly homogeneous oxidation of the electrodes during cycling and quantitative analysis of the observed phases is carried out by Rietveld analysis. Long‐term material behavior completes the investigations.     

Very High Surface Capacity Observed Using Si Negative Electrodes Embedded in Copper Foam as 3D Current Collectors

Cu foam is evaluated as a replacement for metal foil current collectors to create 3D composite electrodes with the objective to produce Si‐based anodes with high loadings. The electrodes are prepared by casting the slurry into the porosity of the foam. With such a design, the loading and the surface capacity can reach values as high as 10 mg cm^?2 and 10 mAh cm^?2. Compared to the common 2D design, the 3D copper framework shows a great advantage in the cycle life (more than 400 cycles at a Si loading of 10 mg cm^?2 with commercial micrometric particles) and power performance. The thinness of the composite coating on the foam walls favors a better preservation of the electronic wiring upon cycling and fast lithium ion diffusion. A higher coulombic efficiency in half cells with lithium metal as the counter electrode is achieved by using carbon nanofibers (CNF) rather than carbon black (CB). The possibility to reach, in practice, higher surface capacity could allow a significant increase in both the volumetric and gravimetric energy densities by 23% and 19%, respectively, for the Cu foam‐silicon//LiFePO₄ stack compared to the graphite/LiFePO₄ stack of traditional design.     

Definitive Structural Identification toward Molecule‐Type Sites within 1D and 2D Carbon‐Based Catalysts

Developing facile preparation routes and atomic‐level characterization methods for single‐atom catalysts is highly desirable but still challenging. Herein, a general strategy is proposed to construct transition metal single atoms within 1D and 2D carbon supports. The carbon supports, typically graphene and carbon nanotubes, are coated with various transition metal‐containing bimetal hydroxides, followed by polydopamine coating and high‐temperature pyrolysis. X‐ray absorption fine structure spectroscopy measurements and simulations efficiently indicate that single atoms (Co, Fe, or Cu) are captured within the applied carbon supports, distinctively forming exclusive molecule‐type sites. As a proof‐of‐concept application, the obtained catalysts exhibit remarkable performance for electrochemical oxygen reduction reaction, even surpassing commercial Pt/C catalyst. The developed versatile route opens up new avenues for the design of carbon‐based catalysts with definite molecular active sites. The atomic‐level structural identifications provide significant guidance for mechanistic studies toward single‐atom catalysts.     

Structural Characterization of a Composition Tolerant Bulk Heterojunction Blend

The ratio of the donor and acceptor components in bulk heterojunction (BHJ) organic solar cells is a key parameter for achieving optimal power conversion efficiency (PCE). However, it has been recently found that a few BHJ blends have compositional tolerance and achieve high performance in a wide range of donor to acceptor ratios. For instance, the X2 :PC₆₁BM system, where X2 is a molecular donor of intermediate dimensions, exhibits a PCE of 6.6%. Its PCE is relatively insensitive to the blend ratio over the range from 7:3 to 4:6. The effect of blend ratio of X2 /PC₆₁BM on morphology and device performance is therefore systematically investigated by using the structural characterization techniques of energy‐filtered transmission energy microscopy (EF‐TEM), resonant soft X‐ray scattering (R‐SoXS) and grazing incidence wide angle X‐ray scattering (GIWAXS). Changes in blend ratio do not lead to obvious differences in morphology, as revealed by R‐SoXS and EF‐TEM. Rather, there is a smooth evolution of a connected structure with decreasing domain spacing from 8:2 to 6:4 blend ratios. Domain spacing remains constant from 6:4 to 4:6 blend ratios, which suggests the presence of continuous phases with proper domain size that may provide access for charge carriers to reach their corresponding electrodes.     

The integrative role of cryo electron microscopy in molecular and cellular structural biology

After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo‐EM) is now heading off at unprecedented speed towards high‐resolution analysis of biological objects of various sizes. This ‘revolution in resolution’ is happening largely thanks to new developments of new‐generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo‐EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo‐EM in synergy with other methods such as X‐ray crystallography, fluorescence imaging or focussed‐ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi‐scale and multi‐resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.