Unraveling the Potassium Storage Mechanism in Graphite Foam

Potassium‐intercalated graphite intercalation compounds (K‐GICs) are of particular physical and chemical interest due to their versatile structures and fascinating properties. Fundamental insights into the K⁺ storage mechanism, and the complex kinetics/thermodynamics that control the reactions and structural rearrangements allow manipulating K‐GICs with desired functionalities. Here operando studies including in situ Raman mapping and in situ X‐ray diffraction (XRD) characterizations, in combination with density‐functional theory simulations are carried out to correlate the real‐time electrochemical K⁺ intercalation/deintercalation process with structure/component evolution. The experimental results, together with theoretical calculations, reveal the reversible K‐GICs staging transition: C ? stage 5 (KC₆₀) ? stage 4 (KC₄₈) ? stage 3 (KC₃₆) ? stage 2 (KC₂₄/KC₁₆) ? stage 1 (KC₈). Moreover, the staging transition is clearly visualized and an intermediate phase of stage 2 with the stoichiometric formula of KC₁₆ is identified. The staging transition mechanism involving both intrastage transition from KC₂₄ (stage 2) to KC₁₆ (stage 2) and interstage transition is proposed. The present study promotes better fundamental understanding of K⁺ storage behavior in graphite, develops a nondestructive technological basis for accurately capture nonuniformity in electrode phase evolution across the length scale of graphite domains, and offers guidance for efficient research in other GICs.     

Predicting CO2 adsorption and reactivity on transition metal surfaces using popular density functional theory methods

ABSTRACT

In this work, with Ni (110) as a model catalyst surface and CO₂ as an adsorbate, a performance study of Density Functional Theory methods (functionals) is performed. CO being a possible intermediate in CO₂ conversion reactions, binding energies of both, CO₂ and CO, are calculated on the Ni surface and are compared with experimental data. OptPBE-vdW functional correctly predicts CO₂ binding energy on Ni (?62?kJ/mol), whereas CO binding energy is correctly predicted by the rPBE-vdW functional (?138?kJ/mol). The difference in computed adsorption energies by different functionals is attributed to the calculation of gas phase CO₂. Three alternate reaction systems based on a different number of C=O double bonds present in the gas phase molecule are considered to replace CO₂. The error in computed adsorption energy is directly proportional to the number of C=O double bonds present in the gas phase molecule. Additionally, both functionals predict similar carbon–oxygen activation barrier (40?kJ/mol) and equivalent C1s shifts for probe species (?2.6?eV for CCH₃ and +1.5?eV CO₃^?), with respect to adsorbed CO₂. Thus, by including a correction factor of 28?kJ/mol for the computed CO₂ gas phase energy, we suggest using rPBE-vdW functional to investigate CO₂ conversion reactions on different metals.     

DFT tests for group 8 transition metal carbonyl complexes

The applicability of several popular density functionals in predicting the geometrical parameters and energetics of transition metal carbonyl complexes of iron, ruthenium and osmium has been studied. The methods tested include pure GGA functionals (BLYP, BP86, OPBE, HCTH, PBE, VSXC) and hybrid GGA functionals (B3PW91, B3LYP, PBE1PBE, MPW1K, B97-2, B1B95, PBE1KCIS). The effect of changing the metal basis set from Huzinaga’s all-electron basis to SDD scECP basis was also studied. The results show, that hybrid functionals are needed in order to describe the back-bonding ability of the carbonyl ligands as well as to deal with metal-metal bonds. The best general performance, when also the computational cost was considered, was obtained with hybrid functionals B3PW91 and PBE1PBE, which therefore provide an efficient tool for solving problems involving large or medium sized transition metal carbonyl compounds. Figure Optimized structure for one of the test molecules, the Ru₃(CO)₁₂ cluster, showing the staggered conformation of the carbonyl ligands     

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

We use free energy functionals that account for the partial ordering of residues in the transition state ensemble to characterize the free energy surfaces for fast folding proteins. We concentrate on chymotrypsin inhibitor and lambda-repressor. We show how the explicit cooperativity that can arise from many body forces, such as side-chain ordering or hydrophobic surface burial, determines the crossover from folding with a large delocalized nucleus and the specific small classical nucleus of the type envisioned in nucleation growth scenarios. We compare the structural correlations present in the transition state ensemble obtained from free energy functionals with those inferred from experiment using extrathermodynamic free energy relations for folding time obtained via protein engineering kinetics experiments. We also use the free energy functionals to examine both the size of barriers and multidimensional representations of the free energy profiles in order to address the question of appropriate reaction coordinates for folding.     

Validation of density functional modeling protocols on experimental bis(μ-oxo)/μ-η<Superscript>2</Superscript>:η<Superscript>2</Superscript>-peroxo dicopper equilibria

The bis(μ-oxo)/μ-η²:η²-peroxo equilibria for seven supported Cu₂O₂ cores were studied with different hybrid and nonhybrid density functional theory models, namely, BLYP, mPWPW, TPSS, TPSSh, B3LYP, mPW1PW, and MPW1K. Supporting ligands 3,3′-iminobis(N,N-dimethylpropylamine), N,N,N′,N′,N″-pentamethyldipropylenetriamine, N-[2-(pyridin-2-yl)ethyl]-N,N,N′-trimethylpropane-1,3-diamine, bis[2-(2-pyridin-2-yl)ethyl]methylamine, bis[2-(4-methoxy-2-pyridin-2-yl)ethyl]methylamine, bis[2-(4-N,N-dimethylamino-2-pyridin-2-yl)ethyl]methylamine, and 1,4,7-triisopropyl-1,4,7-triazacyclononane were chosen on the basis of the availability of experimental data for comparison. Density functionals were examined with respect to their ability accurately to reproduce experimental properties, including, in particular, geometries and relative energies for the bis(μ-oxo) and side-on peroxo forms. While geometries from both hybrid and nonhybrid functionals were in good agreement with experiment, the incorporation of Hartree–Fock (HF) exchange in hybrid density functionals was found to have a large, degrading effect on predicted relative isomer energies. Specifically, hybrid functionals predicted the μ-η²:η²-peroxo isomer to be too stable by roughly 5–10 kcal mol⁻¹ for each 10% of HF exchange incorporated into the model. Continuum solvation calculations predict electrostatic effects to favor bis(μ-oxo) isomers by 1–4 kcal mol⁻¹ depending on ligand size, with larger ligands having smaller differential solvation effects. Analysis of computed molecular partition functions suggests that nonzero measured entropies of isomerization are likely to be primarily associated with interactions between molecular solutes and their first solvation shell. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Assembly of Collagen Matrices as a Phase Transition Revealed by Structural and Rheologic Studies

We have studied the structural and viscoelastic properties of assembling networks of the extracellular matrix protein type-I collagen by means of phase contrast microscopy and rotating disk rheometry. The initial stage of the assembly is a nucleation process of collagen monomers associating to randomly distributed branched clusters with extensions of several microns. Eventually a sol-gel transition takes place, which is due to the interconnection of these clusters. We analyzed this transition in terms of percolation theory. The viscoelastic parameters (storage modulus G′ and loss modulus G″) were measured as a function of time for five different frequencies ranging from ω = 0.2 rad/s to 6.9 rad/s. We found that at the gel point both G′ and G″ obey a scaling law , with the critical exponent Δ = 0.7 and a critical loss angle being independent of frequency as predicted by percolation theory. Gelation of collagen thus represents a second order phase transition.     

Mn‐Rich P′2‐Na0.67[Ni0.1Fe0.1Mn0.8]O2 as High‐Energy‐Density and Long‐Life Cathode Material for Sodium‐Ion Batteries

Herein, P′2‐type Na_0.67[Ni_0.1Fe_0.1Mn_0.8]O₂ is introduced as a promising new cathode material for sodium‐ion batteries (SIBs) that exhibits remarkable structural stability during repetitive Na⁺ de/intercalation. The O? Ni? O? Mn? O? Fe? O bond in the octahedra of transition‐metal layers is used to suppress the elongation of the Mn? O bond and to improve the electrochemical activity, leading to the highly reversible Na storage mechanism. A high discharge capacity of ≈220 mAh g^?1 (≈605 Wh kg^?1) is delivered at 0.05 C (13 mAg^?1) with a high reversible capacity of ≈140 mAh g^?1 at 3 C and excellent capacity retention of 80% over 200 cycles. This performance is associated with the reversible P′2–OP4 phase transition and small volume change upon charge and discharge (≈3%). The nature of the sodium storage mechanism in a full cell paired with a hard carbon anode reveals an unexpectedly high energy density of ≈542 Wh kg^?1 at 0.2 C and good capacity retention of ≈81% for 500 cycles at 1 C (260 mAg^?1).     

Optical properties of P3HT and N2200 polymers: a performance study of an optimally tuned DFT functional

The optical properties of systems composed of the polymers PolyeraActivInk? N2200 and P3HT are experimentally and theoretically investigated using UV-Vis spectroscopy and time-dependent density functional theory calculations, respectively. From a theoretical point of view, we carried out an analysis considering several functionals and model oligomers of different sizes to mimic the polymers. As our studies were performed with and without solvents, a first important result regards the fact that, by considering solvent effects, a better agreement between theoretical and experimental results could be achieved. Our findings also show that an optimally tuned functional is better suited to describe the experimental absorption profile than a hybrid one for the flexible polymer (P3HT). For the almost rigid polymer considered here (N2200), on the other hand, hybrid functionals may perform better than tuned functionals.     

Insights into Ionic Transport and Structural Changes in Magnetite during Multiple‐Electron Transfer Reactions

Metal oxides, such as Fe₃O₄, hold promise for future battery applications due to their abundance, low cost, and opportunity for high lithium storage capacity. In order to better understand the mechanisms of multiple‐electron transfer reactions leading to high capacity in Fe₃O₄, a comprehensive investigation on local ionic transport and ordering is made by probing site occupancies of anions (O^2?) and cations (Li⁺, Fe³⁺/Fe²⁺) using multiple synchrotron X‐ray and electron‐beam techniques, in combination with ab‐initio calculations. Results from this study provide the first experimental evidence that the cubic‐close‐packed (ccp) O‐anion array in Fe₃O₄ is sustained throughout the lithiation and delithiation processes, thereby enabling multiple lithium intercalation and conversion reactions. Cation displacement/reordering occurs within the ccp O‐anion framework, which leads to a series of phase transformations, starting from the inverse spinel phase and turning into intermediate rock‐salt‐like phases (Li_xFe₃O₄; 0 < x < 2), then into a cation‐segregated phase (Li₂O?FeO), and finally converting into metallic Fe and Li₂O. Subsequent delithiation and lithiation processes involve interconversion between metallic Fe and FeO‐like phases. These results may offer new insights into the structure‐determined ionic transport and electrochemical reactions in metal oxides, and those of other compounds sharing a ccp anion framework, reminiscent of magnetite.     

Effect of Confinement on Melting in Slit-Shaped Pores: Experimental and Simulation Study of Aniline in Activated Carbon Fibers

Abstract

We report both experimental and molecular simulation studies of the melting behavior of aniline confined within an activated carbon fiber having slit-shaped pores. Dielectric relaxation spectroscopy is used to determine the transition temperatures and also the dielectric relaxation times over the temperature range 240 to 340 K. For the confined system two transitions were observed, one at 298 K and a second transition at 324 K. The measured relaxation times indicate that the low temperature phase (below 298 K) is a crystalline or partially crystalline solid phase, while that above 324 K is a liquid-like phase; for the intermediate phase, in the range 298–324 K, the relaxation times are of the order 10^?5s, which is typical of a hexatic phase. The melting temperature of the confined system is well above that of bulk aniline, which is 267 K. The simulations are carried out using the Grand Canonical Monte Carlo method together with Landau free energy calculations, and phase transitions are located as state points where the grand free energies of two confined phases are equal. The nature of these phases is determined by analysis of in-plane pair positional and orientational correlation functions. The simulations also show two transitions. The first is a transition from a two-dimensional hexagonal crystal phase to a hexatic phase at 296 K; the second transition is from the hexatic to a liquid-like phase at 336 K. Confinement within the slit-shaped pores appears to stabilize the hexatic phase, which is the stable phase over a wider temperature range than for quasi-two-dimensional thin films.     

Membrane potential, action potential and activation potential of eggs of the sea urchin, Lytechinus variegatus

Unfertilized Lytechinus variegatus eggs in sea water in their normal physiological state have membrane potentials that approximate ?70 to ?80 mV. This conclusion is based on microelectrode measurements and on computation from the Na⁺ and K⁺ fluxes. The ?8 to ?15 mV values for the membrane potential previously reported and which are generally measured are the consequence of depolarization by impalement. The activation potential in inseminated eggs with an initial membrane potential more negative than ?60 mV is a compound event involving sperm-induced as well as voltage dependent conductance changes. The sperm-induced mechanism is a two-phase conductance increase which involves both Na⁺ and Ca²⁺ during the first phase, and Na⁺ alone during the second phase. In addition, the sperm-induced depolarization at the beginning of the first phase activates a voltage dependent Ca²⁺-conductance mechanism resulting in generation of an action potential.     

Fast charge translocations associated with partial reactions of the Na,K-pump: II. Microscopic analysis of transient currents

Summary Nonstationary pump currents which have been observed in K⁺-free Na⁺ media after activation of the Na,K-ATPase by an ATP-concentration jump (see the preceding paper) are analyzed on the basis of microscopic reaction models. It is shown that the behavior of the current signal at short times is governed by electrically silent reactions preceding phosphorylation of the protein; accordingly, the main information on charge-translocating processes is contained in the declining phase of the pump current. The experimental results support the Albers-Post reaction scheme of the Na,K-pump, in which the translocation of Na⁺ precedes translocation of K⁺. The transient pump current is represented as the sum of contributions of the individual transitions in the reaction cycle. Each term in the sum is the product of a net transition rate times a dielectric coefficient describing the amount of charge translocated in a given reaction step. Charge translocation may result from the motion of ion-binding sites in the course of conformational changes, as well as from movement of ions in access channels connecting the binding sites to the aqueous media. A likely interpretation of the observed nonstationary currents consists in the assumption that the principal electrogenic step is the E₁-P/P-E₂ conformational transition of the protein, followed by a release of Na⁺ to the extracellular side. This conclusion is supported by kinetic data from the literature, as well as on the finding that chymotrypsin treatment which is known to block the E₁-P/P-E₂ transition abolishes the current transient. By numerical simulation of the Albers-Post reaction cycle, the proposed mechanism of charge translocation has been shown to reproduce the experimentally observed time behavior of pump currents.     

Alterations in hepatitis B virus nucleotide sequences in a chronic virus carrier from immunotolerant to immunoactive phase

Factors involved in transition from the immunotolerant to immunoactive phase in chronic hepatitis B virus (HBV) infection remain unclear. We investigated viral mutations occurring during transition and elucidated their virological and immunological significance. Full-length HBV DNA sequences were serially determined in a chronic HBV carrier from the immunotolerant to immunoactive phase. Viral replicative competence was examined by transfection analysis. HBV-specific CD8⁺ T cell response was evaluated by coculture of CD8⁺ T cells with autologous dendritic cells followed by interferon-γ Elispot assay. Eleven point mutations and two deletions appeared around the onset of the immunoactive phase. Viral replicative competence declined significantly after the onset of active hepatitis. Examination of the CD8⁺ T cell response against two putative T-cell epitopes, which contained substituted amino acids from the immunotolerant to immunoactive phase, showed that mutant HBV epitopes gave a lesser T cell response than wild-type HBV ones. In summary, point mutations and deletions may occur prior to or concurrent with the onset of the immunoactive phase during chronic HBV infection. These mutations may result in a significant decrease in both viral replicative competence and HBV-specific CD8⁺ T cell response, suggesting a possible adaptation for the maintenance of viral persistence.     

The calculation of structural,elastic and phase stability properties of minerals using first principles techniques: A comparison of HF,DFT and Hybrid functional treatments of exchange and correlation

We benchmark the performance of four treatments of electron exchange and correlation in the prediction of structural and elastic properties of a range of minerals. The treatments used are the Hartree-Fock (HF) theory, the local density approximation (LDA) and the generalised gradient approximation (GGA) to the density functional theory (DFT) and Becke's three parameter hybrid functional (B3LYP). We find that the hybrid functional, B3LYP method yields computed elastic properties in significantly better agreement to experiment than HF or DFT-LDA and performs at least as well, if not better than the most successful DFT-GGA functionals. We suggest that B3LYP is a simple, reliable and computationally efficient tool for the ab initio simulation of mineral systems.     

Performance of density functionals for the structure and energetics of (M–O)0,± (M=Al,Si, Sc–Zn)

We report the results of the performance of 20 exchange–correlation functionals of density functional theory (DFT) in the structure (Metal–Oxygen bond length) and energetical properties (bond dissociation energy, adiabatic ionisation energy, and adiabatic electron affinity) of twelve metal monoxides (M–O, M=Al, Si, Sc–Zn). The calculated results show that the selected DFT functionals have the ability to reproduce the M–O bond length with a mean deviation of 0.01–0.05 Å, the energy values are reproduced with a mean deviation of 0.20–1.00?eV. In general, the functionals with significant HF exchange show decent performance in the calculation of bond length and harmonic vibrational frequency. These functionals show poor performance in energetics. Our calculated results show that the M06-L, B3LYP, and TPSSh functionals give good performance in both structure and energetical properties of metal monoxides. These functionals are recommended for the studies of structure and energetics in metal oxide systems. Further, our studies indicate that M06-L can be used for the studies in larger molecular systems. Among the 20 DFT functionals, the recently developed N12 functional gives poor performance in the studies of metal monoxides. Hence this functional is not recommended for the studies of structure and energetics in metal oxide systems.     

Evidence for the regulation of the activity of protein kinase C through changes in membrane properties

We measured the effects of two branched-chain analogs of distearoyl-phosphatidylcholine, containing either a methyl or an n-butyl group at the 8 position, on the bilayer to hexagonal phase transition temperature of dielaidoylphosphatidylethanolamine. The former compound raised the bilayer to hexagonal phase transition temperature while the latter compound lowered it. The opposite effects of these amphiphiles on protein kinase C activity (inhibition and activation, respectively) correlated with their effects on lipid polymorphism. Because of the similarity of the structures of these two compounds, it seems likely that their opposite effects on the activity of protein kinase C is a result of their alteration of the lipid environment of the membrane rather than to binding to a specific site on the protein.We also compared the effects of hexachlorophene on lipid polymorphism and protein kinase C activity at high and at low calcium concentrations. We also found that the effect of hexachlorophene forming a complex with Ca²⁺ is to increase both the hexagonal phase forming propensity of the membrane as well as to increase the activity of protein kinase C, again demonstrating the correlation between lipid phase propensity and effects on protein kinase C activity.Abbreviations DSPC distearoylphosphatidylcholine - DSPC-8M and DSPC-8B the 8-methyl and 8-n-butyl derivatives of DSPC, respectively - PKC protein kinase C - DSC differential scanning calorimetry     

A comparison of spin probe ESR, 2H- and 31P-nuclear magnetic resonance for the study of hexagonal phase lipids

We have investigated the feasibility of the various possible magnetic resonance probes of lipids which form non-bilayer phases. As a model system we have used equimolar mixtures of phosphatidylethanolamine (PE) and cholesterol, which exhibit a thermotropic transition from a bilayer to a hexagonal phase. Variable temperature electron spin resonance (ESR) spin probe spectra were obtained using random dispersion and oriented lipid systems. Simultations of the ESR spectra were performed in order to aid in the interpretation of the experimental results for the oriented system. ³¹P- and ²H-nuclear magnetic resonance (NMR) studies were carried out using a deuterated PE. The ESR spin probes in the random dispersions show essentially no effect attributable to the phase transition. However, there are large, reversible effects in the temperature-dependent behaviour for the oriented system. The orientation dependence of the spectra above the transition temperature indicate that the hexagonal phase lipids may spontaneously assume a macroscopic organization on a flat surface. We find, however, that such an organization cannot be unambiguously assigned from the ESR spin probe spectra, and point out a potential difficulty in the interpretation of spin probe spectra in oriented systems. In contrast, the ²H-NMR method provides a reliable monitor of the phase transformation. Taken together, the ²H and ³¹P data indicate that the structure of the headgroup in PE is quite similar in both the bilayer and hexagonal phase. ²H-NMR should be very useful in probing the structural and dynamic characteristics of lipids in non-bilayer phases.     

A Brillouin scattering study of the hydration of Li- and Na-DNA films

We have used Brillouin spectroscopy to study the velocities and attenuation of acoustic phonons in wet-spun films of Na-DNA and Li-DNA as a function of the degree of hydration at room temperature. Our data for the longitudinal acoustic (LA) phonon velocity vs water content display several interesting features and reveal effects that we can model at the atomic level as interhelical bond softening and relaxation of the hydration shell. The model for interhelical softening makes use of other physical parameters of these films, which we have determined by gravimetric, x-ray, and optical microscopy studies. We extract intrinsic elastic constants for hydrated Na-DNA molecules of c₁₁ ? 8.0 × 10¹⁰ dynes/cm² and c₃₃ ? 5.7 × 10¹⁰ dynes/cm², which corresponds to a Young's modulus, E ? 1.1 × 10¹⁰ dynes/cm² (with Poisson's ratio, σ = 0.44). The negative velocity anisotropy of the LA phonons indicates that neighboring DNA molecules are held together by strong interhelical bonds in the solid state. The LA phonon attenuation data can be understood by the relaxational model in which the acoustic phonon is coupled to a relaxation mode of the water molecules. Na-DNA undergoes the A to B phase transition at a relative humidity (rh) of 92% while Li-DNA (which remains in the B form in this range) decrystallizes at an rh of 84%. We find that our Brillouin results for Na- and Li-DNA are remarkably similar, indicating that the A to B phase transition does not play an important role in determining the acoustic properties of these two types of DNA.     

Fundamental Insights from a Single‐Crystal Sodium Iridate Battery

Electrochemically driven chemical transformations play the key role in controlling storage of energy in chemical bonds and subsequent conversion to power electric vehicles and consumer electronics. The promise of coupling anionic oxygen redox with cationic redox to achieve a substantial increase in capacities has inspired research in a wide range of electrode materials. A key challenge is that these studies have focused on polycrystalline materials, where it is hard to perform precise structural determinations, especially related to the location of light atoms. Here a different approach is utilized and a highly ordered single crystal, Na_2?xIrO₃ is harnessed, to explore the role of defects and structural transformations in layered transition metal oxide materials on redox‐activity, capacity, reversibility, and stability. Within a combined experimental and theoretical framework, it is demonstrated that 1) it is possible to cycle Na_2?xIrO₃, offering proof of principle for single‐crystal based batteries 2) structural phase transitions coincide with Ir ⁴⁺/Ir ⁵⁺ redox couple with no evident contribution from anionic redox 3) strong irreversibility and capacity fade observed during cycling correlates with the Na ⁺ migration resulting in progressive growth of an electrochemically inert O3‐type NaIrO₃ phase.