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Banner Highlight for Structure-Dependent Doppler Broadening Using a Generalized Thermal Scattering Law [DOI 10.3390/jne2020013].
We present a study of the lithium nickel manganese cobalt oxide (LiNi 0.6 Mn 0.2 Co 0.2 O 2 , NMC622) cathode-electrolyte interphase (CEI) during galvanostatic charging and discharging using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) methods to investigate the voltage dependent electrolyte solution structure changes at the interface, transition metal (TM) redox chemistry, and cathode/electrolyte interfacial layer evolution. Furthermore, our in situ cell design provides both reliable electrochemical device testing and strong FTIR vibrational absorption signals near the cathode surface. Specifically, advanced spectral analysis elucidates changes of near-surface Li+ ion (de)solvation by solvent molecules during galvanostatic cycling. Moreover, cathode metal-oxygen vibrational absorptions, sensitive to TM redox behaviors and subsequent local structural variations, were correlated to cathode de-lithiation (and lithiation) and electrolyte solution structure changes. In addition, we have detected the formation and evolution of a CEI surface layer on the NMC622 cathode that contributes to the cell's capacity fade.
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The rotational spectrum of the normal isotopologue of 1,3-oxazole (c-C 3 H 3 NO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic centrifugally distorted-rotor Hamiltonians. The measured frequencies and resulting spectroscopic constants from this extended spectral range, combined with previous measurements of the nuclear quadrupole coupling constants, will facilitate astronomical searches for oxazole across the majority of the range of modern radiotelescopes. Spectra for a set of 30 oxazole isotopologues, which include multiple isotopic substitutions of each atom, are used to determine the first semi-experimental equilibrium ($r$$^{SE}_{e}$) structure and semi-experimental substitution structure ($r$$^{SE}_{e}$), each using CCSD(T) computed values for the vibration–rotation interaction and electron-mass corrections. The large number of isotopologues, including 21 isotopologues observed for the first time, and the redundant substitutions of each atom provide sufficient spectroscopic information to determine the $r$$^{SE}_{e}$ structure with the expected high level of accuracy and precision (0.0001 or 0.0002 Å in bond distances and 0.013 to 0.025° in bond angles). In the course of this study, we analyzed a known issue for some $r$$^{SE}_{e}$ structure determinations of near-oblate asymmetric tops in which inclusion of individual isotopologues degrades the structure determination. We demonstrate that this problem primarily arises from the difference in the values of the computed vibration–rotation interaction corrections as evaluated at the computed re geometry vs the $r$$^{SE}_{e}$ geometry of the “real” molecule. Our solution to this problem substantially improves the $r$$^{SE}_{e}$ structure of oxazole and likely can be generalized to many other molecules.
The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI{sup −}), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.
We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Our results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.
Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na) for three different crystal structures, namely tetragonal (P42{sub 1}c), tetragonal (P4{sub 2}/nmc) and monoclinic (P2{sub 1}/c). Among the considered structures, tetragonal (P42{sub 1}c) phase is found to be the most stable phase for these hydrides at normal pressure. A pressure induced structural phase transition from tetragonal (P42{sub 1}c) to tetragonal (P4{sub 2}/nmc) is observed. The electronic structure reveals that these hydrides are insulators. The calculated elastic constants indicate that these ternary imides are mechanically stable at normal pressure.
In this work, we present an efficient energy-based method for structural optimization with stochastic electronic structure theories, such as diffusion quantum Monte Carlo (DMC). This method is based on robust line-search energy minimization in reduced parameter space, exploiting approximate but accurate Hessian information from a surrogate theory, such as density functional theory. The surrogate theory is also used to characterize the potential energy surface, allowing for simple but reliable ways to maximize statistical efficiency while retaining controllable accuracy. We demonstrate the method by finding the minimum DMC energy structures of the selected flake-like aromatic molecules, such as benzene, coronene, and ovalene, represented by 2, 6, and 19 structural parameters, respectively. In each case, the energy minimum is found within two parallel line-search iterations. The method is near-optimal for a line-search technique and suitable for a broad range of applications. It is easily generalized to any electronic structure method where forces and stresses are still under active development and implementation, such as diffusion Monte Carlo, auxiliary-field Monte Carlo, and stochastic configuration interaction, as well as deterministic approaches such as the random-phase approximation. Accurate and efficient means of geometry optimization could shed light on a broad class of materials and molecules, showing high sensitivity of induced properties to structural variables.
The complex crystal chemistry of elemental boron has led to numerous proposed structures with distinctive motifs as well as contradictory findings. Herein, evolutionary structure searches performed at 100 GPa have uncovered a series of metastable phases of boron, and bonding analyses were carried out to elucidate their electronic structure. These polymorphs, dynamically stable at 100 GPa, were grouped into two families. Here, the first was derived from the thermodynamic minimum at these conditions, α-Ga, whereas channels comprised the second. Two additional intergrowth structures were uncovered, and it was shown they could be constructed by stacking layers of α-Ga-like and channel-like allotropes on top of each other. A detailed bonding analysis revealed networks of four-center σ-bonding functions linked by two-center B-B bonds in the α-Ga based structures, and networks that were largely composed of three-center σ-bonding functions in the channel-based structures. Seven of these high-pressure phases were found to be metastable at atmospheric conditions, and their Vickers hardnesses were estimated to ≈ 36 GPa.
A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.
The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with these quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.
Plutonium(IV) oxalate hexahydrate (Pu(C 2 O 4 ) 2 ∙ 6H 2 O; PuOx) is an important intermediate in the recovery of plutonium from used nuclear fuel. Its formation via precipitation is well studied, yet its crystal structure remains unknown. Instead, the crystal structure of PuOx is assumed to be isostructural with neptunium(IV) oxalate hexahydrate (Np(C 2 O 4 ) 2 ∙ 6H 2 O; NpOx) and uranium(IV) oxalate hexahydrate (U(C 2 O 4 ) 2 ∙ 6H 2 O; UOx) despite the high degree of unresolved disorder that exists when determining water positions in the crystal structures of the latter two compounds. Such assumptions regarding the isostructural behavior of the actinide elements have been used to predict the structure of PuOx for use in a wide range of studies. Herein, we report the first crystal structures for PuOx and Th(C 2 O 4 ) 2 · 6H 2 O (ThOx). This data, along with new characterization of UOx and NpOx, has resulted in the full determination of the structures and resolution of the disorder around the water molecules. Specifically, we identify the coordination of two water molecules with each metal center, which necessitates a change in oxalate coordination mode from axial to equatorial that has not been reported in the literature. Here this work exemplifies the need to revisit previous assumptions regarding fundamental actinide chemistry, which are heavily relied upon within the current nuclear field.
The structure of γ-Al2O3 remains largely undetermined despite decades of research. This is due to the high degree of disorder, which poses significant challenges for structural analysis using conventional crystallographic approaches. Herein, we study the structure of γ-Al2O3 with Scanning Transmission Electron Microscopy (STEM) and ab-initio calculations to provide a complete structural description. We show that the microstructure can be understood in terms of two key structural features of nanoscale spinel domains and finite thickness segments termed as complex antiphase boundaries (cAPB) that provide the domain interconnectivity. The spinel domains have a distinctive preference for vacancy ordering, which can be rationalized in terms of a structure with a stacking disorder. Tetragonal P4 1 2 1 2 or monoclinic P2 1 models, all based on the identical motif, can be considered as representative ordered forms. Individual spinel domains are interconnected via cAPBs, which adopt a distinct non-spinel bonding environment of δ-Al 2 O 3 . The most common cAPB consists of a single delta motif with thickness of just 0.6 nm on (001), with the resulting displacement a/4 [101]. Remarkably, the cAPBs are shown to energetically stabilize the spinel domains of γ-Al 2 O 3 explaining their high abundance. We demonstrate how the tetragonal distortions naturally arise in this intricate microstructure and place the proposed model in the context of phase transformations to high temperature transition aluminas.
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We report the structure of the metallic high-temperature (ht) form of V{sub 9}O{sub 17}, determined from single crystal X-ray diffraction: space group=P-1 a=5.4219(7) A, b=7.0142(9) A, c=14.5252(19) A, {alpha}=97.0310(10) Degree-Sign , {beta}=90.9900(10) Degree-Sign , {gamma}=108.9630(10) Degree-Sign , V=517.53(12) A{sup 3}, and Z=2. We also report refinement of the structure of metallic ht-V{sub 8}O{sub 15}, space group=P-1, a=5.4315(17) A, b=7.015(2) A, c=13.147(5) A, {alpha}=100.144(4) Degree-Sign , {beta}=95.776(4) Degree-Sign , {gamma}=108.965(3) Degree-Sign , V=459.6(3) A{sup 3}, and Z=2. The structure of metallic V{sub 9}O{sub 17} is interpreted and discussed in the context of the V{sub n}O{sub 2n-1} Magneli phases, yielding trends about how the underlying forces contribute to the metal to insulator transition (MIT). The manner in which structural features of the metallic phases change as a function of n supports previous arguments that there is a turnover in the forces leading to the MIT between n=6 and n=8. - Graphical abstract: Left: The crystal structures of V{sub 8}O{sub 15} and V{sub 9}O{sub 17} shown in context of the crystallographic shear family V{sub n}O{sub 2n-1}. Right: The lattice parameters of V{sub n}O{sub 2n-1} as a function of n. The anamolous trend in b exhibits similar behavior as the metal to insulator (MIT) transition temperature (red). Highlights: Black-Right-Pointing-Pointer Crystal structures of the metallic forms of V{sub 8}O{sub 15} and V{sub 9}O{sub 17}. Black-Right-Pointing-Pointer General trends across the V{sub n}O{sub 2n-1} allow designation of two chain types in all phases. Black-Right-Pointing-Pointer Triclinic b lattice parameter varies anomalously with n, in V{sub n}O{sub 2n-1}. Black-Right-Pointing-Pointer Trend in b matches the metal to insulator transition temperature trend.
The structure of the wurtzite-derived β-AgGaO{sub 2} was refined by Rietveld analysis of high-resolution powder diffraction data obtained using synchrotron X-ray radiation. The space group of the crystal is Pna2{sub 1} with lattice parameters of a{sub 0}=5.56175 Å, b{sub 0}=7.14749 Å, and c{sub 0}=5.46875 Å. The deviation of O–Ag–O and M–O–M bond angles from the regular tetrahedral angle of 109.5° was very large at ∼8° and ∼11°, respectively. The electronic structure of β-AgGaO{sub 2} is discussed based on its structure, and the indirect band gap of β-AgGaO{sub 2} was related to significant tetrahedral distortion. Although β-AgGaO{sub 2} decomposes into metallic silver and Ga{sub 2}O{sub 3} at a high temperature in any atmosphere, β-AgGaO{sub 2} is stable up to 690 °C under an O{sub 2} atmosphere. No direct transformation from the wurtzite-derived phase to a delafossite phase occurs in β-AgGaO{sub 2}. - Graphical abstract: Crystal structure of β-AgGaO{sub 2} was refined by Rietveld analysis. AgO{sub 4} and O(Ag,Ga){sub 4} tetrahedra are significantly distorted from ideal tetrahedron. - Highlights: • Orthorhombic β-AgGaO{sub 2} with a wurtzite-derived β-NaFeO{sub 2} structure was synthesized. • Its structure was refined by Rietveld analysis of high-resolution XRD data. • Silver and oxygen tetrahedra are significantly distorted from an ideal tetrahedron. • The extent of this tetrahedral distortion is related to the band gap nature. • β-AgGaO{sub 2} is a metastable phase but is stable up to 690 °C in an O{sub 2} atmosphere.