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Thermodynamics of Phase Selection in MnO 2 Framework Structures through Alkali Intercalation and Hydration
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Universal Relationship between Molecular Structure and Crystal Structure in Peptoid Polymers and Prevalence of the cis Backbone Conformation
Peptoid polymers are often crystalline in the solid-state as examined by X-ray scattering, but thus far, there has been no attempt to identify a common structural motif among them. In order to probe the relationship between molecular structure and crystal structure, we synthesized and analyzed a series of crystalline peptoid copolymers, systematically varying peptoid side-chain length (S) and main-chain length (N). We also examined X-ray scattering data from 18 previously reported peptoid polymers. In all peptoids, we found that the unit cell dimensions, a, b, and c, are simple functions of S and N: a (Å) = 4.55, b (Å) = [2.98]N + 0.35, and c (Å) = [1.86]S + 5.5. These relationships, which apply to both bulk crystals and self-assembled nanosheets in water, indicate that the molecules adopt extended, planar conformations. Furthermore, we performed molecular dynamics simulations (MD) of peptoid polymer lattices, which indicate that all backbone amides adopt the cis conformation. This is a surprising conclusion, because previous studies on isolated molecules indicated an energetic preference for the trans conformer. Finally, this study demonstrates that when packed into supramolecular lattices or crystals, peptoid polymers prefer to adopt a regular, extended, all-cis secondary structure.
Structure of photosystem II and substrate binding at room temperature
Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions
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The molecular structure of plant sporopollenin
Sporopollenin is a ubiquitous and extremely chemically inert biopolymer that constitutes the outer wall of all land-plant spores and pollen grains. Sporopollenin protects the vulnerable plant gametes against a wide range of environmental assaults, and is considered as a prerequisite for the migration of early plants onto land2. Despite its importance, the chemical structure of plant sporopollenin has remained elusive1. Using a newly developed thioacidolysis degradative method together with state-of-the-art solid-state NMR techniques, we determined the detailed molecular structure of pine sporopollenin. We show here that pine sporopollenin is primarily composed of aliphatic-polyketide-derived polyvinyl alcohol units and 7-O-p-coumaroylated C16 aliphatic units, crosslinked through a distinctive dioxane moiety featuring an acetal. Naringenin was also identified as a minor component of pine sporopollenin. This discovery answers the long-standing question about the chemical makeup of plant sporopollenin, laying the foundation for future explorations of sporopollenin biosynthesis and for design of new biomimetic polymers with desirable inert properties.
Measurement of the proton spin structure at long distances
Measuring the spin structure of protons and neutrons tests our understanding of how they arise from quarks and gluons, the fundamental building blocks of nuclear matter. At long distances, the coupling constant of the strong interaction becomes large, requiring non-perturbative methods to calculate quantum chromodynamics processes, such as lattice gauge theory or effective field theories. In this work, we report proton spin structure measurements from scattering a polarized electron beam off polarized protons. The spin-dependent cross-sections were measured at large distances, corresponding to the region of low momentum transfer squared between 0.012 and 1.0GeV 2 . This kinematic range provides unique tests of chiral effective field theory predictions. Our results show that a complete description of the nucleon spin remains elusive, and call for further theoretical works, for example, in lattice quantum chromodynamics. Finally, our data extrapolated to the photon point agree with the Gerasimov–Drell–Hearn sum rule, a fundamental prediction of quantum field theory that relates the anomalous magnetic moment of the proton to its integrated spin-dependent cross-sections.
Proton spin structure and generalized polarizabilities in the strong quantum chromodynamics regime
The strong interaction is not well understood at low energies or for interactions with low momentum transfer. Chiral perturbation theory gives testable predictions for the nucleonic generalized polarizabilities, which are fundamental quantities describing the nucleon’s response to an external field. We report a measurement of the proton’s generalized spin polarizabilities extracted with a polarized electron beam and a polarized solid ammonia target in the region where chiral perturbation theory is expected to be valid. The investigated structure function g2 characterizes the internal spin structure of the proton. From its moments, we extract the longitudinal–transverse spin polarizability δLT and twist-3 matrix element and polarizability d2¯. Our results provide discriminating power between existing chiral perturbation theory calculations and will help provide a better understanding of this strong quantum chromodynamics regime.
Modified structure of protons and neutrons in correlated pairs
The atomic nucleus is made of protons and neutrons (nucleons), which are themselves composed of quarks and gluons. Understanding how the quark-gluon structure of a nucleon bound in an atomic nucleus is modified by the surrounding nucleons is an outstanding challenge. Although evidence for such modification-known as the EMC effect-was first observed over 35 years ago, there is still no generally accepted explanation for its cause. Recent observations suggest that the EMC effect is related to close-proximity short-range correlated (SRC) nucleon pairs in nuclei. Here we report simultaneous, high-precision measurements of the EMC effect and SRC abundances. We show that EMC data can be explained by a universal modification of the structure of nucleons in neutron-proton SRC pairs and present a data-driven extraction of the corresponding universal modification function. This implies that in heavier nuclei with many more neutrons than protons, each proton is more likely than each neutron to belong to an SRC pair and hence to have distorted quark structure. This universal modification function will be useful for determining the structure of the free neutron and thereby testing quantum chromodynamics symmetry-breaking mechanisms and may help to discriminate between nuclear physics effects and beyond-the-standard-model effects in neutrino experiments.
Curie-Weiss behavior of liquid structure and ideal glass state
We present the results of a structural study of metallic alloy liquids from high temperature through the glass transition. We use high energy X-ray scattering and electro-static levitation in combination with molecular dynamics simulation and show that the height of the first peak of the structure function, S(Q) -1, follows the Curie-Weiss law. The structural coherence length is proportional to the height of the first peak, and we suggest that its increase with cooling may be related to the rapid increase in viscosity. The Curie temperature is negative, implying an analogy with spin-glass. The Curie-Weiss behavior provides a pathway to an ideal glass state, a state with long-range correlation without lattice periodicity, which is characterized by highly diverse local structures, reminiscent of spin-glass.
Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure
We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.
Structural and Na-ion conduction characteristics of Na 3 PS x Se 4–x
The recent discovery of the isostructrual cubic Na 3 PS 4 and Na 3 PSe 4 as fast Na-ion conductors provided a general structural framework for the exploration of new sodium superionic conductors. In this work, we systematically investigated the structures and ionic conduction characteristics of a series of compounds with the general chemical formula of Na 3 PS x Se 4–x . Synthesis of Na 3 PS 4 under different conditions (e.g., temperature, reaction vessel, mass of the precursors) reveals the reactivity of the precursors with the reaction tubes, producing different polymorphs. X-ray diffraction studies on the solid solution phases Na 3 PS x Se 4–x identified a tetragonal-to-cubic phase transition with increasing Se concentration. This observation is consistent with the computed stability of the tetragonal and cubic polymorphs, where the energy difference between the two polymorphs becomes very close to zero in Se-rich compositions. Furthermore, ab initio molecular dynamic simulations suggest that the fast Na-ion conduction in Na 3 PS x Se 4–x may not be causally related with the symmetry or the composition of these phases. The formation of defects, instead, enables fast Na-ion conduction in this class of materials.
Effect of nucleoside analogue antimetabolites on the structure of PEO–PPO–PEO micelles investigated by SANS
In this work, the effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strength of the effect was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.
A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry
The confident identification of metabolites and xenobiotics in biological and environmental studies is an analytical challenge due to their immense dynamic range, vast chemical space and structural diversity. Ion mobility spectrometry (IMS) is widely used for small molecule analyses since it can separate isomeric species and be easily coupled with front end separations and mass spectrometry for multidimensional characterizations. However, to date IMS metabolomic and exposomic studies have been limited by an inadequate number of accurate collision cross section (CCS) values for small molecules, causing features to be detected but not confidently identified. In this work, we utilized drift tube IMS (DTIMS) to directly measure CCS values for over 450 small molecules including primary metabolites, secondary metabolites and xenobiotics. Since DTIMS measurements do not need calibrates, they avoid calibration errors which can cause CCS accuracy problems and difficulties identifying structurally similar molecules. Furthermore, all measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and seven different electric fields, so that relative standard deviations (RSD) could be assessed for each molecule and structural differences studied. The primary metabolites selected for the database are from key metabolism pathways such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle, while the secondary metabolites consist of classes such as terpenes and flavonoids, and the xenobiotics represent a range of molecules from antibiotics to polycyclic aromatic hydrocarbons. Different CCS trends were observed for several of the diverse small molecule classes, allowing insight in their separations and a possible why of classifying unknowns. This CCS database and structural information are freely available for download at http://panomics.pnnl.gov/metabolites/ with new molecules being added monthly.
Pressure-induced structural phase transition in Li 4 Ge
The structural, dynamic, elastic, and electronic properties of Li 4 Ge were investigated by means of evolutionary crystal structure prediction in conjunction with first-principles calculations.
Structural origins of the electronic properties of materials via time-resolved infrared spectroscopy
Time-resolved mid-infrared (TRIR) spectroscopy offers new opportunities to investigate how the molecular and structural properties of optoelectronic materials influence their electronic and transport states. This capability emerges from the ability to measure low energy electronic transitions in the mid-infrared that are related to delocalized states in materials and to simultaneously detect the vibrational properties of the materials that influence those states. Furthermore, the ability to simultaneously measure electronic and vibrational transitions in materials offers unprecedented opportunities to correlate structural dynamics of materials with their electronic and transport properties. Here, these capabilities are introduced by first describing the basic principles of TRIR spectroscopy used to examine electronic processes in materials. Then, several applications of TRIR spectroscopy are described in which measurements of the vibrational spectra of electronic excited states are probed as a means to correlate the structural properties of materials with the delocalization of their electronic states. In one example, exciton localization mechanisms in organic semiconductors are probed through vibrational spectra of the molecules in their excited states and correlated with their crystalline packing arrangements. Another example highlights the use of TRIR spectroscopy to examine singlet fission reaction dynamics through a combination of low energy electronic transitions and the vibrational spectra that are unique to the electronic states involved in the reaction. Finally, the use of TRIR spectroscopy to investigate charge carrier localization mechanisms in lead-halide perovskites is described, followed by an outlook of future applications of the technique in optoelectronic materials research.
Elemental iron: reduction of pertechnetate in the presence of silica and periodicity of precipitated nano-structures
Enhanced TcO 4 − reduction by metallic Fe 0 in the presence of particulate and structural Si. Rhythmical precipitation of dissolved iron leads to formation of layered structures related to geological phenomena such as orbicular rocks and Liesegang rings.
Structural instability of the CoO 4 tetrahedral chain in SrCoO 3-δ thin films
Raman scattering experiments together with detailed lattice dynamic calculations are performed to elucidate crystallographic and electronic peculiarities of SrCoO 3-δ films. We observe that the 85 cm -1 phonon mode involving the rotation of a CoO 4 tetrahedron undergoes a hardening by 21 cm -1 when the temperature is decreased. In addition, new phonon modes appear at 651.5 and 697.6 cm -1 . The latter modes are attributed to the Jahn-Teller activated modes. Upon cooling from room temperature, all phonons exhibit an exponential-like increase of intensity with a characteristic energy of about 103–107 K. We attribute this phenomenon to an instability of the CoO 4 tetrahedral chain structure, which constitutes a key ingredient to understand the electronic and structural properties of the brownmillerite SrCoO 2.5 .