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At least 1,027 records · Page 57

Materials Data on CuC3N2O5 by Materials Project

NNCuCO(CO2)2 crystallizes in the triclinic P-1 space group. The structure is zero-dimensional and consists of four carbon dioxide molecules and two NNCuCO clusters. In each NNCuCO cluster, Cu2+ is bonded in a distorted single-bond geometry to one O2- atom. The Cu–O bond length is 2.02 Å. C4+ is bonded in a 1-coordinate geometry to two N2- and one O2- atom. Both C–N bond lengths are 1.36 Å. The C–O bond length is 1.23 Å. There are two inequivalent N2- sites. In the first N2- site, N2- is bonded in a distorted single-bond geometry to one C4+ atom. In the second N2- site, N2- is bonded in a 1-coordinate geometry to one C4+ atom. O2- is bonded in a bent 120 degrees geometry to one Cu2+ and one C4+ atom.

36 MATERIALS SCIENCE↗

Materials Data on OsN5Cl3 by Materials Project

(OsN)2N2(N2Cl)2(NCl2)2 crystallizes in the orthorhombic Pnma space group. The structure is zero-dimensional and consists of four ammonia molecules, four azanylidyneosmium molecules, four dichloramine molecules, and four N2Cl clusters. In each N2Cl cluster, N+0.20+ is bonded in a single-bond geometry to one Cl1- atom. The N–Cl bond length is 1.70 Å. Cl1- is bonded in a linear geometry to two equivalent N+0.20+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on CoBr2N6O by Materials Project

CoN5NO(Br)2 crystallizes in the orthorhombic Cmcm space group. The structure is zero-dimensional and consists of eight hydrobromic acid molecules, four nitroxyl molecules, and four CoN5 clusters. In each CoN5 cluster, Co2+ is bonded in a distorted single-bond geometry to five N+1.67- atoms. There is one shorter (1.50 Å) and four longer (1.96 Å) Co–N bond length. There are three inequivalent N+1.67- sites. In the first N+1.67- site, N+1.67- is bonded in a distorted T-shaped geometry to one Co2+ and two equivalent N+1.67- atoms. Both N–N bond lengths are 1.42 Å. In the second N+1.67- site, N+1.67- is bonded in a distorted T-shaped geometry to one Co2+ and two equivalent N+1.67- atoms. In the third N+1.67- site, N+1.67- is bonded in a single-bond geometry to one Co2+ atom.

36 MATERIALS SCIENCE↗

Materials Data on Fe4AgP(XeF3)2 by Materials Project

(Xe)2Fe4AgF4PF2 crystallizes in the tetragonal I-4c2 space group. The structure is zero-dimensional and consists of four difluorophosphine molecules, eight xenon molecules, and four Fe4AgF4 clusters. In each Fe4AgF4 cluster, Fe is bonded in a distorted single-bond geometry to one F atom. The Fe–F bond length is 1.85 Å. Ag is bonded in a 4-coordinate geometry to four equivalent F atoms. All Ag–F bond lengths are 2.40 Å. F is bonded in an L-shaped geometry to one Fe and one Ag atom.

36 MATERIALS SCIENCE↗

Materials Data on CdCN2 by Materials Project

CdCN2 crystallizes in the trigonal R3m space group. The structure is zero-dimensional and consists of three hydrogen cyanide molecules and three CdN clusters. In each CdN cluster, Cd2+ is bonded in a distorted single-bond geometry to one N3- atom. The Cd–N bond length is 2.13 Å. N3- is bonded in a single-bond geometry to one Cd2+ atom.

36 MATERIALS SCIENCE↗

Materials Data on LiB12PC by Materials Project

LiB6CP(B)6 crystallizes in the orthorhombic Ima2 space group. The structure is zero-dimensional and consists of twenty-four boron molecules and four LiB6CP clusters. In each LiB6CP cluster, Li1+ is bonded in a distorted single-bond geometry to one C4- and one P3- atom. The Li–C bond length is 2.74 Å. The Li–P bond length is 2.68 Å. There are four inequivalent B+0.50+ sites. In the first B+0.50+ site, B+0.50+ is bonded in a single-bond geometry to one C4- atom. The B–C bond length is 1.67 Å. In the second B+0.50+ site, B+0.50+ is bonded in a single-bond geometry to one P3- atom. The B–P bond length is 1.91 Å. In the third B+0.50+ site, B+0.50+ is bonded in a single-bond geometry to one C4- atom. The B–C bond length is 1.66 Å. In the fourth B+0.50+ site, B+0.50+ is bonded in a single-bond geometry to one P3- atom. The B–P bond length is 1.91 Å. C4- is bonded in a tetrahedral geometry to one Li1+, three B+0.50+, and one P3- atom. The C–P bond length is 1.87 Å. P3- is bonded in a 5-coordinate geometry to one Li1+, three B+0.50+, and one C4- atom.

36 MATERIALS SCIENCE↗

Phase Behavior and Ionic Conductivity of Blended, Ion-Condensed Electrolytes with Ordered Morphologies

In this study, the amphiphilic salt lithium trifluoromethanesulfonylimide octadecane (C18LiTFSI) was used as a basis to investigate the effects of anion density and cation coordination sites within blended electrolytes with strong ionic aggregation. C18LiTFSI was previously reported as a single-component, ion-condensed electrolyte with a wide layered liquid crystalline phase regime. Three additive molecules with varyingly sized polar sulfonyl groups attached to an octodecane-tail were synthesized and mixed with C18LiTFSI. The thermal properties, morphology, and ionic conductivity of the blended electrolytes were characterized. It was found that the blended electrolytes exhibited layered liquid crystalline morphology over a narrower temperature range than the pure salt, and the ionic conductivity of the blended liquid crystalline electrolytes were generally lower than that of the pure salt. Surprising, the additives were found to have the greatest effect on the bulk ionic conductivity of the semicrystalline phase of the electrolytes. Addition of minor fractions of methylsulfonyloctadecane to C18LiTFSI resulted in increases in conductivity of over two orders of magnitude at room temperature, while addition of ethylsulfonyloctadecane or isopropylsulfonyloctadecane with the larger head group resulted in decreased ionic conductivity over the entire composition space and temperature range investigated.

Collins, Hannah (ORCID:0000000338858136)↗

Spectrophotometry of compact H II regions from 4 to 8 microns

Spectrophotometric observations from 4 to 8 microns of the compact H II regions W51-IRS 2 and K3-50 are reported. Two broad absorption features at approximately 6.0 and 6.8 microns are observed in the spectra of W51-IRS 2, and the 6.0-micron feature is seen in K3-50. These features may be due to absorption by silicate grains. A more speculative identification is absorption by hydrocarbon molecules. The continuum flux from 2 to 13 microns is broader than emission from a single-temperature blackbody; this suggests a distribution of dust temperatures within the H II regions. Failure to detect hydrogen Pfund-alpha in W51-IRS 2 indicates significant 7.5-micron extinction. Upper limits are placed on the abundance of Ar(+).

Puetter, R. C.↗

Condensed-matter energetics from diatomic molecular spectra

Analyses of molecular spectra and compression data from crystals show that a single function successfully describes the dependence on interatomic separation of both the potential energy of diatomic molecules and the cohesive binding energy of condensed matter. The empirical finding that one function describes interatomic energies for such diverse forms of matter and over a wide range of conditions can be used to extend condensed-matter equations of state but warrants further theoretical study.

Kim, In H.↗

New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces. Measuring these units was not attempted before and most studies have assumed that the growth unit consisted of individual protein molecules. The linescan mode of AFM instruments allows the crystal surface to be scanned along a single line. By scanning across a growth step an image showing the motion of the step is obtained. Normally such an image shows a straight line for continuous and constant step velocity. In this study by increasing the scan rate and by decreasing the step velocity (by decreasing the supersaturation), we were able to capture images of individual growth events, shown by jump discontinuities in the step line. By suitable integration of the image the growth unit dimension in the scanned direction can be obtained. Since multiple units can be involved in the growth process it is necessary to collect a statistically relevant sample before drawing conclusions about the growth mechanism. This technique was successfully employed to obtain the dimensions of growth units for the (110) face, showing that they consisted of various aggregates corresponding to the 43 helices in the crystal structure.

Li, Huayu↗

Dynamics of molecular associates in methanol/water mixtures

The dynamics of molecular associates in a methanol/water mixture was investigated using quasielastic neutron scattering. By measuring the signal from four methanol/water samples differing only by their isotopic composition, the relative motion of the water to methanol molecules, i.e. their mutual dynamics, was determined at the nanoscale. The thus obtained nanoscopic mutual diffusion coefficient signals a significantly slower process than the single particle diffusion of either methanol or water in the system as well as their macroscopic mutual diffusion. The data do not provide any indication of microsegregation in this preeminent alcohol/water mixture; however, they do indicate the existence of long lived but dynamic molecular associates of water and methanol molecules. Our analysis of the structural relaxation shows that the lifetime of molecular association through hydrogen bonding determines the fact that viscosity of the mixtures at intermediate concentrations is higher than that of both pure components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Disorderly Conduct of Benzamide IV: Crystallographic and Computational Analysis of High Entropy Polymorphs of Small Molecules

Benzamide, a simple derivative of benzoic acid and a common intermediate of pharmaceutical compounds, was reported to form two polymorphs in 1832, but the single crystal structure of the more stable form was not solved until 1959. Nearly 50 years later, the second form was characterized by powder diffraction, followed shortly thereafter by characterization of a third form, a polytype of the most thermodynamically stable Form I. These two new forms, Forms II and III, are metastable. Herein, we describe a fourth polymorph, Form IV, discovered by melt crystallization concurrently with its crystallization under confinement at small length scales (<10 nm), where it is stable indefinitely. Form III exists under confinement in larger pores, and melting point data for different pore sizes corroborate the existence of Form IV below 10 nm. Form IV is highly disordered, precluding indexing of powder diffraction data other than hk0 reflections. Nonetheless, a combination of powder X-ray diffraction and computational crystal structure prediction reveals that Form IV contains a 2D motif resembling that of Form II, but with longrange order in the third dimension masked by ubiquitous stacking faults. This approach relies on distilling a large number of candidate structures to a few possible disorder models based on benzamide tetrads that organize in 2D parquet-like tiles, with organization along the third dimension, that can be modeled with various stacking fault configurations having distinct intermolecular interactions and translations in the dimension orthogonal to the tiling planes. These observations reveal a bewildering crystallographic complexity for such a simple molecule. Nonetheless, the approach described herein demonstrates that challenging structures that may be abandoned prematurely because of poor crystallinity, twinning, or disorder can be solved.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Exobiological Role of Interstellar Polycyclic Aromatic Hydrocarbons and Ices

Tremendous strides have been made in our understanding of interstellar material over the past twenty years thanks to significant, parallel developments in observational astronomy and laboratory astrophysics. Before this time, the composition of interstellar dust was largely guessed-at, the presence of ices in interstellar clouds ignored, and the notion that large, gas phase, carbon rich molecules might be abundant and widespread throughout the interstellar medium (ISM) considered impossible. Today, the composition of dust in the ISM is reasonably well constrained to micron-sized cold refractory materials comprised of amorphous and crystalline silicates mixed with an amorphous carbonaceous material containing aromatic structural units and short, branched aliphatic chains. Shrouded within the protective confines of cold, opaque molecular clouds--the birthplace of stars and planets--these cold dust particles secrete mantles of mixed molecular ices whose compositions are also well constrained. Finally, amidst the molecular inventory of these ice mantles are likely to be found polycyclic aromatic hydrocarbons (PAHs), shockingly large molecules by the standards of interstellar chemistry, the telltale infrared spectral signature of which is now recognized throughout the Universe. In the first part of this talk, we will review the spectroscopic evidence that forms the basis for the currently accepted abundance and ubiquity of PANs in the ISM. We will then look at a few specific examples which illustrate how experimental and theoretical data can be applied to interpret the interstellar spectra and track how the PAN population evolves as it passes from its formation site in the circumstellar outflows of dying stars, through the various phases of the ISM, and into forn~iing planetary systems. Nevertheless, despite the fact that PANs likely represent the single largest molecular reservoir of organic carbon in evolving planetary systems, they are not what would be considered "biogenic" molecules. Although interesting from a chemical and astrophysical standpoint, in the absence of a mechanism by which this population can be dislodged from the precipitous thermodynamic well afforded by their extensive aromatic networks, they are of little Astrobiological significance. Consequently, for the remainder of the talk, we will consider the photochemical evolution of PANS under conditions similar to those found in the ISM and in proto-planetary systems with an eye toward means by which this rich repository of pre-biotic organic "ore" might be converted into materials of greater importance to Astrobiology.

Hudgins, Douglas M.↗

Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

The human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond single crystals: Imaging rubrene polymorphism across crystalline batches through lattice phonon Raman microscopy

Polymorphism is an issue troubling numerous scientific fields. A phenomenon where molecules can arrange in different orientations in a crystal lattice, polymorphism in the field of organic photovoltaic materials can dramatically change electronic properties of these materials. Rubrene is a benchmark photovoltaic material showing high carrier mobility in only one of its three polymorphs. To use rubrene in devices, it is important to quantify the polymorph distribution arising from a particular crystal growth method. However, current methods for characterizing polymorphism are either destructive or inefficient for batch scale characterization. Lattice phonon Raman spectroscopy has the ability to distinguish between polymorphs based on low frequency intermolecular vibrations. Here, we present here the addition of microscopy to lattice phonon Raman spectroscopy, which allows us to not only characterize polymorphs efficiently and nondestructively through Raman spectroscopy but also concurrently gain information on the size and morphology of the polymorphs. We provide examples for how this technique can be used to perform large, batch scale polymorph characterization for crystals grown from solution and physical vapor transport.We end with a case study showing how Raman microscopy can be used to efficiently optimize a green crystal growth method, selecting for large orthorhombic crystals desired for rubrene electronic device applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Detection of Strand Cleavage And Oxidation Damage Using Model DNA Molecules Captured in a Nanoscale Pore

We use a biological nano-scale pore to distinguish among individual DNA hairpins that differ by a single site of oxidation or a nick in the sugar-phosphate backbone. In earlier work we showed that the protein ion channel alpha-hemolysin can be used as a detector to distinguish single-stranded from double-stranded DNA, single base pair and single nucleotide differences. This resolution is in part a result of sensitivity to structural changes that influence the molecular dynamics of nucleotides within DNA. The strand cleavage products we examined here included a 5-base-pair (5-bp) hairpin with a 5-prime five-nucleotide overhang, and a complementary five-nucleotide oligomer. These produced predictable shoulder-spike and rapid near-full blockade signatures, respectively. When combined, strand annealing was monitored in real time. The residual current level dropped to a lower discrete level in the shoulder-spike blockade signatures, and the duration lengthened. However, these blockade signatures had a shorter duration than the unmodified l0bp hairpin. To test the pore sensitivity to nucleotide oxidation, we examined a 9-bp hairpin with a terminal 8-oxo-deoxyguanosine (8-oxo-dG), or a penultimate 8-oxo-dG. Each produced blockade signatures that differed from the otherwise identical control 9bp hairpins. This study showed that DNA structure is modified sufficiently by strand cleavage or oxidation damage at a single site to alter in a predictable manner the ionic current blockade signatures produced. This technique improves the ability to assess damage to DNA, and can provide a simple means to help characterize the risks of radiation exposure. It may also provide a method to test radiation protection.

Vercoutere, W.↗

One Collision—Two Substituents: Gas–Phase Preparation of Xylenes under Single–Collision Conditions

The fundamental reaction pathways to the simplest dialkylsubstituted aromatics—xylenes (C 6 H 4 (CH 3 ) 2 )—in high-temperature combustion flames and in low-temperature extraterrestrial environments are still unknown, but critical to understand the chemistry and molecular mass growth processes in these extreme environments. Exploiting crossed molecular beam experiments augmented by state-of-the-art electronic structure and statistical calculations, this study uncovers a previously elusive, facile gas-phase synthesis of xylenes through an isomer-selective reaction of 1-propynyl (methylethynyl, CH 3 CC) with 2-methyl-1,3-butadiene (isoprene, C 5 H 8 ). The reaction dynamics are driven by a barrierless addition of the radical to the diene moiety of 2-methyl-1,3-butadiene followed by extensive isomerization (hydrogen shifts, cyclization) prior to unimolecular decomposition accompanied by aromatization via atomic hydrogen loss. This overall exoergic reaction affords a preparation of xylenes not only in high-temperature environments such as in combustion flames and around circumstellar envelopes of carbon-rich Asymptotic Giant Branch (AGB) stars, but also in low-temperature cold molecular clouds (10 K) and in hydrocarbon-rich atmospheres of planets and their moons such as Triton and Titan. Furthermore, our study established a hitherto unknown gas-phase route to xylenes and potentially more complex, disubstituted benzenes via a single collision event highlighting the significance of an alkyl-substituted ethynyl-mediated preparation of aromatic molecules in our Universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

One Collision—Two Substituents: Gas–Phase Preparation of Xylenes under Single–Collision Conditions

The fundamental reaction pathways to the simplest dialkylsubstituted aromatics—xylenes (C 6 H 4 (CH 3 ) 2 )—in high-temperature combustion flames and in low-temperature extraterrestrial environments are still unknown, but critical to understand the chemistry and molecular mass growth processes in these extreme environments. Exploiting crossed molecular beam experiments augmented by state-of-the-art electronic structure and statistical calculations, this study uncovers a previously elusive, facile gas-phase synthesis of xylenes through an isomer-selective reaction of 1-propynyl (methylethynyl, CH 3 CC) with 2-methyl-1,3-butadiene (isoprene, C 5 H 8 ). The reaction dynamics are driven by a barrierless addition of the radical to the diene moiety of 2-methyl-1,3-butadiene followed by extensive isomerization (hydrogen shifts, cyclization) prior to unimolecular decomposition accompanied by aromatization via atomic hydrogen loss. This overall exoergic reaction affords a preparation of xylenes not only in high-temperature environments such as in combustion flames and around circumstellar envelopes of carbon-rich Asymptotic Giant Branch (AGB) stars, but also in low-temperature cold molecular clouds (10 K) and in hydrocarbon-rich atmospheres of planets and their moons such as Triton and Titan. Furthermore, our study established a hitherto unknown gas-phase route to xylenes and potentially more complex, disubstituted benzenes via a single collision event highlighting the significance of an alkyl-substituted ethynyl-mediated preparation of aromatic molecules in our Universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗