Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HCN polymers characterized by solid state NMR: chains and sheets formed in the neat liquid.

ABSTRACT: Hydrogen cyanide polymerizes readily under a variety of conditions and significant prebiotic roles have been suggested for these polymers due to the abundance of HCN in universe. However, the structures of HCN polymers have been more speculative than grounded in experimental data. Here we show that (13)C and (15)N solid state NMR spectra of polymers formed in neat HCN are inconsistent with the previously proposed structures and suggest instead that the polymers are formed by simple monomer addition, first in head-to-tail fashion to form linear, conjugated chains, and then laterally to form saturated two-dimensional networks. This interpretation of the NMR spectra finds support in other information about the polymerization of neat HCN, including the presence of free radicals. As expected from the literature, formation of the HCN tetramer, diaminomaleonitrile, is also observed, but only when the reaction is catalyzed exclusively by base and then in crystalline form.

SUBMITTER: Mamajanov I

PROVIDER: S-EPMC2832022 | biostudies-other | 2009 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

DNP-enhanced solid-state NMR spectroscopy of chromatin polymers.

Project description:Chromatin is a DNA-protein polymer that represents the functional form of the genome. The main building block of chromatin is the nucleosome, a structure that contains 147 base pairs of DNA and two copies each of the histone proteins H2A, H2B, H3 and H4. Previous work has shown that magic angle spinning (MAS) NMR spectroscopy can capture the nucleosome at high resolution although studies have been challenging due to low sensitivity, the presence of dynamic and rigid components, and the complex interaction networks of nucleosomes within the chromatin polymer. Here, we use dynamic nuclear polarization (DNP) to enhance the sensitivity of MAS NMR experiments of nucleosome arrays at 100 K and show that well-resolved 13C-13C MAS NMR correlations can be obtained much more efficiently. We evaluate the effect of temperature on the chemical shifts and linewidths in the spectra and demonstrate that changes are relatively minimal and clustered in regions of histone-DNA or histone-histone contacts. We also compare samples prepared with and without DNA and show that the low temperature 13C-13C correlations exhibit sufficient resolution to detect chemical shift changes and line broadening for residues that form the DNA-histone interface. On the other hand, we show that the measurement of DNP-enhanced 15N-13C histone-histone interactions within the nucleosome core is complicated by the natural 13C abundance network in the sample. Nevertheless, the enhanced sensitivity afforded by DNP can be used to detect long-range correlations between histone residues and DNA. Overall, our experiments demonstrate that DNP-enhanced MAS NMR spectroscopy of chromatin samples yields spectra with high resolution and sensitivity and can be used to capture functionally relevant protein-DNA interactions that have implications for gene regulation and genome organization.

| S-EPMC9191766 | biostudies-literature

Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR.

Project description:We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as (1)H-(13)C and (1)H-(15)N HETCOR or (13)C-(13)C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs.

| S-EPMC4699642 | biostudies-literature

Solid-State NMR characterization of autofluorescent fibrils formed by the elastin-derived peptide GVGVAGVG.

Project description:The characterization of the molecular structure and physical properties of self-assembling peptides is an important aspect of optimizing their utility as scaffolds for biomaterials and other applications. Here we report the formation of autofluorescent fibrils by an octapeptide (GVGVAGVG) derived via a single amino acid substitution in one of the hydrophobic repeat elements of human elastin. This is the shortest and most well-defined peptide so far reported to exhibit intrinsic fluorescence in the absence of a discrete fluorophore. Structural characterization by FTIR and solid-state NMR reveals a predominantly ?-sheet conformation for the peptide in the fibrils, which are likely assembled in an amyloid-like cross-? structure. Investigation of dynamics and the effects of hydration on the peptide are consistent with a rigid, water excluded structure, which has implications for the likely mechanism of intrinsic fibril fluorescence.

| S-EPMC3089984 | biostudies-literature

Donor-acceptor stacking arrangements in bulk and thin-film high-mobility conjugated polymers characterized using molecular modelling and MAS and surface-enhanced solid-state NMR spectroscopy.

Project description:Conjugated polymers show promising properties as cheap, sustainable and solution-processable semiconductors. A key challenge in the development of these materials is to determine the polymer chain structure, conformation and packing in both the bulk polymer and in thin films typically used in devices. However, many characterisation techniques are unable to provide atomic-level structural information owing to the presence of disorder. Here, we use molecular modelling, magic-angle spinning (MAS) and dynamic nuclear polarisation surface-enhanced NMR spectroscopy (DNP SENS) to characterise the polymer backbone group conformations and packing arrangement in the high-mobility donor-acceptor copolymer diketopyrrolo-pyrrole-dithienylthieno[3,2-b]thiophene (DPP-DTT). Using conventional 1H and 13C solid-state MAS NMR coupled with density functional theory calculations and molecular dynamics simulations, we find that the bulk polymer adopts a highly planar backbone conformation with a laterally-shifted donor-on-acceptor stacking arrangement. DNP SENS enables acquisition of 13C NMR data for polymer films, where sensitivity is limiting owing to small sample volumes. The DNP signal enhancement enables a two-dimensional 1H-13C HETCOR spectrum to be recorded for a drop-cast polymer film, and a 13C CPMAS NMR spectrum to be recorded for a spin-coated thin-film with a thickness of only 400 nm. The results show that the same planar backbone structure and intermolecular stacking arrangement is preserved in the films following solution processing and annealing, thereby rationalizing the favourable device properties of DPP-DTT, and providing a protocol for the study of other thin film materials.

| S-EPMC5413886 | biostudies-literature

Solid-state NMR spectroscopy.

Project description:Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.

| S-EPMC8341432 | biostudies-literature

Homogeneous nanoparticles to enhance the efficiency of a hydrophobic drug, antihyperlipidemic probucol, characterized by solid-state NMR.

Project description:A low absorption in the gastrointestinal tract of hydrophobic pharmaceutical compounds in use today considerably limits their bioavailability, and therefore they are taken in large doses in order to reach the therapeutic plasma concentration, which inevitably results in undesired side effects. In this study, we demonstrate a new nanoparticle approach to overcome this problem, and our experimental results show that this approach has a high efficiency of drug loading and is easily adaptable to industrial scale. Characterization of nanoparticles containing a cholesterol-lowering hydrophobic drug, probucol, using a variety of biophysical techniques revealed higher homogeneity of these particles compared to those prepared using other approaches. Intermolecular interactions of these nanoparticles are probed at high resolution by magic angle spinning solid-state NMR experiments.

| S-EPMC2814972 | biostudies-literature

Porous honeycomb structures formed from interconnected MnO2 sheets on CNT-coated substrates for flexible all-solid-state supercapacitors.

Project description:The use of lightweight and easily-fabricated MnO2/carbon nanotube (CNT)-based flexible networks as binder-free electrodes and a polyvinyl alcohol/H2SO4 electrolyte for the formation of stretchable solid-state supercapacitors was examined. The active electrodes were fabricated from 3D honeycomb porous MnO2 assembled from cross-walled and interconnected sheet-architectural MnO2 on CNT-based plastic substrates (denoted as honeycomb MnO2/CNT textiles).These substrates were fabricated through a simple two-step procedure involving the coating of multi-walled carbon nanotubes (MWCNTs) onto commercial textiles by a dipping-drying process and subsequent electrodeposition of the interconnected MnO2 sheets onto the MWCNT-coated textile. With such unique MnO2 architectures integrated onto CNT flexible films, good performance was achieved with a specific capacitance of 324 F/g at 0.5 A/g. A maximum energy density of 7.2 Wh/kg and a power density as high as 3.3 kW/kg were exhibited by the honeycomb MnO2/CNT network device, which is comparable to the performance of other carbon-based and metal oxide/carbon-based solid-state supercapacitor devices. Specifically, the long-term cycling stability of this material is excellent, with almost no loss of its initial capacitance and good Coulombic efficiency of 82% after 5000 cycles. These impressive results identify these materials as a promising candidate for use in environmentally friendly, low-cost, and high-performance flexible energy-storage devices.

| S-EPMC4750103 | biostudies-other

"CLASSIC NMR": an in-situ NMR strategy for mapping the time-evolution of crystallization processes by combined liquid-state and solid-state measurements.

Project description:A new in-situ NMR strategy (termed CLASSIC NMR) for mapping the evolution of crystallization processes is reported, involving simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time. This combined strategy allows complementary information to be obtained on the evolution of both the solid and liquid phases during the crystallization process. In particular, as crystallization proceeds (monitored by solid-state NMR), the solution state becomes more dilute, leading to changes in solution-state speciation and the modes of molecular aggregation in solution, which are monitored by liquid-state NMR. The CLASSIC NMR experiment is applied here to yield new insights into the crystallization of m-aminobenzoic acid.

| S-EPMC4227553 | biostudies-other

?-Sheet nanocrystalline domains formed from phosphorylated serine-rich motifs in caddisfly larval silk: a solid state NMR and XRD study.

Project description:Adhesive silks spun by aquatic caddisfly (order Trichoptera) larvae are used to build both intricate protective shelters and food harvesting nets underwater. In this study, we use (13)C and (31)P solid-state NMR and wide angle X-ray diffraction (WAXD) as tools to elucidate molecular protein structure of caddisfly larval silk from the species Hesperophylax consimilis . Caddisfly larval silk is a fibroin protein based biopolymer containing mostly repetitive amino acid motifs. NMR and X-ray results provide strong supporting evidence for a structural model in which phosphorylated serine repeats (pSX)4 complex with divalent cations Ca(2+) and Mg(2+) to form rigid nanocrystalline ?-sheet structures in caddisfly silk. (13)C NMR data suggests that both phosphorylated serine and neighboring valine residues exist in a ?-sheet conformation while glycine and leucine residues common in GGX repeats likely reside in random coil conformations. Additionally, (31)P chemical shift anisotropy (CSA) analysis indicates that the phosphates on phosphoserine residues are doubly ionized, and are charge-stabilized by divalent cations. Positively charged arginine side chains also likely play a role in charge stabilization. Finally, WAXD results finds that the silk is at least 7-8% crystalline, with ?-sheet interplane spacings of 3.7 and 4.5 Å.

| S-EPMC3643008 | biostudies-literature

Single-molecule bonds characterized by solid-state nanopore force spectroscopy.

Project description:Weak molecular interactions drive processes at the core of living systems, such as enzyme-substrate interactions, receptor-ligand binding, and nucleic acid replication. Single-molecule force spectroscopy is a remarkable tool for revealing molecular scale energy landscapes of noncovalent bonds, by exerting a mechanical force directly on an individual molecular complex and tracking its survival as a function of time and applied force. In principle, force spectroscopy methods can also be used for highly specific molecular recognition assays, by directly characterizing the strength of bonds between probe and target molecules. However, complexity and low throughput of conventional force spectroscopy techniques render such biosensing applications impractical. Here we demonstrate a straightforward single-molecule approach, suitable for both biophysical studies and molecular recognition assays, in which a approximately 3 nm silicon nitride nanopore is used to determine the bond lifetime spectrum of the biotin-neutravidin complex. Thousands of individual molecular complexes are captured and dissociated in the solid-state nanopore under constant applied forces, ranging from 400 to 900 mV, allowing us to extract the location of the energy barrier that governs the interaction, mapped at Deltax approximately 0.5 nm. These results highlight the capacity of a solid-state nanopore to detect and characterize intermolecular interactions and demonstrate how this could be applied to rapid, highly specific molecular detection assays.

| S-EPMC2800075 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data