SciCombinator

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Concept: Circular dichroism

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Knots may ultimately prove just as versatile and useful at the nanoscale as at the macroscale. However, the lack of synthetic routes to all but the simplest molecular knots currently prevents systematic investigation of the influence of knotting at the molecular level. We found that it is possible to assemble four building blocks into three braided ligand strands. Octahedral iron(II) ions control the relative positions of the three strands at each crossing point in a circular triple helicate, while structural constraints on the ligands determine the braiding connections. This approach enables two-step assembly of a molecular 819 knot featuring eight nonalternating crossings in a 192-atom closed loop ~20 nanometers in length. The resolved metal-free 819 knot enantiomers have pronounced features in their circular dichroism spectra resulting solely from topological chirality.

Concepts: Knot, Chirality, Topology, Circular dichroism, Loop, Rope, Ropework, Knots

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Semiconductors with chiral geometries at the nanoscale and mesoscale provide a rich materials platform for polarization optics, photocatalysis, and biomimetics. Unlike metallic and organic optical materials, the relationship between the geometry of chiral semiconductors and their chiroptical properties remains, however, vague. Homochiral ensembles of semiconductor helices with defined geometries open the road to understanding complex relationships between geometrical parameters and chiroptical properties of semiconductor materials. We show that semiconductor helices can be prepared with an absolute yield of ca 0.1% and an enantiomeric excess (e.e.) of 98% or above from cysteine-stabilized cadmium telluride nanoparticles (CdTe NPs) dispersed in methanol. This high e.e. for a spontaneously occurring chemical process is attributed to chiral self-sorting based on the thermodynamic preference of NPs to assemble with those of the same handedness. The dispersions of homochiral self-assembled helices display broadband visible and near-infrared (Vis-NIR) polarization rotation with anisotropy (g) factors approaching 0.01. Calculated circular dichroism (CD) spectra accurately reproduced experimental CD spectra and gave experimentally validated spectral predictions for different geometrical parameters enabling de novo design of chiroptical semiconductor materials. Unlike metallic, ceramic, and polymeric helices that serve predominantly as scatterers, chiroptical properties of semiconductor helices have nearly equal contribution of light absorption and scattering, which is essential for device-oriented, field-driven light modulation. Deconstruction of a helix into a series of nanorods provides a simple model for the light-matter interaction and chiroptical activity of helices. This study creates a framework for further development of polarization-based optics toward biomedical applications, telecommunications, and hyperspectral imaging.

Concepts: Optics, Chirality, Cadmium, Solar cell, Electrical conductivity, Tellurium, Circular dichroism, Dichroism

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The helical structure is experimentally determined by circular dichroism (CD) spectra. The sign and shape of the CD spectra are different between B-DNA with a right-handed double-helical structure and Z-DNA with a left-handed double-helical structure. In particular, the sign at around 295 nm in CD spectra is positive for B-DNA, which is opposite to that of Z-DNA. However, it is difficult to determine the helical structure from the UV absorption spectra. Three important factors that affect the CD spectra of DNA are 1) the conformation of dG monomer, 2) the hydrogen-bonding interaction between two helices and 3) the stacking interaction between nucleic acid bases. We calculated the CD spectra of 1) the dG monomer at different conformations, 2) the composite of dG and dC monomers, 3) two dimer models that simulate separately the hydrogen-bonding interaction and the stacking interaction and 4) the tetramer model that includes both hydrogen-bonding and stacking interactions simultaneously. The helical structure of DNA can be clarified by a comparison of the experimental and SAC-CI theoretical CD spectra of DNA and that the sign at around 295 nm of the CD spectra of Z-DNA reflects from the strong stacking interaction characteristic of its helical structure.

Concepts: DNA, Protein, Nucleic acid, Monomer, Double helix, Circular dichroism, Alpha helix, Helices

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The solution-dispersed-state and polymer-dispersed-state circular dichroism (CD) and circularly polarized luminescence (CPL) properties of chiral binaphthyl fluorophores could be controlled by the choice of open- or closed-type substituents on the binaphthyl units and by the axial chirality of the binaphthyls.

Concepts: Optics, Stereochemistry, Chirality, Polarization, Circular polarization, Circular dichroism, Axial chirality

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Terpecurcumins A-I (1-9), together with three known analogues (10-12), were isolated from the rhizomes of Curcuma longa (turmeric). They were derived from the hybridization of curcuminoids and bisabolanes. The structures and absolute configurations of 1-9 were elucidated on the basis of extensive spectroscopic data analysis, including NMR and electronic circular dichroism spectra. The configuration of 10 was further confirmed by X-ray crystallography. A plausible biogenetic relationship for 1-12 is proposed. Compounds 4, 6, 7, 10, and 11 showed higher cytotoxic activities (IC(50), 10.3-19.4 μM) than curcumin (IC(50), 31.3-49.2 μM) against human cancer cell lines (A549, HepG2, and MDA-MB-231).

Concepts: Cell, X-ray, X-ray crystallography, Circular dichroism, Curcuma, Turmeric, Curcumin, Zingiberaceae

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Circular dichroism spectra reveal that sodium dodecyl benzene sulfonate (SDBS) at low concentrations can effectively prevent the aggregation of lysozyme molecules, while SDBS at high concentrations can lead to conformational and structural change of the protein. SDBS is able to inhibit the enzymatic activity of lysozyme in a highly efficient dose-dependent manner. The interaction mechanism of SDBS with lysozyme has been investigated by measuring optical spectra. Based on fluorescence and UV-vis spectra, microenvironmental change in and around the active site region induced by SDBS has been revealed and explained. Two-dimensional FTIR spectra have been analyzed to identify the secondary structures and residues of lysozyme, which have a preferential interaction with SDBS. Hydroxypropyl β-cyclodextrin (HP-β-CD) was used to detach SDBS from the inactivated enzyme, and complete recovery of enzymatic activity was achieved. Thus, the enzymatic activity of lysozyme can be regulated by SDBS and HP-β-CD.

Concepts: Protein, Metabolism, Enzyme, Catalysis, Chemical equilibrium, Enzyme inhibitor, Circular dichroism, Active site

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Collagen-nanoparticle interactions are vital for many biomedical applications including drug delivery and tissue engineering applications. Iron oxide nanoparticles synthesized using starch template according to our earlier reported procedures were functionalized by treating them with Gum Arabic (GA), a biocompatible polysaccharide, so as to enhance the interaction between nanoparticle surfaces and collagen. Viscosity, circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) techniques have been used to study the collagen-nanoparticle interactions. The relative viscosity for collagen-nanoparticle conjugate was found to increase with increase in concentration of the nanoparticle within the concentration range investigated, which is due to the aggregation of protein onto the surface of nanoparticle. The CD spectra for the collagen-nanoparticle at different concentration ratios do not have much variation in the Rpn values (ratio of positive peak intensity over negative peak intensity) after functionalization with GA. The variation of molar ellipticity values for collagen-nanoparticle is due to the glycoprotein present in GA. The collagen triple helical structure is maintained after interaction with nanoparticles. The FTIR spectra of native collagen, Coll-Fs (nanoparticle without functionalization) and Coll-FsG (nanoparticle functionalized with GA) show clearly the amide I, II, III bands, with respect to collagen. The ability of polysaccharide stabilized/functionalized nanoparticles to maintain the collagen properties would help in its biomedical applications.

Concepts: Protein, Spectroscopy, Ultraviolet, Fourier transform, Infrared spectroscopy, Fourier transform spectroscopy, Circular dichroism, Alpha helix

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Class IIa bacteriocins are potent antimicrobial peptides produced by lactic acid bacteria to destroy competing microorganisms. The N-terminal domain of these peptides consists of a conserved YGNGV sequence and a disulphide bond. The YGNGV motif is essential for activity, whereas, the two cysteines involved in the disulphide bond can be replaced with hydrophobic residues. The C-terminal region has variable sequences, and folds into a conserved amphipathic α-helical structure. To elucidate the structure-activity relationship in the N-terminal domain of these peptides, three analogues (1-3) of a class IIa bacteriocin, Leucocin A (LeuA), were designed and synthesized by replacing the N-terminal β-sheet residues of the native peptide with shorter β-turn motifs. Such replacement abolished the antibacterial activity in the analogues, however, analogue 1 was able to competitively inhibit the activity of native LeuA. Native LeuA (37-mer) was synthesized using native chemical ligation method in high yield. Solution conformation study using circular dichroism spectroscopy and molecular dynamics simulations suggested that the C-terminal region of analogue 1 adopts helical folding as found in LeuA, while the N-terminal region did not fold into β-sheet conformation. These structure-activity studies highlight the role of proper folding and complete sequence in the activity of class IIa bacteriocins.

Concepts: Protein, Protein structure, Bacteria, Microbiology, Sequence, Peptide synthesis, N-terminus, Circular dichroism

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From the fruits of the tropical tree Aphanamixis grandifolia, five new evodulone-type limonoids, aphanalides I-M (1-5), one new apo-tirucallane-type triterpenoid, polystanin E (6), and three new chain-like diterpenoids, nemoralisins A-C (7-9), along with 12 known compounds were identified. The absolute configurations were determined by a combination of single-crystal X-ray diffraction studies, Mo2(OAc)4-induced electronic circular dichroism (ECD) data, the Mosher ester method, and calculated ECD data. The cytotoxicities of all the isolates and the insecticidal activities of the limonoids were evaluated.

Concepts: DNA, Diffraction, X-ray, Absolute, Terpenoid, Circular dichroism

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Determination of the absolute configuration (AC) is often a challenging aspect in the structure elucidation of natural products. When chiral compounds possess appropriate chromophore(s), electronic circular dichroism (ECD) may provide a powerful approach to the determination of their absolute configuration. Recently, ECD calculations by time-dependent density functional theory (TDDFT) have come to be used more commonly. In the present review, we give several examples of recent studies using TDDFT-calculated ECD spectra for the AC determination of natural products.

Concepts: Stereochemistry, Chirality, Density functional theory, Circular dichroism, Time-dependent density functional theory