X-ray crystal and molecular structure of a hydrated lithium picrate complex of benzo-15-crown-5; An example of non-chelation of the crown

Complexation of alkali and alkaline earth metal ions with crown ethers is well known (1) and chemical and crystallographic studies have been carried out for number of complexes (2,3). The interaction of the metal with the crown ether depends on the nature of the cation and particularly on the basicity of the anion (4) , In this paper we report the crystal and molecular structure of a lithium picrate complex of benzo-15-crown-5, the first x-ray crystallographic study of a lithlum-crown system.

The non-planar peptide unit II. Comparison of theory with crystal structure datastar, open

The theoretical results derived in Part I (Ramachandran, G.N., Lakshminarayan, A.V. and Kolaskar, A.S. (1973) Biochim. Biophys. Acta 303, 8–13) that the three bonds of the peptide unit meeting at N can have a pyramidal structure is confirmed by an analysis of 14 published crystal structures of small peptides. It is shown that the dihedral angles θN and Δω are correlated, while θC, is small and is uncorrelated with Δω, showing that the non-planar distortion at C′ is generally small.

Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (ϕ-ψ) may be used as folding nuclei in the design of helices and β-hairpins. α-Amino-isobutyric acid (Aib) and related Cαα dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II’ turn conformations, which serve to nucleate registered β-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel β-sheet structures. Mixed (α/β) secondary structures can be generated by linking rigid modules of helices and β-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization.

A self-consistent formulation for analysis and generation of non-uniform DNA structure

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

Molecular structure-activity relationship study of some non-steroidal antiinflammatory agents using electrostatic potential mapping

A series of 6,11-dihydro-11-oxodibenz[b,e]oxepin-2-acetic acids (DOAA) which are known to be anti-inflammatory agents were studied. The geometries of some of the molecules obtained from X-ray crystallography were used in the calculations as such while the geometries of their derivatives were obtained by local, partial geometry optimization around the Sites of substitution employing the AMI method, keeping the remaining parts of the geometries the same as those in the parent molecules. Molecular electrostatic potential (MEP) mapping was performed for the molecules using optimized hybridization displacement charges (HDC) combined with Lowdin charges, as this charge distribution has been shown earlier to yield near ab initio quality results. A good correlation has been found between the MEP values near the oxygen atoms of the hydroxyl groups of the carboxy groups of the molecules and their anti-inflammatory activities. The result is broadly in agreement with the model proposed earlier by other authors regarding the structure-activity relationship for other similar molecules.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Empirical torsional potential functions from protiesn structure DATA Phi- and Psi-Potentials for Non-glycyl Amino Acid Residues

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα-C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)-plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l-configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°). The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Beta-structure of polypeptides in non-aqueous solutions. I. Spectral characteristics of the polypeptide backbone

The optical rotatory features of the beta-structure of the polypeptides in non-aqueous solutions and films cast from these solutions have been investigated. The beta-structure of poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-O-carbo-bands of their films. The optical rotatory dispersion (ORD) and circular dichroism (CD) spectra of these polypeptides are found to be very similar in both film and solution. In solvents promoting the beta-structure, the polypeptides are characterized by CD troughs in the n-pi* transition region of the peptide chromophore. The ORD spectra are found to be positive in sign throughout the visible and accessible ultraviolet regions and are interpreted in terms of the possible existence of a relatively much larger positive pi-pi* CD bands as compared with the negative n-pi* band. The rotatory data obtained in the non-aqueous solution are compared with those obtained for other poly peptides in aqueous solutions, with respect to the type and extent of beta-structure present.

Beta-structure of polypeptides in non-aqueous solutions. II. Side-chain orientation

The specific side-chain orientations of the phenyl group in the polypeptides poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-O-carbobenzoxy-L-serine in the beta-structure have been studied by spectral measurements in solutions. All the three polypeptides exhibit aromatic CD bands, indicating the asymmetric placement of the side-chain phenyl rings when the polypeptide backbone takes up the antiparallel beta-structure. Supporting evidence for this is derived from n.m.r. spectra of the polypeptides, which show upfield shift of the phenyl protons due to the stacking of the aromatic rings. Molecular model building studies reveal the stacking of alternate phenyl groups along the polypeptide chain.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Synthesis, and crystal and electronic structure of sodium metal phosphate for use as a hybrid capacitor in non-aqueous electrolyte

Energy storage devices based on sodium have been considered as an alternative to traditional lithium based systems because of the natural abundance, cost effectiveness and low environmental impact of sodium. Their synthesis, and crystal and electronic properties have been discussed, because of the importance of electronic conductivity in supercapacitors for high rate applications. The density of states of a mixed sodium transition metal phosphate (maricite, NaMn1/3Co1/3Ni1/3PO4) has been determined with the ab initio generalized gradient approximation (GGA)+Hubbard term (U) method. The computed results for the mixed maricite are compared with the band gap of the parent NaFePO4 and the electrochemical experimental results are in good agreement. A mixed sodium transition metal phosphate served as an active electrode material for a hybrid supercapacitor. The hybrid device (maricite versus carbon) in a nonaqueous electrolyte shows redox peaks in the cyclic voltammograms and asymmetric profiles in the charge-discharge curves while exhibiting a specific capacitance of 40 F g(-1) and these processes are found to be quasi-reversible. After long term cycling, the device exhibits excellent capacity retention (95%) and coulombic efficiency (92%). The presence of carbon and the nanocomposite morphology, identified through X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) studies, ensures the high rate capability while offering possibilities to develop new cathode materials for sodium hybrid devices.

Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure

The structures of nine independent crystals of bitter gourd seed lectin (BGSL), a non-toxic homologue of type II RIPs, and its sugar complexes have been determined. The four-chain, two-fold symmetric, protein is made up of two identical two-chain modules, each consisting of a catalytic chain and a lectin chain, connected by a disulphide bridge. The lectin chain is made up of two domains. Each domain carries a carbohydrate binding site in type II RIPs of known structure. BGSL has a sugar binding site only on one domain, thus impairing its interaction at the cell surface. The adenine binding site in the catalytic chain is defective. Thus, defects in sugar binding as well as adenine binding appear to contribute to the non-toxicity of the lectin. The plasticity of the molecule is mainly caused by the presence of two possible well defined conformations of a surface loop in the lectin chain. One of them is chosen in the sugar complexes, in a case of conformational selection, as the chosen conformation facilitates an additional interaction with the sugar, involving an arginyl residue in the loop. The N-glycosylation of the lectin involves a plant-specific glycan while that in toxic type II RIPs of known structure involves a glycan which is animal as well as plant specific.

Solute induced liquid crystalline behaviour of a quaternary ammonium salt and its application to structure determination

A new liquid crystalline phase, induced by the addition of small amounts of a non-mesogenic solute (such as dimethyl sulphoxide or methyl iodide) to a quaternary ammonium salt, N-methyl-N,N,N-trioctadecylammonium iodide (MTAI), has been detected by NMR and optical microscopic studies. In some cases, there is a coexistence of nematic and smectic phases. Information on the ordering of the phases in the magnetic field of the spectrometer has been derived from NMR spectra of a dissolved molecule, C-13-enriched methyl iodide. The low order parameter of the pure thermotropic nematic phase of the salt provides first-order spectra of the dissolved oriented molecules. Analyses of spectra of cis,cis-mucononitrile exemplifies the utility of the MTAI nematic phase in the determination of structural parameters of the solute.

Probing the Neutral Edge Modes in Transport across a Point Contact via Thermal Effects in the Read-Rezayi Non-Abelian Quantum Hall States

Non-Abelian quantum Hall states are characterized by the simultaneous appearance of charge and neutral gapless edge modes, with the structure of the latter being intricately related to the existence of bulk quasiparticle excitations obeying non-Abelian statistics. Here we propose a scenario for detecting the neutral modes by having two point contacts in series separated by a distance set by the thermal equilibration length of the charge mode. We show that by using the first point contact as a heating device, the excess charge noise measured at the second point contact carries a nontrivial signature of the presence of the neutral mode. We also obtain explicit expressions for the thermal conductance and corresponding Lorentz number for transport across a quantum point contact between two edges held at different temperatures and chemical potentials.

Similarities in the Genomic Sequence and Coat Protein-Structure of Plant Viruses

The genomic sequences of several RNA plant viruses including cucumber mosaic virus, brome mosaic virus, alfalfa mosaic virus and tobacco mosaic virus have become available recently. The former two viruses are icosahedral while the latter two are bullet and rod shaped, respectively in particle morphology. The non-structural 3a proteins of cucumber mosaic virus and brome mosaic virus have an amino acid sequence homology of 35% and hence are evolutionarily related. In contrast, the coat proteins exhibit little homology, although the circular dichroism spectrum of these viruses are similar. The non-coding regions of the genome also exhibit variable but extensive homology. Comparison of the brome mosaic virus and alfalfa mosaic virus sequences reveals that they are probably related although with a much larger evolutionary distance. The polypeptide folds of the coat protein of three biologically distinct isometric plant viruses, tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been shown to display a striking resemblance. All of them consist of a topologically similar 8-standard β-barrel. The implications of these studies to the understanding of the evolution of plant viruses will be discussed.