Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-beta Gly-NHMe (2), Piv-Pro-beta Gly-OMe (3), Piv-Pro-delta Ava-OMe (4) and Boc-Pro-gamma Abu-OH (5) are described (Piv:pivaloyl; NHMe: N-methylamide; beta Gly:beta-glycine; OMe:O-methyl ester; delta Ava:delta-aminovaleric acid; gamma Abu:gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-beta Gly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the delta Ava residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H center dot center dot center dot O hydrogen bond.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.

Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein

The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.

ESR studies of X-irradiated strontium mixed calcium tartrate crystals

The electron spin resonance spectra of X-ray irradiated single crystals of strontium doped calcium tartrate tetrahydrate (CST) with molecular formula Ca0.88Sr0.12C4H4O6.4H(2)O grown in gels has been investigated. Only one species of free radical but with two magnetically unequivalent sites was observed at room temperature. The free radical was found to be the result of the splitting of a C-II bond adjacent to both the hydroxyl and carboxyl groups. The a factor was found to be slightly anisotropic. Couplings with two H nuclei, believed to be the proton of the OH group attached directly to the unsaturated asymmetric carbon atom and the proton attached directly to the: other asymmetric carbon atom of the molecule were observed. The principal g-values were found to be 2.0030, 2.0017, 2.0027. The principal elements of the nuclear coupling are 7.45, 6.59, 4.28 and 8.56, 7.22, 18.71 G, respectively. The radical was found to be very stable. (C) 2000 Elsevier Science Ltd. All rights reserved.

Surface Structures of Silicon and Germanium

Si and Ge were cleaved on the (111) plane under ultra high vacuum and exposed to O and subsequent heat treatment. LEED and spot photometric measurements were taken. Cleaved surfaces for both Si and Ge gave the expected (2 x 1) structure. Results for O exposure were qualitatively for Si and Ge. The 1/2 orders disappeared after exposure to approx = 10 exp - exp 7. Integral orders started to weaken at 10 exp -6 to 10 exp - exp 2 torr min., disappearing at 10 exp -1 torr min. Heat treatment of Si at 900 deg C for several seconds restored the integral orders and further heating gave a new pattern with 1/3 orders. Exposure to 2 x 10 exp -6 torr min O without further heating weakened the fractional orders and at 10 exp -5 torr min they disappeared. Integral orders remained after further heating in O. For Ge integral orders were not restored after 0 exposure until heat treatment had continued at 550 deg C for several min. The (1 x 1) structure disappeared after heating at 590 deg C in 7 x 10 exp -1 torr O and further heating at 590 deg C without O restored the integral order Variations of intensity with voltage were measured for the (00) and (20) spots. The results supported a model proposed by Haneman (Phys. Rev., 1968, 170, 705) involving two kinds of atom sites on the cleaved surface. 20 ref.--E.J.S.

Structure of columbin, a diterpenoid furanolactone from Tinospora cordifolia Miers

(1S,4R,5R,8S, IOR,12S)-4-Hydroxy-15,16-epoxycleroda-2,13 (16), 14-trieno- 17,12:18,1-biscarbolactone,C20H2206, Mr = 358.2, m.p. = 453-454 K,orthorhombic, P212121, a = 7.3869 (6), b = 11.986 (1),c=19.896(2) A, V=1761.65A 3, Z=4, D x=1.351, Din(by flotation)= 1.349gem -3, 2(CuKa)=1.5418 A, /l = 8.36 cm -1, F(000) = 760, T= 295 K,R = 0.0432 for 1662 observed reflections. Two terpenerings, two ~-lactones, two methyl groups, a tertiary hydroxyl group and a fl-substituted furan ring are present in the structure. The H atoms at C(12) and C(8) are a- and fl-oriented. The terpene ring A is locked into a boat conformation by the C(1)-C(4) lactone bridge. The furan ring is attached equatoriaUy at atom C(12). The hydroxyl group is involved in intramolecular hydrogen bonding.

Tris(tert-butyl 3-oxobutanoato-kappa O-2(1),O- )-aluminium(III) at 153 K

In the title complex, [Al(C8H13O3)(3)], a potential metal-organic chemical vapour deposition (MOCVD) precursor, three bidentate ligand molecules are bound to the metal atom, forming an octahedral geometry. Two non-planar six-membered chelate rings adopt screw-boat conformations, while the third ring has a conformation that lies about halfway between an envelope and a screw-boat.

Chemical-shift of the X-ray K-absorption edge of Co in some compounds, complexes and minerals

The chemical-shift of the X-ray K-absorption edge of Co was studied in a large number of compounds, complexes (spinels) and minerals of Co in its different oxidation states having widely different crystal structures and containing different types of bonding and various types of ligands, and were reported collectively, for the first time, in a single paper. A quadratic relationship was established on the basis of least-squares regression analysis to hold between the chemical-shift and the effective charge on the absorbing atom, but the dominance of the linear term was shown. This relation was utilized in evaluating the charge on the Co-ion in a number of minerals. The effect on chemical-shift of oxidation states of the absorbing atom, of the bond length, crystal structure and higher shell atoms of the molecule, and of electronegativity, atomic number and ionic radius of the ligand was discussed.

Completeness of the Coulomb wave functions in quantum mechanics

We give an explicit, direct, and fairly elementary proof that the radial energy eigenfunctions for the hydrogen atom in quantum mechanics, bound and scattering states included, form a complete set. The proof uses only some properties of the confluent hypergeometric functions and the Cauchy residue theorem from analytic function theory; therefore it would form useful supplementary reading for a graduate course on quantum mechanics.

Dielectric behaviour and ferroelectricity in alums

Introduction The alum family of double salts with the general formula M1+M3+(RO4)2.12H2O where M1+ is a monovalent ion (M1+ = K, Rb, Cs, Tl, NH4, CH3NH3, NH3OH3 NH3NH2, etc.) and M3+ is a trivalent metal such as Al, Fe, Cr, V, In, Ga, etc. and R is S or Se, form an isomorphous series and their general features indicate a common cubic space group Pa3. Lipson1 showed subsequently that there exist three different structure types agr, β and γ and the structure of a particular alum is dependent on the radius of the monovalent atom. The agr structure is typical of medium sized ions, the β of the larger ones and the γ of the small Na atom.2 Ferroelectricity has been reported only in alums containing NH4, CH3NH3, NH3NH3 and NH3OH. Their hindered rotations as well as the influence of sulphate group disorder on the dielectric behaviour of alums is still not clear.3 No study of the temperature dependence of the low frequency dielectric constant of some of the alums, particularly those of Cs, Rb and Tl, have been made so The present investigation was undertaken to correlate their dielectric behaviour with their composition and structural differences. Under the same experimental conditions, methyl ammonium and ammonium alums also were studied and compared with the known data.

Interaction of metal ions with 6-oxopurine nucleotides. Part 1. X-Ray structures of ternary cobalt(III) complexes with inosine 5'-monophosphate or guanosine 5'-monophosphate

The crystal structures of two ternary metal nucleotide complexes of cobalt, [Co(en)2(H2O)2]-[Co(5?-IMP)2(H2O)4]Cl2·4H2O (1) and [Co(en)2(H2O)2][Co(5?-GMP)2(H2O)4]Cl2·4H2O (2), have been analysed by X-ray diffraction (en = ethylenediamine, 5?-IMP = inosine 5?-monophosphate, and 5?-GMP = guanosine 5?-monophosphate). Both complexes crystallize in the orthorhombic space group C2221 with a= 8.725(1), b= 25.891(5), c= 21.212(5)Å, Z= 4 for (1) and a= 8.733(2), b= 26.169(4), c= 21.288(4)Å, Z= 4 for (2). The structure of (1) was solved by the heavy-atom method, while that of (2) was deduced from (1). The structures were refined to R values of 0.09 and 0.10 for 1 546 and 1 572 reflections for (1) and (2) respectively. The two structures are isomorphous. A novel feature is that the chelate ligand en and the nucleotide are not co-ordinated to the same metal ion. One of the metal ions lying on the two-fold a axis is octahedrally co-ordinated by two chelating en molecules and two water oxygens, while the other on the two-fold b axis is octahedrally co-ordinated by two N(7) atoms of symmetry-related nucleotides in a cis position and four water oxygens. The conformations of the nucleotides are C(2?)-endo, anti, and gauche�gauche. In both (1) and (2) the charge-neutralising chloride ions are disordered in the vacant space between the molecules. These structures bear similarities to the mode of nucleotide co-ordination to PtII complexes of 6-oxopurine nucleotides, which are the proposed models for intrastrand cross-linking in DNA by a metal complex.

Investigation of the effect of nonlocal scale on ultrasonic wave dispersion characteristics of a monolayer graphene

In this article, an ultrasonic wave propagation in graphene sheet is studied using nonlocal elasticity theory incorporating small scale effects. The graphene sheet is modeled as an isotropic plate of one-atom thick. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of wave propagation model is also derived for the graphene sheet. The nonlocal scale parameter introduces certain band gap region in in-plane and flexural wave modes where no wave propagation occurs. This is manifested in the wavenumber plots as the region where the wavenumber tends to infinite or wave speed tends to zero. The frequency at which this phenomenon occurs is called the escape frequency. The explicit expressions for cutoff frequencies and escape frequencies are derived. The escape frequencies are mainly introduced because of the nonlocal elasticity. Obviously these frequencies are function of nonlocal scaling parameter. It has also been obtained that these frequencies are independent of y-directional wavenumber. It means that for any type of nanostructure, the escape frequencies are purely a function of nonlocal scaling parameter only. It is also independent of the geometry of the structure. It has been found that the cutoff frequencies are function of nonlocal scaling parameter (e(0)a) and the y-directional wavenumber (k(y)). For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(o)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this paper. (C) 2010 Elsevier B.V. All rights reserved.

Structure of 1,2,4-oxadiazolidine-3,5-dione monohydrate

C2H2N203.H20, Mr= 120.07, monoclinic,P21/c, a= 5.011 (1), b= 11.796(2), c= 7.689 (2)A,fl= 95.22 (2) ° , V= 452.61 A 3, Z= 4, Dx= 1.76, D m = 1.75 gcm -3, /].(Cu Ks) = 1.5418 A, g = 14-0 cm -l,F(000) = 248, T = 293 K, crystal quality was poor and the final R =0.107, wR =0.090 for 881 observed reflections. The compound is derived from a novel form of the monopropellant oxalohydroxamic acid. The two exocyclic C-O bond lengths of 1.240 (3) and 1.228 (4)A indicate double bonds. The C-N bond lengths of 1.334 (4), 1.390 (4) and 1.359 (4) A are characteristic of the amide bond. The N atom covalently bonded to the two carbonyl C atoms acts as a proton donor in an intermolecular hydrogen bond to the ring O atom: N1...O3i = 2.854 ]k (i =x-- 1,y, z), H...O = 2.15 A, N-H...O = 159 °.

Intermolecular Chelate Linkage Isomerism of the Hydroxyimino Group in the Nickel(II), Copper(II), and Palladium(II) Complexes of Quadridentate Schiff-base Ligands

The C-nitrosation of bivalent quadridentate β-imino ketone complexes of nickel(II), copper(II), and palladium(II), with nitrosating reagents has been investigated. The chemical analysis and spectroscopic results reveal that one of the α-CH groups of the coordinated lignad undergoes selective nitrosation forming mono(hydroxyimino) derivative. The hydroxyimino group introduced coordinates through either N- or O- atom to metal(II) by dislodging the carbonyl group already coordinated. This gives rise to two linkage isomers, one with N-bonded and the other with O-bonded hydroxyimino group in the case of nickel(II) (except for 1d) and palladium(II), and a single isomer with O-bonded hydroxyimino group in copper(II) complexes. The isomers obtained from 1b and 1i have been separated by column chromatography. In chloroform each of the isomers of nickel(II) isomerizes to give an equilibrium mixture of two isomers, but not those of copper(II) and palladium(II).

Synthesis and characterization of Pd(0), PdS, and Pd@PdO core-shell nanoparticles by solventless thermolysis of a Pd-thiolate cluster

Colloids of palladium nanoparticles have been prepared by the solvated metal atom dispersion (SMAD) method. The as-prepared Pd colloid consists of particles with an average diameter of 2.8 +/- 0.1 nm. Digestive ripening of the as-prepared Pd colloid, a process involving refluxing the as-prepared colloid at or near the boiling point of the solvent in the presence of a passivating agent, dodecanethiol resulted in a previously reported Pd-thiolate cluster, Pd(SC12H25)(2)](6) but did not render the expected narrowing down of the particle size distribution. Solventless thermolysis of the Pd-thiolate complex resulted in various Pd systems such as Pd(0), PdS, and Pd@PdO core-shell nanoparticles thus demonstrating its versatility. These I'd nanostructures have been characterized using high-resolution electron microscopy and powder X-ray diffraction methods. (C) 2010 Elsevier Inc. All rights reserved.