Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

A New Pathway for the Degradation of a Sesquiterpene Alcohol, Nerolidol by Alcaligenes eutrophus

An oxidative pathway hitherto unknown for tile degradation of a sesquiterpene alcohol, nerolidol (I) by Alcaligenes eutrophus is presented. Fermentation of nerolidol (I) by this organism in a mineral salts medium resulted in the formation of geranylacetone (II) and an optically active alcohol (S)-(+)-geranylacetol (III), as major metabolites. Nerolidol (I) induced cells readily transformed 1,2-epoxynerolidol (IV) and 1,2-dihydroxynerolidol (V) into geranylacetone (II). These cells also exhibited their ability to carry out stereospecific reduction of II into (S)-(+)-geranylacetol (III). Oxygen uptake studies clearly indicated that nerolidol induced cells oxidized compounds II, III, IV, V and ethyleneglycol. Based on these observations a new oxidative pathway for the degradation of I is suggested which envisages the epoxidation of the terminal double bond, opening of the epoxide and cleavage between C-2 and C-3 in a manner similar to the periodate oxidation of diol.

Local polynomial convexity of the union of two totally-real surfaces at their intersection

We consider the following question: Let S (1) and S (2) be two smooth, totally-real surfaces in C-2 that contain the origin. If the union of their tangent planes is locally polynomially convex at the origin, then is S-1 boolean OR S-2 locally polynomially convex at the origin? If T (0) S (1) a (c) T (0) S (2) = {0}, then it is a folk result that the answer is yes. We discuss an obstruction to the presumed proof, and provide a different approach. When dim(R)(T0S1 boolean AND T0S2) = 1, we present a geometric condition under which no consistent answer to the above question exists. We then discuss conditions under which we can expect local polynomial convexity.

Stabilisation of unusual simultaneous binding of four cytosine nucleobases to copper(II) by a novel network of bifurcated hydrogen bonding

The crystal structure of tetrakis(cytosine)copper(II) perchlorate dihydrate has been determined. All the hydrogen atoms were obtained from Fourier-difference synthesis. The geometry around. copper is a bicapped octahedron (4 + 2 + 2*). The adjacent cytosine rings are oriented head-to-tail with respect to each other and are roughly at right angles to the co-ordination plane. The exocyclic oxo groups form an interligand, intracomplex hydrogen-bonding network above and below the co-ordination plane with the exocyclic amino groups of alternate cytosine bases. The EPR and electronic spectra are consistent with the retention of the solid-state structure in solution. The steric effect of the C(2)=O group of cytosine is offset by the presence of the intracomplex hydrogen-bonding network. The trend in Ei values of Cu-II-Cu-I couples for 1.4 complexes of cytosine, cytodine, pyridine, 2-methylpyridine and N-methylimidazole suggests that both steric effects and pi-delocalization in imidazole and pyridine ligands and the steric effect of C(2)=O in pyrimidine ligands are important in stabilising Cu-I relative to Cu-II.

The crystal structure of hydrated barium copper oxalate

BaCu(C2O4)(2) . 6H2O is triclinic, P (1) over bar, with a = 6.5405(9), b = 9.202(3), c = 10.939(1) Angstrom, alpha = 85.46(2), beta = 79.22(1), gamma = 80.45(2), V = 636.99(1) Angstrom(3), Z = 2, D-0 = 2.14, D-c = 2.465 g . cm(-3), R = 0.074, wR = 0.0746 for 2219 significant reflections \F-0\ greater than or equal to 6.0 sigma F-0. The barium has eleven coordinations and the coordination polyhedra is a capped antiprism. Six water oxygen atoms are coordinated whereas the other five are coming from the oxalate group. In the unit cell the molecule's form a polymeric network. One lattice water molecule belongs to the coordinating water. The barium oxygen distances vary from 2.75 Angstrom to 3.15 Angstrom.

Structure of 9[alpha],19-dihydroxy-4-androstene-3,17-dione

C19H26O4, M(r) = 318.41, orthorhombic, P2(1)2(1)2(1), a = 10.591 (1), b = 11.133 (1), c = 13.657 (2) angstrom, V = 1610.29 angstrom 3, Z = 4, D(m) (flotation in KI) = 1.301, D(x) = 1.313 g cm-3, Mo K-alpha, lambda = 0.7107 angstrom, mu = 0.85 cm-1, F(000) = 688, T = 293 K, R = 0.057 for 1253 significant reflections. The A ring is disordered with atoms C(2) and O(19) occupying two possible sites. The molecules are held together by a hydrogen bond [O(9)...O(17) = 2.89 angstrom].

Model studies directed towards the synthesis of functionalised chiral A-ring derivatives of taxanes

Model studies, starting from the monoterpene R-carvone, directed towards the synthesis of chiral A-ring derivatives of taxanes with oxygen functionalities at C-2, 9 and 13 carbon atoms as in taxol is described.

Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.

Weakly non-linear stability of a hydrodynamic accretion disc

When the cold accretion disc coupling between neutral gas and a magnetic field is so weak that the magnetorotational instability is less effective or even stops working, it is of prime interest to investigate the pure hydrodynamic origin of turbulence and transport phenomena. As the Reynolds number increases, the relative importance of the non-linear term in the hydrodynamic equation increases. In an accretion disc where the molecular viscosity is too small, the Reynolds number is large enough for the non-linear term to have new effects. We investigate the scenario of the `weakly non-linear' evolution of the amplitude of the linear mode when the flow is bounded by two parallel walls. The unperturbed flow is similar to the plane Couette flow, but with the Coriolis force included in the hydrodynamic equation. Although there is no exponentially growing eigenmode, because of the self-interaction, the least stable eigenmode will grow in an intermediate phase. Later, this will lead to higher-order non-linearity and plausible turbulence. Although the non-linear term in the hydrodynamic equation is energy-conserving, within the weakly non-linear analysis it is possible to define a lower bound of the energy (alpha A(c)(2), where A(c) is the threshold amplitude) needed for the flow to transform to the turbulent phase. Such an unstable phase is possible only if the Reynolds number >= 10(3-4). The numerical difficulties in obtaining such a large Reynolds number might be the reason for the negative result of numerical simulations on a pure hydrodynamic Keplerian accretion disc.

Icosahedral quasicrystalline and hexagonal approximant phases in the Al-Mn-Be alloy system

We report the formation of a primitive icosahedral quasicrystal with increased stability in Al Mn-Be alloys close to the compound Al15Mn13Be2, by melt spinning and injection casting. The crystal structure of this compound was unknown. We show that in as-cast as well as heat treated condition the intermetallic phase H1 has a hexagonal structure with lattice parameters a = 1.2295 run and c = 2.4634 nm. The space group is P6(3)/mmc In the injection-cast samples, the quasicrystal coexists with another closely related hexagonal phase H2 with a = 1.2295 nm and c = 1.2317 nm with a possible space group of P6/mmm. This phase exhibits specific orientation relationships with the icosahedral quasicrystal given by [0001](hex)//2f(QC) and [01 (1) over bar0](hex)//5f(QC) where 2f(QC) and 5f(QC) represent twofold and fivefold axes respectively. Electron diffraction patterns from both phases exhibit a close resemblance to the quasicrystalline phase. It is shown that the H1 phase is closely related to mu-Al4Mn with the same e parameter while the a parameter is reduced by tau. Following Kreiner and Franzen, it is postulated that both structures (H1 and H2) can be understood by a simple hexagonal packing of I13 clusters.

Dynamics of pulled desorption with effects of excluded-volume interaction: The p-Laplacian diffusion equation and its exact solution

We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force f, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value f(c). We formulate an equation for the average position of the n-th monomer, which takes into account excluded-volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a p-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get tau = tau(0)n(d)(2), where n(d) is the number of monomers that have desorbed at the time tau. tau(0) is known only numerically, but for f close to f(c), it is found to be tau(0) similar to f(c)/(f(2/3) - f(c)(2/3)) If one used simple Rouse dynamics, this result would change to tau similar to f(c)n(d)(2)/(f - f(c)). In the other regimes too, one can find exact solution, and interestingly, in all regimes tau similar to n(d)(2). Copyright (C) EPLA, 2011

Structure of the Pyridine-Chloranil Complex in Solution: A Surprise from Depolarized Hyper-Rayleigh Scattering Measurements

In this article, we report the structure of a 1:1 charge transfer complex between pyridine (PYR) and chloranil (CHL) in solution (CHCl(3)) from the measurement of hyperpolarizability (beta(HRS)) and linear and circular depolarization ratios, D and D', respectively, by the hyper-Rayleigh scattering technique and state-of-the-art quantum chemical calculations. Using linearly (electric field vector along X) and circularly polarized incident light, respectively, we have measured two macroscopic depolarization ratios D = I(X,X)(2 omega)/I(X,Z)(2 omega) and D' = I(X,C)(2 omega)/I(Z,C)(2 omega) in the laboratory fixed XYZ frame by detecting the second harmonic (SH) scattered light in a polarization resolved fashion. The stabilization energy and the optical gap calculated through the MP2/cc-pVDZ method using Gaussian09 were not significantly different to distinguish between the cofacial and T-shape structures. Only when the experimentally obtained beta(HRS) and the depolarization ratios, D and D', were matched with the theoretically computed values from single and double configuration interaction (SDCI) calculations performed using the ZINDO-SCRF technique, we concluded that the room temperature equilibrium structure of the complex is cofacial. This is in sharp contrast to an earlier theoretical prediction of the T-shape structure of the complex.

Polynomial Approximation, Local Polynomial convexity, and Degenerate CR Singularities- II

We provide some conditions for the graph of a Holder-continuous function on (D) over bar, where (D) over bar is a closed disk in C, to be polynomially convex. Almost all sufficient conditions known to date - provided the function (say F) is smooth - arise from versions of the Weierstrass Approximation Theorem on (D) over bar. These conditions often fail to yield any conclusion if rank(R)DF is not maximal on a sufficiently large subset of (D) over bar. We bypass this difficulty by introducing a technique that relies on the interplay of certain plurisubharmonic functions. This technique also allows us to make some observations on the polynomial hull of a graph in C(2) at an isolated complex tangency.

Synthesis, Reactivity Studies, Structural Aspects, and Solution Behavior of Half Sandwich Ruthenium(II) N,N `,N `'-Triarylguanidinate Complexes

[(eta(6)-C(10)H(14))RuCl(mu-Cl)](2) (eta(6)-C(10)H(14) = eta(6)-p-cymene) was subjected to a bridge-splitting reaction with N,N',N `'-triarylguanidines, (ArNH)(2)C=NAr, in toluene at ambient temperature to afford [(eta(6)-C(10)H(14))RuCl{kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (1), C(6)H(4)(OMe)-2 (2), C(6)H(4)Me-2 (3), and C(6)H(3)Me(2)-2,4 (4)) in high yield with a view aimed at understanding the influence of substituent(s) on the aryl rings of the guanidine upon the solid-state structure, solution behavior, and reactivity pattern of the products. Complexes 1-3 upon reaction with NaN(3) in ethanol at ambient temperature afforded [(eta(6)-C(10)H(14))RuN(3){kappa(2)(N,N')((ArN)(2)C-N(H)Ar)}] (Ar = C(6)H(4)Me-4 (5), C(6)H(4)(OMe)-2 (6), and C(6)H(4)Me-2 (7)) in high yield. [3 + 2] cycloaddition reaction of 5-7 with RO(O)C-C C-C(O)OR (R = Et (DEAD) and Me (DMAD)) (diethylacetylenedicarboxylate, DEAD; dimethylacetylenedicarboxylate, DMAD) in CH(2)Cl(2) at ambient temperature afforded [(eta(6)-C(10)H(14))Ru{N(3)C(2)(C(O)OR)(2)}{kappa(2)(N,N')((ArN)(2) C-N(H)Ar)}center dot xH(2)O (x = 1, R = Et, Ar = C(6)H(4)Me-4 (8 center dot H(2)O); x = 0, R = Me, Ar = C(6)H(4)(OMe)-2 (9), and C(6)H(4)Me-2 (10)) in moderate yield. The molecular structures of 1-6, 8 center dot H(2)O, and 10 were determined by single crystal X-ray diffraction data. The ruthenium atom in the aforementioned complexes revealed pseudo octahedral ``three legged piano stool'' geometry. The guanidinate ligand in 2, 3, and 6 revealed syn-syn conformation and that in 4, and 10 revealed syn-anti conformation, and the conformational difference was rationalized on the basis of subtle differences in the stereochemistry of the coordinated nitrogen atoms caused by the aryl moiety in 3 and 4 or steric overload caused by the substituents around the ruthenium atom in 10. The bonding pattern of the CN(3) unit of the guanidinate ligand in the new complexes was explained by invoking n-pi conjugation involving the interaction of the NHAr/N(coord)Ar lone pair with C=N pi* orbital of the imine unit. Complexes 1, 2, 5, 6, 8 center dot H(2)O, and 9 were shown to exist as a single isomer in solution as revealed by NMR data, and this was ascribed to a fast C-N(H)Ar bond rotation caused by a less bulky aryl moiety in these complexes. In contrast, 3 and 10 were shown to exist as a mixture of three and five isomers in about 1:1:1 and 1.0:1.2:2:7:3.5:6.9 ratios, respectively in solution as revealed by a VT (1)H NMR, (1)H-(1)H COSY in conjunction with DEPT-90 (13)C NMR data measured at 233 K in the case of 3. The multiple number of isomers in solution was ascribed to the restricted C-N(H)(o-tolyl) bond rotation caused by the bulky o-tolyl substituent in 3 or the aforementioned restricted C-NH(o-tolyl) bond rotation as well as the restricted ruthenium-arene(centroid) bond rotation caused by the substituents around the ruthenium atom in 10.

Some Aspects of the Kobayashi and Carath,odory Metrics on Pseudoconvex Domains

The purpose of this article is to consider two themes, both of which emanate from and involve the Kobayashi and the Carath,odory metric. First, we study the biholomorphic invariant introduced by B. Fridman on strongly pseudoconvex domains, on weakly pseudoconvex domains of finite type in C (2), and on convex finite type domains in C (n) using the scaling method. Applications include an alternate proof of the Wong-Rosay theorem, a characterization of analytic polyhedra with noncompact automorphism group when the orbit accumulates at a singular boundary point, and a description of the Kobayashi balls on weakly pseudoconvex domains of finite type in C (2) and convex finite type domains in C (n) in terms of Euclidean parameters. Second, a version of Vitushkin's theorem about the uniform extendability of a compact subgroup of automorphisms of a real analytic strongly pseudoconvex domain is proved for C (1)-isometries of the Kobayashi and Carath,odory metrics on a smoothly bounded strongly pseudoconvex domain.