Polybrominated oxydiphenol derivatives from the sponge dysidea herbacea: Structure determination by analysis of 13C spin-lattice relaxation data for quaternary carbons and 13C-1H coupling constants

Five polybrominated oxydiphenol derivatives have been isolated from various Great Barrier Reef collections and one Fijian collection of the sponge Dysidea herbacea: 3,4',5,6,6'-hexabromo-2, 2'-oxydiphenol (11), 3,4',5,6,6'-pentabromo-2,2'-oxydiphenol (12), 3.4',5,6,6'-pentabromo-2,2'-oxydiphenol 1-methyl ether (13), 3,4,4',5,6'-pentabromo-2,2'-oxydiphenol 1,1'-dimethyl ether (14) and 3,4',5,6'-tetrabromo-2,2'-oxydiphenol 1'-methyl ether (15).The structure of the first member of this series is determined by a new method involving ¹³C spin-lattice relaxation data. The contributions of nearby hydrogens to quaternary carbon spin-lattice relaxation times are calculated for various possible structures and compared with the experimental data, leading to an unequivocal proof of structure. The structures of the remaining compounds in the series are established principally by analysis of ¹³C chemical shifts and ¹³C-¹H coupling constants.     

The molecular structure and the puckering potential function of silacyclobutane as determined by gas electron diffraction and relaxation constraints from ab initio calculations

Gas electron diffraction is applied to determine the geometric parameters of the silacyclobutane molecule using a dynamic model where the ring puckering was treated as a large amplitude motion. The structural parameters and the parameters of the potential function were refined taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the MP2/6-311+G(d, p) level of theory. The potential function has been described as V() = V₀[(/_e)² − 1]² with the following parameters V₀ = 0.82 ± 0.60 kcal/mol and _e = 33.5 ± 2.7°, where is a puckering angle of the ring.

The geometric parameters at the minimum V() (r_a in Å, in degrees and uncertainties given as three times the standard deviations including a scale error) are: r(Si–H_ax) = 1.467(96), r(Si–H_eq) = 1.468(96), r(Si–C) = 1.885(2), r(C–C) = 1.571(3), r(C–H) = 1.100(3), CSiC = 77.2(9), HSiH = 108.3, SiCH_eq = 123.5(16), SiCH_ax = 111.9(16), CC₅H_eq = 118.4(24), CC₅H_ax = 112.3(24), HC₃H = 107.7, δ(HSiH) = 6.6, δ(HC₃H) = 7.0, where the tilts δ, HSiH, and HC₃H are estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds.     

The rz structure of 1,2,5-selenadiazole partially oriented in ordered mesophases as determined by PMR spectra including 13C and 77Se satellites

The proton magnetic resonance spectra of 1,2,5-selenadiazole together with the natural abundance ¹³C and ⁷⁷Se satellites have been obtained and analysed in two lyotropic mesophases and in a thermotropic mesophase. The r_z structure of the molecule has been obtained.     

Use of 13C spin-lattice relaxation measurements to determine the structure of a tetrabromo diphenyl ether from the sponge Dysideaherbacea

The structure of a novel tetrabromodiphenyl ether from $\text{D}$. $\text{herbacea}$ is solved principally by analysis of the contributions of non-bonded hydrogens to the spin-lattice relaxation times of quaternary carbons.     

Computational and ESR studies of electron attachment to decafluorocyclopentane, octafluorocyclobutane, and hexafluorocyclopropane: electron affinities of the molecules and the structures of their stable negative ions as determined from 13C and 19F hyperfine coupling constants

High-resolution ESR spectra of the ground-state negative ions of hexafluorocyclopropane (c-C3F6*-), octafluorocyclobutane (c-C4F8*-), and decafluorocyclopentane (c-C5F10*-) are reported and their isotropic 19F hyperfine coupling constants (hfcc) of 198.6 +/- 0.4 G, 147.6 +/- 0.4 G, and 117.9 +/- 0.4 G, respectively, are in inverse ratio to the total number of fluorine atoms per anion. Together with the small value of 5.2 +/- 0.4 G determined for the isotropic 13C hfcc of c-C4F8*-, these results indicate that in each case the singly occupied molecular orbital (SOMO) is delocalized over the equivalent fluorines and possesses a nodal plane through the carbon atoms of a time-averaged D(nh) structure. A series of quantum chemical computations were carried out to further characterize these anions and their neutral counterparts. Both the B3LYP density functional and second-order M?ller-Plesset perturbation theory (MP2) indicate that c-C3F6*- adopts a D(3h) geometry and a (2)A2' ground electronic state, that c-C4F8*- adopts a D(4h) geometry and a (2)A2u ground electronic state, and that c-C5F10*- adopts a C(s) structure and a (2)A' electronic state. Moreover, the 19F hyperfine coupling constants computed with the MP2 method and a high quality triple-zeta basis set are within 1% of the experimental values. Also, the values computed for the 13C hfcc of c-C4F8*- are consistent with the experimental value of 5.2 G. Therefore, in keeping with the ESR results, these negative ions derived from first-row elements can be characterized as pi* species. In addition, the hypervalency of these perfluorocycloalkane radical anions has been clarified.     

The molecular structure of di-t-butylamine, NH[C(CH3)3]2, as determined by gas-phase electron diffraction: an exceptionally sterically hindered amine

Gaseous di-t-butylamine, NHBu^t₂, has been studied by electron diffraction at a nozzle temperature of ca. 293 K. The diffraction data reveal that this amine is exceedingly hindered. Repulsive steric interactions between the Bu^t groups are mainly relieved by an opening of the CNC valence angle to 135(3)°. Evidence of steric strain may also be found in the non-zero tilts (2–3°) of the Bu^t groups, defining the angle of rotation of these groups about axes through the N-bonded carbon atoms orthogonal to the NC₂ plane. The N---C and C---C bonds, 1.467(13) and 1.561(6) Å, respectively, are on the other hand relatively unstrained. Other principal geometrical parameters are unexceptional: C---H = 1.103(10) Å, NCC = 111.3(1.5)° (mean value) and CCH = 106(2)°. The position of the N-bonded hydrogen atom relative to the NC₂ plane could not be determined. The torsional positions of the Bu^t groups, with respect to the N---C bonds, could not be derived from least-squares refinements. A large number of models with Bu^t groups in various fixed positions were considered; the best fit between the observed and theoretical intensity data was obtained with one Bu^t group being twisted 19° away from the position typified by one C---C bond of this group being anti to the remote N---C bond, and the other Bu^t group similarly twisted by 30°. When viewed along the N---C bonds, the Bu^t groups are twisted in the same direction. Viewed along the C(N)C axis, these groups come close to being staggered with respect to each other. The values of the above bond distances are those of r_a parameters. Parenthesized values denote error limits, being least-squares standard deviations multiplied by a factor of three.     

The conformation of 4-phenylcyclohexanone in solution by 1H- and 13C-Lanthanide induced shift (L.I.S.) analysis : Evidence in favour of phenyl over t-butyl as a conformational lock

The degree of pucker of the cyclohexanone ring in 4-phenylcyclohexanone has been refined by L.I.S. analysis. The results indicate puckering intermediate between that in cyclohexanone and 4-t-butylcyclohexanone, suggesting that phenyl may be preferable to t-butyl as a locking group in conformational analysis. The Yb (fod)3 shift reagent, although binding primarily at the carbonyl oxygen atom, also complexes weakly with the phenyl group.     

Redox dependent conformational changes in the mixed valence form of the cytochrome c oxidase from p. The reorganization of glutamic acid 278 is coupled to the electron transfer from/to heme a and the binuclear center. denitrificans

In this work we present the separation of FTIR difference signals induced by electron transfer to/from the redox centers of the cytochrome c oxidase from P. denitrificans and compare electrochemically induced FTIR difference spectra with those induced by CO photolysis. FTIR difference spectra of rebinding of CO to the half reduced (mixed valence) form of the cytochrome c oxidase after photolysis reflect the conformational changes induced by the rebinding of CO and by electron transfer reactions from heme a3 to heme a and further on to CUA. During this process, heme a3 (and CUB) are oxidized, whereas heme a and CuA are reduced. By subtracting these difference spectra from an electrochemically induced FTIR difference spectrum, where all four cofactors are reduced, the contributions for heme a3 (and CuB) could be separated. Correspondingly, the spectral contributions of heme a and CuA have been separated. The comparison of these spectra with the spectra calculated for the hemes on the basis of their redox dependent changes previously published in Hellwig et al., (Biochemistry 38, (1999) 1685-1694) show a high degree of similarity, except for additional signals coupled to the reorganization of the binuclear center upon CO rebinding. The separated spectra clearly show that the signals attributed to Glu278, an amino acid discussed to be crucial for proton pumping, is coupled to electron transfer to/from heme a and the binuclear heme a3-CuB center.     

Arsenic containing heterocycles. II. Confirmation of the structure of benzo[a]-9-chlorophenarsazine 12-chloride by 13C-NMR spectroscopy and spin-lattice relaxation time studies: Possible evidence for the contribution of an 75as-13C mechanism to the relaxation of the arsenic bearing quarternary carbons in the phenarsazine ring system

The product of the reaction of (3-chlorophenyl)-2-naphthylamine with arsenic trichloride has been confirmed to be benzo(a)-9-chlorophenarsazine 12-chloride by ¹³C-nmr spectroscopy and spin-lattice (T₁) relaxation time measurements. A considerable shortening of the spin-lattice relaxation times of the arsenic bearing quaternary carbons, relative to the calculated relaxation times, was observed. This discrepancy has been interpreted in terms of an ⁷⁵As-¹³C dipolar contribution to quaternary carbon relaxation.     

The use of one-bond,heteronuclear coupling constants (1J —C,H) as structure reporters in 13 C-N.M.R. of oligosaccharides containing 3-deoxy-(=D)-manno-2-octulosonic acid

In proton-coupled, ¹³ C-n.m.r.-spectra of 3-deoxy-(=D)-$\text{manno}$-2-octulopyranosylono (KDO$\text{p}$-)derivatives, the ¹$\text{J}$-C-5,H-5 is significantly larger (148 Hz) than the respective coupling constants of the other carbon signals, and the chemical shift of the signal displaying this spacing indicates whether position 5 is glycosidated or unsubstituted.     

The trapping of a spontaneously "flipped-out" base from double helical nucleic acids by host-guest complexation with beta-cyclodextrin: the intrinsic base-flipping rate constant for DNA and RNA

Beta-cyclodextrin, which forms stable host-guest complexes with purine bases, induces the melting of RNA and DNA duplexes below their normal melting temperatures. Alpha-cyclodextrin, which does not form stable complexes, has no effect on either RNA or DNA. Gamma-cyclodextrin, which forms weaker complexes, has no effect on RNA and a smaller effect than beta-cyclodextrin on DNA. The rate of melting is kinetically first-order in duplex and, above about 20 mM beta-cyclodextrin, is independent of the beta-cyclodextrin concentration with a first-order rate constant, common to both RNA and DNA, of (3.5 +/- 0.5) x 10(-3) s(-1) at 61 degrees C (DNA) and at 50 degrees C (RNA). This is taken to be the rate constant for spontaneous "flipping out" of a base from within the duplex structure of the nucleic acids, the exposed base being rapidly trapped by beta-cyclodextrin. Like beta-cyclodextrin, nucleic acid methyltransferases bind the target base for methylation in a site that requires it to have flipped out of its normal position in the duplex. The spontaneous flip-out rate constant of around 10(-3) s(-1) is near the value of k(cat) for the methyltransferases (ca. 10(-3) to 10(-1) s(-1)). In principle, the enzymes, therefore, need effect little or no catalysis of the flipping-out reaction. Nevertheless, the flip-out rate in enzyme/DNA complexes is much faster. This observation suggests that the in vivo circumstances may differ from in vitro models or that factors other than a simple drive toward higher catalytic power have been influential in the evolution of these enzymes.     

Mass spectrometry of pyridine compounds–IV: The formation and decomposition of the [M – methyl]+ ion [C8H10N]+ from 4-t-butylpyridine in comparison with that of the [M – methyl]+ ion [C9H11]+ from t-butylbenzene,as studied by D- and 13C-labelling

A strong secondary isotope effect is observed in the preferred loss of methyl vs. trideutero-methyl from the molecular ions of appropriately labelled 4-t-butylpyridine and t-butylbenzene decomposing in the first and second field free regions of a double focusing mass spectrometer. This has been rationalised by invoking the theory of radiationless transitions², which can account for the higher population of activated states responsible for loss of methyl vs. that for trideuteromethyl. ¹³C-Labelling at the central carbon atom of the t-butyl group indicates that the [M – methyl]⁺ ions, decomposing further by elimination of ethylene, cannot be represented exclusively by a pyridylated (or phenylated) cyclopropane ion if present at all. It is concluded that ions with structures generated by 1,2-hydrogen-, 1,2-pyridyl- (or 1,2-phenyl-) and 1,2-methyl shifts must also play a role. D-labelling further shows an extensive randomisation of side-chain hydrogen atoms in the [M-methyl]⁺ ions of 4-t-butylbenzene; in this case, however, the expelled ethylene also contains ring hydrogen atoms (≤2). Presumably this is caused by exchange between the side-chain and ortho-hydrogen atoms in the initially generated phenyldimethylcarbinyl carbenium ion.     

Ligand displacement reactions from the coordination sphere of cobalt complexes. Part II: The displacement of ligands of [cis-Co(en)2Cl2]Cl by potassium squarate. The crystal and molecular structure of a compound with idealized formula of [cis-Co(en)2(H2O)Br]2[trans-(C2O4 2−(C2O4H−)Co-trans-(H2O)2(OH)2]Br2 (I)

Compound (I), idealized as Br₄Co₃O₁₄N₈C₁₆H₄₁ (see text), crystallizes in the triclinic space groupP¯ 1 (No. 2) with cell constants ofa=7.4470(7),b=7.9648(4),c=15.2223(8),α=96.338(4)?Β=93.504(6)?,γ=112.894(6)?,V=821.328 å³, and d(calc; MW=1065.97,z=1)=2.155 gm-cm^?3. Data (3880 total reflections) were collected over the range 2? ≤ 2θ ≤ 55? and corrected for absorption (Μ=63.69 cm^?1) using data from Psi scans. The unexpectedly isolated compound contains a [cis-Co(en)₂Br(OH)]⁺ cation, while the anion contains a central Co(III) surrounded by two mondentate,trans-squarato ligands, twotrans-hydroxo, and two waters. The waters and hydroxy ligands were identified by determining, experimentally, the presence and positions of their respective hydrogens. Given the need for overall electroneutrality, one squarato ligand must be a dianion (Sq^2?) and the other a monoanion (SqH^?); however, since the ion bearing the squarato ligands sits at an inversion center, the hydrogen of the latter must be disordered. Refinement of the heavy atoms with anisotropic thermal parameters and fixed hydrogen positions (B's fixed at) led to the finalR(F) andR _W(F) factors of 0.036 and 0.042, respectively. (I) was obtained during efforts to prepare [Co(en)₂(squarate)]Br by the displacement of two chloro ligands from the coordination sphere of [cis-Co(en)₂Cl₂]Cl by K₂ (squarate) followed by addition of NaBr. Compound (I) appears to be the first example of a coordination compound in which squarate^2? and squarate H^? anions are present as ligands to a transition metal ion. A search of the Cambridge file (to 1992) produced no known examples of Co(III) squarates. Thus, (I) appears to also be the first example of its kind.