Determination of sugar structures in solution from residual dipolar coupling constants: methodology and application to methyl beta-D-xylopyranoside

We have developed methodology for the determination of solution structures of small molecules from residual dipolar coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl beta-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C(12)E(5) and hexanol in D(2)O. Thirty residual dipolar coupling constants, ranging from -6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 D(HH), 4 (1)D(CH), and 11 (n)D(CH) coupling constants. The accuracy of the dipolar coupling constants is estimated to be < +/- 0.02 Hz. New constant-time HMBC NMR experiments were developed for the measurement of (n)D(CH) coupling constants, the use of which was crucial for the successful structure determination of I, as they allowed us to increase the number of fitted parameters. The structure of I was refined using a model in which the directly bonded interatom distances were fixed at their ab initio values, while 16 geometrical and 5 order parameters were optimized. These included 2 CCC and 6 CCH angles, and 2 CCCC and 6 CCCH dihedral angles. Vibrationally averaged dipolar coupling constants were used during the refinement. The refined solution structure of I is very similar to that obtained by ab initio calculations, with 11 bond and dihedral angles differing by 0.8 degrees or less and the remaining 5 parameters differing by up to 3.3 degrees . Comparison with the neutron diffraction structure showed larger differences attributable to crystal packing effects. Reducing the degree of order by using dilute liquid crystalline media in combination with precise measurement of small residual dipolar coupling constants, as shown here, is a way of overcoming the limitation of strongly orienting liquid crystals associated with the complexity of (1)H NMR spectra for molecules with more than 12 protons.     

Effects of thioamide substitutions on the conformation and stability of alpha- and 3(10)-helices

Thiopeptides, formed by replacing the amide oxygen atom with a sp(2) sulfur atom, are useful in protein engineering and drug design because they confer resistance to enzymatic degradation and are predicted to be more rigid. This report describes our free molecular dynamics simulations with explicit water and free energy calculations on the effects of thio substitutions on the conformation of alpha-helices, 3(10)-helices, and their relative stability. The most prominent structural effect of thio substitution is the increase in the hydrogen bond distance from 2.1 A for normal peptides to 2.7 A for thiopeptides. To accommodate for the longer C[double bond]S...H-N hydrogen bond, the (phi, psi) dihedral angles of the alpha-helix changed from (-66 degrees, -42 degrees) to (-68 degrees, -38 degrees), and the rise per turn increased from 5.5 to 6.3 A. For 3(10)-helices, the (phi, psi) dihedral angles (-60 degrees, -20 degrees) and rise per turn (6.0 A) changed to (-66 degrees, -12 degrees) and 6.8 A, respectively. In terms of relative stability, the most prominent change upon thio substitution is the decrease in the free energy difference, Delta A(alpha --> 3(10)), from 14 to 3.5 kcal/mol. Therefore, normal peptides are less likely to form 3(10)-helix than are thiopeptides. Component analysis of the Delta A(alpha --> 3(10)) reviews that the entropy advantage of the 3(10)-helix for both Ac-Ala(10)-NHMe and Act-Alat(10)-NHMe is attributed to the 3(10)-helix being more flexible than the alpha-helix. Interestingly, upon thio substitution, this differential flexibility is even more apparent because the alpha-helix conformation of Act-Alat(10)-NHMe becomes more rigid due to the bulkier sulfur atom.     

Sulfoxides as ‘traceless’ resolving agents for the synthesis of atropisomers by dynamic or classical resolution

Reacting (−)-menthyl sulfinate with an atropisomeric but racemic aryllithium gives two atropdiastereoisomeric sulfoxides. Separation (by chromatography or crystallisation) and sulfoxide-lithium exchange of each diastereoisomer regenerates the aryllithium in enantiomerically pure form which can be quenched with a range of electrophiles with retention of stereochemical integrity. Overall the reaction sequence is a resolution but without the need for an acidic or basic substituent—a ‘traceless’ method. In certain instances, for example when the nucleophile is an ortholithiated peri-substituted 1-naphthamide, the diastereoisomeric sulfoxides may be interconverted thermally. This allows a dynamic resolution, under thermodynamic control, and hence in principle can give yields of the final products of greater than 50%. The utility of the method is demonstrated by the synthesis of a known atropisomeric phosphine ligand.     

Synthesis, crystal structure, and nonlinear optical behavior of beta-unsubstituted meso-meso E-vinylene-linked porphyrin dimers

[structure: see text] A vinylene-linked porphyrin dimer, with no substituents at the beta-positions, has been synthesized by CuI/CsF promoted Stille coupling. In the crystal structure of this dimer, the C(2)H(2) bridge is twisted by 45 degrees relative to the plane of the porphyrins. The absorption, emission spectra, and electrochemistry reveal substantial porphyrin-porphyrin pi-conjugation. The triplet excited-state absorption spectrum of this dimer makes it suitable for reverse saturable absorption at 710-900 nm.     

Binding Aedes aegypti densonucleosis virus to ion exchange membranes

Experimental and numerical results for binding Aedes aegypti densonucleosis virus (AeDNV) using anion and cation exchange membranes are presented. AeDNV particles are adsorbed by anion and cation exchange membranes providing the virus particles and membranes are oppositely charged. Q membranes which are strongly basic anion exchangers were the most effective. Dynamic and static capacities for Q membranes were found to be similar. A numerical model is proposed which assumes a log normal pore size distribution. By estimating the required parameters from static binding experiments, the model may be used to calculate the breakthrough curve for virus adsorption.     

Methyl, hydrochalcogenido, and phenylchalcogenolate complexes of zinc in a sulfur rich coordination environment: syntheses and structural characterization of the tris(2-mercapto-1-tert-butylimidazolyl)hydroboratozinc complexes [TmBut]ZnMe, [TmBut]ZnEH (E = S, Se) and [TmBut]ZnEPh (E = O, S, Se, Te)

A series of hydrochalcogenido and phenylchalcogenolate complexes of zinc supported by tris(2-mercapto-1-tert-butylimidazolyl)hydroborato ligation, [Tm(Bu(t))]ZnEH (E = S, Se) and [Tm(Bu(t))]ZnEPh (E = O, S, Se, Te) have been synthesized from [Tm(Bu(t))]ZnMe; structural characterization by X-ray diffraction indicates that the variation in Zn-E bonding as a function of the chalcogen is significantly different from that in other series of metal-chalcogenolate compounds.     

Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

First total synthesis of the 7,3'-linked naphthylisoquinoline alkaloid ancistrocladidine

[structure: see text] The first total synthesis of the rare 7,3'-linked naphthylisoquinoline alkaloid, ancistrocladidine, has been completed. The key feature of the synthesis is the formation of the extremely hindered biaryl linkage by Pinhey-Barton ortho-arylation of a naphthol with an aryllead triacetate. The biaryl aldehyde formed is elaborated in 10 steps to form a 1:1 mixture of ancistrocladidine and its atropisomer. Recrystallization of the mixture afforded ancistrocladidine, which was identical in all respects to the reported data.     

Wild ginseng grows in Myanmar

Ginseng, the underground parts of plants of Panax species, has been used in oriental traditional medicine for centuries. Unfortunately, because of extensive exploitation over thousands of years, the natural source of these species has been almost exhausted. Recently, we have found a wild ginseng growing in Myanmar. Here, by a combination of chemical composition study and gene sequence analysis, we unambiguously demonstrate that the wild ginseng is actually P. zingiberensis, commonly known as ginger ginseng. This ginseng was an indigenous to the southwestern China. However, now it is seriously threatened to brink of extinction and is put on the highest level of protection in China. Therefore, an appropriate protection measure is highly recommended to preserve this valuable resource, since this Myanmar ginseng might turn out to be the last P. zingiberensis, which could ever be seen in the planet.