Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures

The ability to discriminate native structures from computer-generated misfolded ones is key to predicting the three-dimensional structure of a protein from its amino acid sequence. Here we describe an assessment of semiempirical methods for discriminating native protein structures from decoy models. The discrimination of decoys entails an analysis of a large number of protein structures, and provides a large-scale validation of quantum mechanical methods and their ability to accurately model proteins. We combine our analysis of semiempirical methods with a comparison of an AMBER force field to discriminate decoys in conjunction with a continuum solvent model. Protein decoys provide a rigorous and reliable benchmark for the evaluation of scoring functions, not only in their ability to accurately identify native structures but also to be computationally tractable to sample a large set of non-native models.     

Design and synthesis of aromatic inhibitors of anthranilate synthase

Aromatic analogues of chorismate were synthesised as potential inhibitors of anthranilate synthase. Molecular modelling using GOLD2.1 showed that these analogues docked into the active site of Serratia marcescens anthranilate synthase in the same conformation as chorismate. Most compounds were found to be micromolar inhibitors of S. marcescens anthranilate synthase. The most potent analogue, 3-(1-carboxy-ethoxy)-4-hydroxybenzoate (K(I) 3 microM), included a lactyl ether side chain. This appears to be a good replacement for the enol-pyruvyl side chain of chorismate.     

Multiple nitrene insertions into metal-sulfur bonds of dithiocarbamate complexes: synthesis of sulfido-amido and zwitterionic tetraamido complexes

The iodine(III) reagent, PhI[double bond, length as m-dash]NTs, acts as a source of the nitrene fragment NTs, which undergoes facile insertion into the metal-sulfur bonds of a range of dithiocarbamate complexes. Addition of two equivalents of PhI=NTs to [M(S(2)CNR2)2] affords sulfido-amido complexes [M{SC(NR2)SNTs}2](M=Ni, Cu), which insert two further nitrene fragments to afford zwitterionic tetraamido complexes [M{TsNSC(NR2)SNTs}2](M=Co, Ni, Cu). Crystallographic studies have been carried out on both types of complex allowing possible resonance hydrids of the new ligand types to be assessed.     

Selective cleavage of P-N bonds and the conversion of rhodium N-pyrrolyl phosphine complexes into diphosphoxane-bridged dimers

Rhodium(I) complexes trans-[RhCl(CO)(PR(2)[NC(4)H(3)C(O)Me-2])(2)] (R = Ph, NC(4)H(4)) react with water to give the diphosphoxane-bridged dimers [Rh(2)Cl(2)(CO)(2)(mu-PR(2)OPR(2))(2)] following cleavage of the P-N bonds to the 2-acetyl-N-pyrrolyl groups. The two dimers have been crystallographically characterized and show a number of structural differences, with the PPh(2)OPPh(2) compound possessing semibridging chloride and carbonyl ligands whereas the P(NC(4)H(4))(2)OP(NC(4)H(4))(2) compound contains only terminal chlorides and carbonyls. No evidence for cleavage of the P-N bonds involving the unfunctionalized N-pyrrolyl groups in trans-[RhCl(CO)(P[NC(4)H(4)](2)[NC(4)H(3)C(O)Me-2])(2)] was observed.     

The structural characteristics of organozinc complexes incorporating N,N'-bidentate ligands

Dimethylzinc reacts with an excess of N-2-pyridylaniline 6 to give the homoleptic species, Zn[PhN(2-C(5)H(4)N)](2) 8. Single crystal X-ray diffraction reveals a solid-state dimer based on an 8-membered (NCNZn)(2) core motif. Zn[CyN(2-C(5)H(4)N)]Me (Cy =c-C(6)H(11)) 10, prepared by the combination of ZnMe(2) with the corresponding cyclohexyl-substituted pyridylamine, is also dimeric in the solid state but reveals a central (ZnN)(2) metallacycle. Employment of (p-Tol)NH(2-C(5)H(4)N)(p-Tol = 4-MeC(6)H(4)) 11 yielded the tris(zinc) adduct Zn(3)[(p-Tol)N(2-C(5)H(4)N)](4)Me(2) 12, which incorporates a central chiral molecule of 'Zn[(p-Tol)N(2-C(5)H(4)N)](2)' 12a, that bridges two 'Zn[(p-Tol)N(2-C(5)H(4)N)]Me' 12b units. A similar trimetallic structure is noted when the pyridylaniline substrate 11 is replaced with the bicyclic guanidine 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine (hppH), affording Zn(3)(hpp)(4)Me(2) 13. Spectroscopic studies point to retention of the solid-state structure of in hydrocarbon solution. Reaction of 13 with dimesityl borinic acid, Mes(2)BOH (Mes = mesityl), affords Zn(3)(hpp)(4)(OBMes(2))(2) 14 in which the trimetallic core is retained. This reactivity is in contrast to the closely related reaction of dimeric Zn[Me(2)NC[N(i)Pr](2)]Me 15 with Mes(2)BOH, which yielded Zn[Me(2)NC[N(i)Pr](2)][OBMes(2)].Me(2)NC[N(i)Pr][NH(i)Pr] 16 as a result of protonation at the guanidine ligand in addition to the Zn-Me bond.     

A study of [Co2(alkyne)(binap)(CO)4] complexes (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine))

Understanding the interaction of chiral ligands, alkynes, and alkenes with cobaltcarbonyl sources is critical to learning more about the mechanism of the catalytic, asymmetric Pauson-Khand reaction. We have successfully characterized complexes of the type [Co2(alkyne)(binap)(CO)4] (BINAP=(1,1'-binaphthalene)-2,2'-diylbis(diphenylphosphine)) and shown that diastereomer interconversion occurs under Pauson-Khand reaction conditions when alkyne=HC[triple bond]CCO2Me. Attempts to isolate [Co2(alkyne)(binap)(CO)x] complexes with coordinated alkenes led to the formation of cobaltacyclopentadiene species.     

Dynamic light scattering studies of poly(ethylene oxide) adsorbed on Laponite: layer conformation and its effect on particle stability

Dynamic light scattering has been used to determine the hydrodynamic thickness of poly(ethylene oxide) (PEO) adsorbed on synthetic anisotropic clay particles (Laponite) as a function of molecular weight. The layer thicknesses, and their increase with molecular weight, indicate that the conformation of the adsorbed layer is very compact and is much smaller than those normally observed for polymer adsorption on flat interfaces. The aggregation kinetics of the polymer coated particles in 5 mM NaCl was analyzed in a quantitative manner, revealing that the potential barrier to aggregation is strongly enhanced when polymer is present.     

Rearrangement of 5-trimethylsilylthebaine on treatment with L-selectride: an efficient synthesis of (+)-bractazonine

Treatment of 5-trimethylsilylthebaine with L-Selectride gave rise to a rearrangement to 10-trimethylsilylbractazonine through migration of the phenyl group, whereas treatment of thebaine with strong Lewis acids is known to lead to a similar rearrangement through migration of the alkyl bridge to give, after reduction, (+)-neodihydrothebaine. It is suggested that the rearrangement of the alkyl group of thebaine is favored due to the formation of a tertiary benzylic cation. However, for 5-trimethylsilylthebaine, the lithium ion of L-Selectride acts as the Lewis acid and the beta-silyl effect dominates in the stabilization of any positive charge. This rearrangement provides a clear example of the greater relative migratory aptitude of phenyl groups over alkyl groups, and provides an efficient synthesis of (+)-bractazonine from thebaine.     

Organic nanoparticles whose size and rigidity are finely tuned by cross-linking the end groups of dendrimers

Dendrimers with molecular weights ranging from ca. 2700 to 11 000 and from 16 to 64 homoallyl ether end groups were cross-linked using the Grubbs ring-closing metathesis reaction. A combination of SEC, MALDI-TOF-MS, and AFM were used to characterize the cross-linked nanoparticles. The data suggest a significant decrease in volume with cross-linking and a concomitant increase in rigidity, both of which can be controlled independently with a fair degree of precision.