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.     

Anion-controlled nuclearity in nickel complexes with potentially dinucleating, poly(oxime) amine ligands

Two new ligands consisting of bis(oxime) amine units tethered by a bridge have been synthesized. Their nickel chloride and nickel nitrate complexes have also been synthesized and characterized by X-ray crystallography, FTIR, mass spectrometry, and elemental analysis. One of these ligands, L1 (N,N,N',N'-tetra(1-propan-2-onyl oxime)-diamino-m-xylene), is always dinucleating, while the other ligand, L2 (N,N,N',N'-tetra(1-propan-2-onyl-oxime)-1,3-diaminopropane), shows an unusual anion dependence on the nuclearity. When nickel chloride is used, the ligand acts in a dinucleating manner and coordinates two nickels; however, when nickel nitrate is used, the ligand acts in a monodentate fashion and coordinates only one nickel. Once the mononuclear complex is formed, it is not possible to add a second nickel if Ni(NO(3))(2) is used as the nickel source; it is possible, however, to add a second nickel if NiCl(2) is used as the nickel source. The dinuclear complex can be converted to the mononuclear one by either using silver nitrate to exchange the chloride anions for nitrates or by dissolving the complex in water. Ni(2)(L1)Cl(4)(DMF)(2).DMF: orthorhombic, P2(1)2(1)2(1), a = 12.2524(11) A, b = 16.6145(15) A, c = 20.1234(19) A, V = 4096.5(6) A(3), Z = 4. [Ni(2)(L2)Cl(4)(DMF)](2).2DMF: triclinic, P-1, a = 12.5347(5) A, b = 12.5403(5) A, c = 14.3504(6) A, alpha = 67.348(1) degrees , beta = 69.705(1) degrees , gamma = 81.549(1) degrees , V = 1952.25(14) A(3), Z = 1. Ni(L2).(NO(3))(2): monoclinic, P2(1)/n, a = 9.6738(3) A, b = 30.2229(9) A, c = 15.8238(5) A, beta = 97.995(1) degrees , V = 4581.4(2) A(3), Z = 8.     

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.     

Two dimensional reversed-phase-reversed-phase separations isomeric separations incorporating C18 and carbon clad zirconia stationary phases

Informational theory and a geometric approach to factor analysis were employed to evaluate the degree of orthogonality of a two-dimensional reversed-phase-reversed-phase chromatographic system. The system incorporated a C18 column as one dimension and a carbon clad zirconia column as the second dimension. In order to study the resolving power of this system, the separation of a sample matrix containing an artificial mix of 32 isomers (structural and diastereoisomers) was evaluated. Using this system, between 25 and 28 of the 32 isomers could be separated, depending on the mobile phase combinations--with resolution that could not possibly be achieved in a single one dimensional separation. The results from this study indicate that in order to fully evaluate the resolving power of a 2D system multiple methods of analysis are most appropriate. This becomes increasingly important when the sample contains components that are very closely related and the retention of solutes is clustered in one quadrant of the 2D space. Ultimately, the usefulness of the 2D separation is determined by the goals of analyst.     

Intramolecular fluorescence quenching in luminescent copolymers containing fluorenone and fluorene units: a direct measurement of intrachain exciton hopping rate

The quenching process of fluorescence emission in polyfluorene (PF) due to the presence of intramolecular 9-fluorenone (9 FL) moieties is studied in dilute toluene solution as a function of 9 FL content in eight copolymers containing both fluorene and fluorenone units (PF/FL(x)). The absorption spectrum of PF/FL(x) copolymers clearly shows a new absorption band, redshifted relatively to the PF and 9-fluorenone absorption, which increases in intensity when the fluorenone fraction increases and also decreases with solvent polarity. Fluorescence emission spectra of PF/FL(x) show that this redshifted and unstructured emission does not coincide with the 9-fluorenone emission and, with increasing solvent polarity, it further redshifts and decreases in intensity. An isoemissive point is clearly observed on the fluorescence emission spectra of PF/FL(x) as a function of fluorenone content, showing that the new emission band is formed at the expense of PF. We propose the formation of an intramolecular charge transfer complex (ICTC) between PF units and 9-fluorenone to explain the appearance of the new emission band. Global analysis of time resolved fluorescence decays collected at 415 nm (PF emission) and 580 nm (the ICTC emission) show that three exponentials are generally needed to achieve excellent fits. Two of the components (420 ps and 6.5 ns) are independent of 9-fluorenone fraction. A further fast component is strongly dependent on fluorenone fraction and ranges between 280 and 70 ps. This component appears as a decay time at 415 nm and as a rise time at 580 nm and is ascribed to the migration of exciton to quenching sites (formation of intramolecular CT complex or exciton ionization at CT complex). A kinetic mechanism involving three different kinetic species, quenched PF units kinetically coupled with the ICTC complex, and unquenched PF units is proposed to explain the experimental data and the quenching rate constant is obtained, k(1) congruent with 10(11) s(-1). This is an experimental measurement of the intrachain exciton hopping rate.