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.     

AB initio calculations of 2H and 14N quadrupolar coupling constants in hydrogen bonded dimers

SCF MO calculations at the 6-31G^** level of approximation are reported for ²H and ¹⁴N electric field gradients in HCN?HCN, HCN?HF, and CH₃CN?HF dimers, with emphasis on the configurational dependence of these quantities in (HCN)₂. In comparison with available experimental nuclear quadrupolar coupling constants, the calculated values for the monomers and dimers exhibit an accuracy of ≈ 10%, which is comparable to that of other spectroscopic parameters. The implications of hydrogen bonding for quadrupolar spin-lattice relaxation rates are briefly discussed.     

Basis set and density functional dependence of vibrational Raman optical activity calculations

We present an extensive investigation of the dependence of the scattering intensity difference of right and left circularly polarized light observed in vibrational Raman optical activity (VROA) on the choice of basis set and exchange-correlation functional. These dependencies are investigated for five molecules for which accurate experimental data are available: (S)-methyloxirane, (R)-epichlorhydrin, (S)-glycidol, (M)-spiro[2,2]pentane-1,4-diene, and (M)-sigma-[4]-helicene. Calculations are presented using the SVWN exchange-correlation functional (LDA), the BLYP exchange-correlation functional, and the B3LYP hybrid functional, using six different basis sets: the cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, aug-cc-pVTZ, Sadlej's polarized basis set, and a minimal VROA basis set recently proposed by Zuber and Hug. It is demonstrated that results from pure gradient-corrected and hybrid functionals are comparable and that the aug-cc-pVDZ and aug-cc-pVTZ basis sets yield similar results. Furthermore, the combination of the small basis set by Zuber and Hug with an accurate force field represents the best compromise between computational accuracy and computational efficiency.     

Direct, stereoselective substitution in [Rh(CO)(2)Cl](2)-catalyzed allylic alkylations of unsymmetrical substrates

[Rh(CO)(2)Cl](2) has been found to possess the unusual property of catalyzing allylic alkylations of unsymmetrical allylic carbonates with high levels of regioselectivity to provide products arising from substitution at the carbon atom bearing the leaving group, irrespective of the structure of the starting carbonate. The substitution reaction occurs with retention of stereochemistry at the reacting center, and the carbon-carbon double-bond stereochemistry of primary (Z)-allylic carbonates is maintained. [reaction: see text]     

Desorption ionization combined with tandem mass spectrometry: Advantages for investigating complex lipids,disaccharides and organometallic complexes

Combining desorption ionization with tandem mass spectrometry overcomes the disadvantage of limited fragmentation accompanying desorption and permits mixtures of closely related substances to be investigated directly. These features of the combination are illustrated by completing the structure-proof of a minor component of an ornithine-containing lipid mixture isolated from Thiobacillus thiooxidans. The minor component is a homolog of the major constituent and differs from the principal component owing to the presence of a double bond in lieu of a cyclopropyl ring in one of the constituent fatty acids. Another feature of the combined method is the potentially complementary nature of collision-activated dissociation spectra of protonated and cationized biomolecules. This is illustrated by the differences in the collision-activated dissociations of the [M + Na]⁺ of sucrose, desorbed by field desorption, and [M + H]⁺, desorbed by fast atom bombardment. A third illustration is the application of field desorption and tandem mass spectrometry to an organometallic compound. The combined approach allows the ligands to be identified and the relative ligand binding energies to be approximated.     

Bromination of sydnones. I. Reaction with 3-arylsydnones containing electron-donors on the aryl ring

Bromination has been examined for a series of 3-arylsydnones (1) with electron donors (dimethyl to dimethoxy) on the aryl ring. In no example was exclusive aryl ring bromination observed, however, exclusive sydnone ring bromination could be realized in every case. For two dimethoxyphenyl examples both aryl and sydnone ring bromination occurred.     

Voltammetric, chronocoulometric and spectroelectrochemical studies of electropolymerized films based on Co(III/II)- and Zn(II)-4,9,16,23-tetraaminophthalocyanine: effect of high pH

Electropolymerized thin films of Co(III/II)- and Zn(II)-4,9,16,23-tetraaminophthalocyanine, immersed in solutions of relatively high pH, have been studied electro- and spectroelectrochemically. Cyclic voltammetry and chronocoulometry were used to characterize films deposited on glassy carbon electrodes. Spectroelectrochemistry and ellipsometry measurements were performed on indium tin oxide (ITO) surfaces coated with the zinc and cobalt complexes and correlated to the electrochemical information collected using glassy carbon electrodes. Studies at high pH are motivated by the efficient increase in luminol chemiluminescence at high OH⁻ concentration, and by potential application in luminescence sensors. Although the films are not removed, some structural changes occur when they are exposed to solutions of high pH. In addition, an estimation of the number of monolayers has also been calculated. The atomic diameters of cobalt and zinc are very close in value, but the estimated number of monolayers, based on cyclic voltammetric data, for a given number of electropolymerization cycles is approximately four-fold higher in the zinc-based film. This would correspond to three-fold thicker films when zinc is the central metal ion. Ellipsometry measurements have been correlated with cyclic voltammetric data to confirm that film thickness varies among the different complexes, even though the conditions of electropolymerization are the same.     

Nordesferriferrithiocin. Comparative Coordination Chemistry of a Prospective Therapeutic Iron Chelating Agent(1)

Nordesferriferrithiocin, NDFFTH(2), is a derivative of the siderophore desferriferrithiocin, DFFTH(2), in which the methyl group is substituted by a hydrogen atom. Both compounds show high oral activity as possible drugs for the treatment of iron overload. While DFFTH(2) is significantly toxic, NDFFTH(2) exhibits a lower toxicity and offers a much better therapeutic window than other orally active iron chelators. In this study, complexes of DFFTH(2) and NDFFTH(2) with various trivalent metals have been synthesized and characterized. Five isomers (the maximum possible) have been observed in the case of [Co(DFFT)(2)](-) in solution, as proved by (1)H-NMR measurements. Although normally labile, complexes of Al(3+) ([Al(DFFT)(2)](-)) have been separated by HPLC. In general, DFFTH(2) forms kinetically inert complexes whereas complexes of NDFFTH(2) tend to isomerize quickly in solution, as indicated by CD spectroscopy of separated HPLC fractions of [Cr(NDFFT)(2)](-). The most stable isomers of the aluminum complexes of both ligands have been characterized by X-ray crystallography; K[Al(DFFT)(2)] crystallizes from methanol/diethyl ether in the orthorhombic space group P2(1)2(1)2 with a = 11.238(3) ?, b = 31.719(11) ?, c = 7.684(2) ?, V = 2739.2(24) ?(3), and Z = 4. This isomer has the mer-(N,O-Lambda)(S,S) configuration, while K[Al(NDFFT)(2)] crystallizes from methanol/diethyl ether in the space group P6(1) (a = 21.269(8) ?, c = 9.643(3) ?, V = 3777.8(42) ?(3), Z = 6) and has the same coordination geometry. The solution thermodynamics of the Al(3+), Ga(3+), and Fe(3+) complexes have been studied by spectrophotometric titration. The stability constants (log K) are 23.6(1), 29.2(3), and 31.04(3), respectively, for the DFFTH(2) complexes and 22.0(1), 27.8(2), and 29.09(3), respectively, for the NDFFTH(2) complexes. Cyclic voltammograms of both iron complexes have been recorded in water at a carbon disk working electrode and in DMF at a graphite working electrode. The reduction waves measured in DMF indicate no reversibility whereas in water a quasi-reversible reduction is observed. The reduction potentials (E(1/2)'s) in water are -166 mV for [Fe(DFFT)(2)](-) and -97 mV for [Fe(NDFFT)(2)](-) versus NHE. These potentials are well in the range for biological reductants, which makes possible an in vivo reduction mechanism for the iron removal from the siderophore.     

Conversion of Allylic Alcohols into Allylic Nitromethyl Compounds via a Palladium-Catalyzed Solvolysis: An Enantioselective Synthesis of an Advanced Carbocyclic Nucleoside Precursor(1)

A two-step reaction sequence to homoallylic nitro compounds from allylic alcohols is presented. Ethoxy carbonylation of the alcohols with ethyl chloroformate provides the corresponding allylic ethyl carbonates in high yields. Exposure of these substrates to catalytic palladium(0) in CH(3)NO(2) initiates a reaction sequence, ionization-decarboxylation-nitromethylation, that culminates with the formation of nitroalkenes. The regio- and stereochemical outcomes of the nitromethyl allylation reaction can be explained by the behavior of the transient pi-allylpalladium complexes. This methodology serves as a centerpiece for the synthesis of an important carbocyclic nucleoside intermediate.     

Transparent conducting oxides: texture and microstructure effects on charge carrier mobility in MOCVD-derived CdO thin films grown with a thermally stable, low-melting precursor

A series of low-melting, thermally stable cadmium metal-organic chemical vapor deposition (MOCVD) precursors have been synthesized, structurally and spectroscopically characterized, and implemented in growth of highly conductive and transparent CdO thin films. One member of the series, bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)(N,N-diethyl-N',N'-dimethyl-ethylenediamine)cadmium(II), Cd(hfa)(2)()(N,N-DE-N',N'-DMEDA), represents a particularly significant improvement over previously available Cd precursors, owing to the low melting point and robust thermal stability. High-quality CdO films were grown by MOCVD on glass and single-crystal MgO(100) between 300 and 412 degrees C. Film growth parameters and substrate surface have large effects on microstructure and electron carrier transport properties. Enhanced mobilities observed for highly biaxially textured films grown on MgO(100) vs glass are attributed, on the basis of DC charge transport and microstructure analysis, to a reduction in neutral impurity scattering and/or to a more densely packed grain microstructure. Although single-grained films grown on MgO(100) exhibit greater mobilities than analogues with discrete approximately 100 nm grains and similar texture, this effect is attributed, on the basis of charge transport and Hall effect measurements as well as optical reflectivity analysis, to differences in carrier concentration rather than to reduced grain boundary scattering. Unprecedented conductivities and mobilities as high as 11,000 S/cm and 307 cm(2)/V.s, respectively, are obtained for epitaxial single-grained films (X-ray diffraction parameters: fwhm(omega) = 0.30 degrees, fwhm(phi) = 0.27 degrees ) grown in situ on MgO(100) at a relatively low temperature (400 degrees C).