Virtual Screening and Structure Generation Applied to Drug Design

The methods of computer-aided drug design can be divided into two categories according to whether or not the structures of receptors are known1, corresponding to two principal strategies: (1) searching the bio-active ligands against virtual combinatorial libraries and calculating the affinity energy between ligand and receptor by docking ; (2) QSAR and 3D-structure data-mining. 3D-QSAR method is now applied widely to drug discovery, but this method is generally limited to refine the structu…     

1H and 13C chemical shifts for acridines: Part XIX. N,N'-diacylproflavine derivatives

The 1H and 13C NMR resonances of 15 N,N'-diacylproflavines were assigned completely and unequivocally using a concerted application of one- and two-dimensional experiments (DEPT, gs-COSY, gs-HMQC and gs-HMBC).     

Diastereoselective hydroxylation of 6-substituted piperidin-2-ones. An efficient synthesis of (2S,5R)-5-hydroxylysine and related alpha-amino acids

The synthesis of (2S,5R)-5-hydroxy-6-oxo-1,2-piperidinedicarboxylates (5) and related (3S,6R)-3-hydroxy-6-alkyl-2-oxo-1-piperidinecarboxylates has been developed. The approach is based on the asymmetric hydroxylation of enolates generated from the corresponding N-protected-6-substituted piperidin-2-ones. The utility of 5a as a precursor in the synthesis of (2S,5R)-5-hydroxylysine (1), an amino acid unique to collagen and collagen-like proteins, has also been demonstrated. (2S)-6-oxo-1,2-piperidinedicarboxylates (6) required for hydroxylation studies were prepared in 38-74% yield, starting from conveniently protected aspartic acid as inexpensive chiral adduct. Hydroxylation of 6 to 5 proceeds in high yield and excellent diastereoselectivity by treatment of their Li-enolate with (+)-camphorsulfonyloxaziridine at -78 degrees C. Ring opening of di-tert-butyl (2S,5R)-6-oxo-1,2-piperidinedicarboxylate ((5R)-5a) under reductive conditions afforded the corresponding 1,2-diol (17) in 91%, which was further transformed to (2S,5R)-5-hydroxylysine in four steps (84%). 17 is also a versatile intermediate in the preparation of tert-butyl (2S,5R)-2-[(tert-butoxycarbonyl)amino]-5-hydroxy-6-iodohexanoate (3) and tert-butyl (2S)-2-[(tert-butoxycarbonyl)amino]-4-[(2R)-oxiranyl]butanoate (4), two amino acid derivatives used in the total synthesis of the bone collagen cross-link (+)-pyridinoline (2a).     

Importance of backdonation in [M-(CO)]p+ complexes isoelectronic to [Au-(CO)]+

In this contribution, we study several monocarbonyl-metal complexes in order to unravel the contribution of relativistic effects to the metal-ligand bond length and complexation energy. Using scalar density functional theory (DFT) constrained space orbital variation (CSOV) energy decomposition analysis supplemented by all-electron four-component DFT computations, we describe the dependency of relativistic effects on the orbitals involved in the complexation for the Au(+) isoelectronic series, namely, the fully occupied 5d orbitals and the empty 6s orbitals. We retrieve the well-known sensitivity of gold toward relativity. For platinum and gold, the four-component results illustrate the simultaneous relativistic expansion of the 5d orbitals and the contraction of the 6s orbitals. The consequences of such modifications are evidenced by CSOV computations, which show the importance of both donation and backdonation within such complexes. This peculiar synergy fades away with mercury and thallium for which coordination becomes driven by the accepting 6s orbitals only, which makes the corresponding complexes less sensitive toward the relativistic effects.     

New and old NMR experiments for the resonance assignment of complex oligosaccharides--application to a cyclodextrin derivative

The complete assignment of the (1)H and (13)C sugar resonances in mono-3,6-anhydro-heptakis(2,3-O-methyl)-hexakis(6-O-methyl)-β-cyclodextrin, an asymmetrically functionalized β-cyclodextrin, was carried out by means of 2D NMR experiments. The TOCSY and the homonuclear multiple relay COSY spectra provided most of the (1)H assignments. The multiplicity edited HSQC and a set of F(1) selective HSQC-TOCSY and multiple relay HSQC-COSY spectra gave access to most of the (13)C chemical shifts. The latter were fully and accurately determined by means of a pair of complementary, highly folded HSQC-TOCSY spectra. The TOCSY-ROESY and ROESY-TOCSY spectra yielded the sequential assignment of the sugar units. A high resolution F(1) selective F(1) decoupled version of the TOCSY-ROESY experiment was recorded.     

2,3-di-n-decyloxy-6,7-dichloroanthracene (Cl2DDOA), a new low-molecular-mass fluorescent organogelator: physical properties and structures

To extend the family of 2,3-didecyloxyanthracene (DDOA, 1), an organogelator having a rodlike shape, a high polarity, and fluorescing properties, the 6,7-dichloro derivative (Cl2DDOA, 2), was designed and prepared. Compound 2 forms gels in alcohols, nitriles, and alkanes. The electronic absorption spectra of the gel show a finer structure than those of the isotropic solutions, pointing to a specific degree of packing of the molecules; such an aggregation mode is also supported by fluorescence data. The gel-to-sol temperatures (Tm) were determined as a function of gelator concentration and the corresponding enthalpies (DeltaHm) were extracted. Scattering experiments have shown that the molecular packing in aggregates of 2 organogels is less reminiscent of the crystalline state than was the situation with DDOA gels. 2 organogels in butanol are made up of 120 A radius fibers much thinner than those observed in DDOA gels (r ca. 300 A) and with rather monodisperse cross sections. In 1-octanol, dodecane, or cyclohexane, the fibrillar organogel networks involve a broader distribution of the related cross sections through anisometric sections of the fibers and/or formation of bundles.     

Comment on “The electron‐pair origin of anti‐aromaticity: Spectroscopic manifestations”

In the article by Zilberg and Haas, “The Electron‐Pair Origin of Anti‐aromaticity: Spectroscopic Manifestations,” the relative sign of the two Kekulé valence bond functions, R and L, in conjugated cyclic hydrocarbons was discussed. It was proposed that in the ground‐state wave function of aromatic compounds, the two functions contribute with like sign, while in the ground state of anti‐aromatic compounds, the two functions contribute with opposite sign. In this Comment, it is shown that the two functions enter with like sign also into the ground‐state wave function of anti‐aromatic compounds. Furthermore, it was argued that resonance tends to (de)stabilize a symmetric ground‐state geometry in case of the (anti‐)aromatic compounds. The expression derived by Zilberg and Haas for the stabilization energy shows an unusual dependence on the ring size and distortion coordinate. An alternative formula is derived for the stabilization energy, in which the energy depends quadratically on the distortion coordinate. Without further numerical calculations, it is not possible to predict whether this term will (de)stabilize a symmetric geometry of the ground state of (anti‐)aromatic molecules. Rather, we are led to believe that the influence of term in question on the geometric stability may be small, thus not providing the main reason for the geometric distortion of anti‐aromatic compounds. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Synthése d'époxydes et d'éthers glycidiques á chaîne chlorofluorée

Epoxides of general formula

(II, V) (R_F,Cl = Cl ; CF₃ ; Cl(CFClCF₂)_n?) are prepared from chlorohydrines R_F,ClCCl₂CH₂CHClCH₂OH (I).These chlorhydrines are monoadducts of carbon tetrachloride 1,1,1 trichlorotrifluoroethane, telomers Cl(CFClCF₂)_nCCl₃, with allyl alcohol.Reactions of these epoxides with lithium aluminium hydride and/or sulfuric acid lead to corresponding secondary alcohols and/or diols. Glycidyl ethers of (I) and (II,n) with epichlorhydrin could not be obtained. However, epichlorhydrin reacts with the more acidic chlorofluorinated alcohol CFCl₂CF₂CH₂OH. Thus, the glycidyl ether

is prepared.     

Norbornane: an investigation into its valence electronic structure using electron momentum spectroscopy, and density functional and Green's function theories

We report on the results of an exhaustive study of the valence electronic structure of norbornane (C(7)H(12)), up to binding energies of 29 eV. Experimental electron momentum spectroscopy and theoretical Green's function and density functional theory approaches were all utilized in this investigation. A stringent comparison between the electron momentum spectroscopy and theoretical orbital momentum distributions found that, among all the tested models, the combination of the Becke-Perdew functional and a polarized valence basis set of triple-zeta quality provides the best representation of the electron momentum distributions for all of the 20 valence orbitals of norbornane. This experimentally validated quantum chemistry model was then used to extract some chemically important properties of norbornane. When these calculated properties are compared to corresponding results from other independent measurements, generally good agreement is found. Green's function calculations with the aid of the third-order algebraic diagrammatic construction scheme indicate that the orbital picture of ionization breaks down at binding energies larger than 22.5 eV. Despite this complication, they enable insights within 0.2 eV accuracy into the available ultraviolet photoemission and newly presented (e,2e) ionization spectra, except for the band associated with the 1a(2) (-1) one-hole state, which is probably subject to rather significant vibronic coupling effects, and a band at approximately 25 eV characterized by a momentum distribution of "s-type" symmetry, which Green's function calculations fail to reproduce. We note the vicinity of the vertical double ionization threshold at approximately 26 eV.     

A study of the spectral emissions in laser-irradiated microdot targets at 0.53 and 0.27 μm wavelengths with micron resolution

Using a knife-edge technique, we have determined the spatial extension of H-like and He-like emissions and the time-integrated axial electron density profile in laser-irradiated aluminium microdot targets at 0.53 and 0.25 μm wavelengths with about 3 μm resolution.