Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity

Mitomycin C (MMC) is a potent antitumour agent that forms a covalent bond with the 2-amino group of selected guanines in the minor groove of double-stranded DNA following intracellular reduction of its quinone ring and opening of its aziridine moiety. At some 5'-CG-3' (CpG) steps the resulting monofunctional adduct can evolve towards a more deleterious bifunctional lesion, which is known as an interstrand crosslink (ICL). MMC reactivity is enhanced when the cytosine bases are methylated (5 MC) and decreased when they are replaced with 5-F-cytosine (5FC) whereas the stereochemical preference of alkylation changes upon decarbamoylation. We have studied three duplex oligonucleotides of general formula d(CGATAAXGCTAACG) in which X stands for C, 5MC or 5FC. Using a combination of molecular dynamics simulations in aqueous solution, quantum mechanics and continuum electrostatics, we have been able to (i) obtain a large series of snapshots that facilitate an understanding in atomic detail of the distinct stereochemistry of monoadduct and ICL formation by MMC and its decarbamoylated analogue, (ii) provide an explanation for the altered reactivity of MMC towards DNA molecules containing 5MC or 5FC, and (iii) show the distinct accommodation in the DNA minor groove of the different covalent modifications, particularly the most cytotoxic C1α and C1β ICLs.     

New ternary germanides La4Mg5Ge6 and La4Mg7Ge6: crystal structure and chemical bonding

The synthesis, structural characterization, and chemical-bonding peculiarities of the two new polar lanthanum-magnesium germanides La(4)Mg(5)Ge(6) and La(4)Mg(7)Ge(6) are reported. The crystal structures of these intermetallics were determined by single-crystal X-ray diffraction analysis. The La(4)Mg(5)Ge(6) phase crystallizes in the orthorhombic Gd(4)Zn(5)Ge(6) structure type [Cmc2(1), oS60, Z = 4, a = 4.5030(7) ?, b = 20.085(3) ?, c = 16.207(3) ?, wR2 = 0.0451, 1470 F(2) values, 93 variables]. The La(4)Mg(7)Ge(6) phase represents a new structure type with a monoclinic unit cell [C2/m, mS34, Z = 2, a = 16.878(3) ?, b = 4.4702(9) ?, c = 12.660(3) ?, β = 122.25(3)°, wR2 = 0.0375, 1466 F(2) values, 54 variables]. Crystallographic analysis together with linear muffin-tin orbital band structure calculations reveals the presence of strongly bonded 3D polyanionic [Mg-Ge] networks balanced by positively charged La atoms in both stoichiometric compounds. The La(4)Mg(5)Ge(6) compound is related to Zintl phases, showing a prominent density of states pseudogap at the Fermi level. A distinctive feature of the La(4)Mg(5)Ge(6) structure is the presence of Ge-Ge covalent dumbbells; in La(4)Mg(7)Ge(6), the higher Mg content generates a polyanionic network consisting exclusively of Mg-Ge heterocontacts. Nevertheless, the frameworks of the two phases are structurally similar, as is highlighted in this work.     

Polar-Covalent Bonding Beyond the Zintl Picture in Intermetallic Rare-Earth Germanides

A comparative chemical bonding analysis for the germanides La₂MGe₆ (M=Li, Mg, Al, Zn, Cu, Ag, Pd) and Y₂PdGe₆ is presented, together with the crystal structure determination for M=Li, Mg, Cu, Ag. The studied compounds adopt the two closely related structure types oS72-Ce₂(Ga_0.1Ge_0.9)₇ and mS36-La₂AlGe₆, containing zigzag chains and corrugated layers of Ge atoms bridged by M species, with La/Y atoms located in the biggest cavities. Chemical bonding was studied by means of the quantum chemical position-space techniques QTAIM (quantum theory of atoms in molecules), ELI-D (electron localizability indicator), and their basin intersections. The new penultimate shell correction (PSC0) method was introduced to adapt the ELI-D valence electron count to that expected from the periodic table of the elements. It plays a decisive role to balance the Ge−La polar-covalent interactions against the Ge−M ones. In spite of covalently bonded Ge partial structures formally obeying the Zintl electron count for M=Mg²⁺, Zn²⁺, all the compounds reveal noticeable deviations from the conceptual 8−N picture due to significant polar-covalent interactions of Ge with La and M ≠ Li, Mg atoms. For M=Li, Mg a formulation as a germanolanthanate M[La₂Ge₆] is appropriate. Moreover, the relative Laplacian of ELI-D was discovered to reveal a chemically useful fine structure of the ELI-D distribution being related to polyatomic bonding features. With the aid of this new tool, a consistent picture of La/Y−M interactions for the title compounds was extracted.     

Determination of urinary S-phenylmercapturic acid, a specific metabolite of benzene, by liquid chromatography/single quadrupole mass spectrometry

A high-performance liquid chromatography/single quadrupole mass spectrometry (LC/MS) method is described for the determination of urinary S-phenylmercapturic acid (S-PMA), a specific metabolite of benzene. Urine samples were spiked with [13C6]S-PMA (used as the internal standard) and acidified; then they were purified by solid-phase extraction (SPE) on C18 cartridges. Analyses were conducted on a reversed-phase column by gradient runs with 1% aqueous acetic acid/methanol mixtures at different proportions as the mobile phase. The detector was used in electrospray negative ion mode (ESI-), the ions m/z 238 for S-PMA and 244 for [13C6]S-PMA being recorded simultaneously. The detection limit (for a signal-to-noise ratio = 3) was 0.2 microg/L, thus allowing for the measurement of background excretion of S-PMA in the general population. The use of the internal standard allowed us to obtain good precision (CV% values < 3%) and a linear calibration curve within the range of interest for monitoring occupational exposure to benzene (up to 500 microg/L). The method was applied to assay the metabolite concentration in a group of 299 workers (68 smokers and 231 non-smokers) occupationally exposed to relatively low levels of benzene (environmental concentration = 0.4-220 microg/m3, mean 11.4 microg/m3 and 236 non-exposed subjects (134 smokers and 102 non-smokers). The results clearly showed that smoking must be taken into account for the correct interpretation of the results of S-PMA measurements for the assessment of work-related benzene exposure. When only non-smokers were selected, the mean excretion of S-PMA was significantly higher in workers exposed to benzene (1.2 +/- 0.9 microg/g creatinine) than in the control group (0.7 +/- 0.6 microg/g creatinine) (p < 0.001), thus confirming the role of S-PMA as a biomarker of benzene on a group basis, even for relatively low exposure degrees.     

Enantioselective addition of phenyl and alkyl acetylenes to imines catalyzed by chiral Cu(I) complexes

The stereoselective addition of phenyl acetylene and alkyl acetylenes to imines, catalyzed by chiral bis-imines-Cu(I) complexes was studied. A very simple experimental procedure allowed to obtain at room temperature optically active propargyl amines in very good yields and enantioselectivity up to 81%.     

Crystallochemistry of the novel two-layer RECuMg4 (RE=La, Tb) ternary compounds

The crystal structures of the new ternary compounds LaCuMg₄ and TbCuMg₄ were studied by X-ray powder diffraction and single-crystal methods, respectively. Scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDXS) was used for examining microstructure and phase composition. LaCuMg₄ crystallizes in the UCoAl₄ structure type (space group P6¯2m, Pearson code hP18, a=1.03911(1), c=0.45126(1) nm, Z=3, R_F=0.0654), while TbCuMg₄ exhibits a new structure (space group Cmmm, Pearson code oS48, a=1.35797(6), b=2.03333(9), c=0.39149(2) nm, Z=8, wR₂=0.0426). Both structures represent a family of two-layer compounds. All interatomic distances indicate metallic type bonding. The structural peculiarities of these compounds and their relations are discussed.     

Lithium intercalation of phenyl-capped aniline dimers: a study by photoelectron spectroscopy and quantum chemical calculations

Structural and electronic properties of pristine and lithium-intercalated, phenyl-capped aniline dimers as a model for the lithium-polyaniline system have been studied by photoelectron spectroscopy and quantum chemical calculations. It was found that the electronic structure of reduced and oxidized forms of oligoanilines is only weakly affected by isomerism. Upon intercalation, charge transfer from the Li-atoms is remarkable and highly localized at N-atomic sites, where configurations are energetically favored in which both N atoms of the dimers are bound to Li atoms. Conversion of nitrogen sites is different for the two forms of aniline dimers and incomplete up to high intercalation levels, indicating a pronounced role of solid-state effects in the formation of such compounds.     

Opioid peptides: synthesis and biological properties of [(N gamma-glucosyl,N gamma-methoxy)-alpha, gamma-diamino-(S)-butanoyl]4-deltorphin-1-neoglycopeptide and related analogues

The [D-Ala2]deltorphin 1 sequence in which the aspartic acid residue is replaced by the N gamma-OCH3-alpha, gamma-diamino (S) butanoyl residue was synthesized using the Fmoc-chemistry-based solid phase procedure. The resulting deltorphin analogue was chemoselectively glucosylated by reaction with unprotected D-glucose (Glc). The Asn4-, (2-acetamido-3,4,6-tri-O-acetyl-2-deoxy-beta-D-galactopyranosyl)-Asn4- and the (2-acetamido-2-deoxy-D-galactopyranosyl)-Asn4-deltorphin I were also prepared for comparison. The affinity of the new compounds for the delta-opioid receptor was expressed by the inhibition constant (Ki) of the binding of the delta-receptor selective ligand [3H]naltrindole (NTI) to rat brain membrane preparations. The in vitro biological activity of the synthetic peptides was compared with that of the mu-opioid receptor agonist dermorphin in guinea pig ileum (GPI) preparations and with that of the delta-opioid receptor agonist deltorphin I in mouse vas deferens (MVD) preparations. The substitution of Asp4 with Asn failed to affect drastically the Ki and IC50 values for delta-sites, suggesting that an electrostatic interaction does not play an essential role in the binding to delta-opioid sites. The steric hindrance of the side chain of the residue in position 4 affects binding to delta-sites. The increase of the Ki value is smaller when the sugar-peptide linkage involves the gamma-nitrogen of the Dab residue in comparison with the Asn amide side chain.     

High-performance liquid chromatographic assay of bacterial collagenase

Summary The activity of bacterial collagenase Clostridiopeptidase A was estimated using a labelled synthetic peptide, 4-phenylazobenzyloxycarbonyl-L-Pro-L-Leu-Gly-L-Pro-D-Arg, as substrate. The N-protected dipeptide obtained after enzymatic hydrolysis of Leu-Gly peptide bond was quantified by reversed-phase, high-performance liquid chromatography using 4-phenylazobenzyloxycarbonyl-L-Pro-L-Phe as internal standard. The time dependence of the appearance of the hydrolysis product and the dependence of rates of hydrolysis on collagenase concentration were linear. Kinetic parameters for collagenase were determined to test the suitability of the described procedure.