Molecular single-bond covalent radii for elements 1-118

Miscoding properties of 8-chloro-2'-deoxyguanosine, a hypochlorous acid-induced DNA adduct, catalysed by human DNA polymerases

Many chronic inflammatory conditions are associated with an increased risk of cancer development. At the site of inflammation, cellular DNA is damaged by hypochlorous acid (HOCl), a potent oxidant generated by myeloperoxidase. 8-Chloro-2'-deoxyguanosine (8-Cl-dG) is a major DNA adduct formed by HOCl and has been detected from the liver DNA and urine of rats administered lipopolysaccharide in an inflammation model. Thus, the 8-Cl-dG lesion may be associated with the carcinogenesis of inflamed tissues. In this study, we explored the miscoding properties of the 8-Cl-dG adduct generated by human DNA polymerases (pols). Site-specifically modified oligodeoxynucleotide containing a single 8-Cl-dG was prepared and used as a template in primer extension reactions catalysed by human pol α, ĸ or η. Primer extension reactions catalysed by pol α and ĸ in the presence of all four dNTPs were slightly retarded at the 8-Cl-dG site, while pol η readily bypassed the lesion. The fully extended products were analysed to quantify the miscoding frequency and specificity of 8-Cl-dG using two-phased polyacrylamide gel electrophoresis (PAGE). During the primer extension reaction in the presence of four dNTPs, pol ĸ promoted one-base deletion (6.4%), accompanied by the misincorporation of 2'-deoxyguanosine monophosphate (5.5%), dAMP (3.7%), and dTMP (3.5%) opposite the lesion. Pol α and η, on the other hand, exclusively incorporated dCMP opposite the lesion. The steady-state kinetic studies supported the results obtained from the two-phased PAGE assay. These results indicate that 8-Cl-dG is a mutagenic lesion; the miscoding frequency and specificity varies depending on the DNA polymerase used. Thus, HOCl-induced 8-Cl-dG adduct may be involved in inflammation-driven carcinogenesis.

Improving biogas separation and methane storage with multilayer graphene nanostructure via layer spacing optimization and lithium doping: a molecular simulation investigation

Methane is a desirable alternative to conventional fossil fuels, and also a main component of biogas from anaerobic fermentation of organic wastes. However, its relatively lower purity and poor storage by existing adsorbent materials negatively affect its wide application. Thus, efficient, cost-effective, and safe adsorbent materials for methane purification and storage are highly desired. In this study, multilayer graphene nanostructures (MGNs) with optimized structure are investigated as a potential adsorbent for this purpose. The effects of layer distance and Li doping on MGN performance in terms of methane storage and acid gas (H(2)S and CO(2)) separation from biogas are examined by molecular simulations. The mechanisms for the interactions between gas molecules and substrates are elucidated by analyzing the binding energy, geometric structures, and charge distribution from the first-principles calculations. The results show that nonhydrocarbons in biogas can be effectively separated using Li-doped MGNs with the optimal layer distance of 0.68 nm, and then the pure methane gas can be stored in MGNs with capacity satisfying the DOE target. This work offers a molecular-level insight into the interactions between gas molecules and MGNs and might provide useful information for development of new materials for methane purification and storage.

[Co(η5-P5){η2-P2H(mes)}]2-: a phospha-organometallic complex obtained by the transition-metal-mediated activation of the heptaphosphide trianion

A carbon copy: The chemical activation of the heptaphosphide trianion with [Co(PEt(2)Ph)(2)(mes)(2)] (see picture; 1) yields the novel phospha-organometallic complex [Co(η(5)-P(5)){η(2)-P(2)H(mes)}](2-) (2). The reaction product maintains the nuclearity of the parent cluster, but extensive cage fragmentation takes place to yield a diamagnetic "inorganometallic" cobalt complex.

Bonding between strongly repulsive metal atoms: an oxymoron made real in a confined space of endohedral metallofullerenes

Endohedral metallofullerenes (EMFs) are able to encapsulate up to four metal atoms. In EMFs, metal atoms are positively charged because of the electron transfer from the endohedral metal atoms to the carbon cage. It results in the strong Coulomb repulsion between the positively charged ions trapped in the confined inner space of the fullerene. At the same time, in many EMFs, such as Lu(2)@C(76), Y(2)@C(79)N, M(2)@C(82) (M = Sc, Y, Lu, etc.), Y(3)@C(80), or Sc(4)O(2)@C(80), metals do not adopt their highest oxidation states, thus yielding a possibility of the covalent metal-metal bonding. In some other EMFs (e.g., La(2)@C(80)), metal-metal bonding evolves as the result of the electrochemical or chemical reduction, which leads to the population of the metal-based LUMO with pronounced metal-metal bonding character. This article highlights different aspects of the metal-metal bonding in EMFs. It is concluded that the valence state of the metal atoms in dimetallofullerenes is not dependent on their third ionization potential, but is determined by their ns(2)(n- 1)d(1)→ns(1)(n- 1)d(2) excitation energies. Peculiarities of the metal-metal bonding in EMFs are described in terms of molecular orbital analysis as well as topological approaches such as Quantum Theory of Atoms in Molecules and Electron Localization Function. Interplay of Coulomb repulsion and covalent bonding is analyzed in the framework of the Interacting Quantum Atom approach.

A substrate-driven approach to determine reactivities of α,β-unsaturated carboxylic esters towards asymmetric bioreduction

The degree of C=C bond activation in the asymmetric bioreduction of α,β-unsaturated carboxylic esters by ene-reductases was studied, and general recommendations to render these "borderline-substrates" more reactive towards enzymatic reduction are proposed. The concept of "supported substrate activation" was developed. In general, an additional α-halogenated substituent proved to be beneficial for enzymatic activity, whereas β-alkyl or β-aryl substituents were detrimental for the reactivity of nonhalogenated substrates, and α-cyano groups showed little effect. The alcohol moiety of the ester functionality was found to have a strong influence on the reaction rate. Overall, activities were determined by both steric and electronic effects.

Are N-heterocyclic carbenes "better" ligands than phosphines in main group chemistry? A theoretical case study of ligand-stabilized E2 molecules, L-E-E-L (L = NHC, phosphine; E = C, Si, Ge, Sn, Pb, N, P, As, Sb, Bi)

A theoretical examination of the L-E-E-L class of molecules has been carried out (E = group 14, group 15 element; L = N-heterocyclic carbene, phosphine), for which Si, Ge, P, and As-NHC complexes have recently been synthesized. The focus of this study is to predict whether it is possible to stabilize the elusive E(2) molecule via formation of L-E-E-L beyond the few known examples, and if the ligand set for this class of compounds can be extended from the NHC to the phosphine class of ligands. It is predicted that thermodynamically stable L-E-E-L complexes are possible for all group 14 and 15 elements, with the exception of nitrogen. The unknown ligand-stabilized Sn(2) and Pb(2) complexes may be considered attractive synthetic targets. In all cases the NHC complexes are more stable than the phosphines, however several of the phosphine derivatives may be isolable. The root of the extra stability conferred by the NHC ligands over the phosphines is determined to be a combination of the NHCs greater donating ability, and for the group 15 complexes, superior π acceptor capability from the E-E core. This later factor is the opposite as to what is normally observed in transition metal chemistry when comparing NHC and phosphine ligands, and may be an important consideration in the ongoing "renaissance" of low-valent main group compounds supported by ligands.

Borylene complexes (BH)L2 and nitrogen cation complexes (N+)L2: isoelectronic homologues of carbones CL2

Quantum chemical calculations using DFT (BP86, M05-2X) and ab initio methods (CCSD(T), SCS-MP2) have been carried out on the borylene complexes (BH)L(2) and nitrogen cation complexes (N(+))L(2) with the ligands L=CO, N(2), PPh(3), NHC(Me), CAAC, and CAAC(model). The results are compared with those obtained for the isoelectronic carbones CL(2). The geometries and bond dissociation energies of the ligands, the proton affinities, and adducts with the Lewis acids BH(3) and AuCl were calculated. The nature of the bonding has been analyzed with charge and energy partitioning methods. The calculated borylene complexes (BH)L(2) have trigonal planar coordinated boron atoms which possess rather short B-L bonds. The calculated bond dissociation energies (BDEs) of the ligands for complexes where L is a carbene (NHC or CAAC) are very large (D(e) =141.6-177.3 kcal mol(-1)) which suggest that such species might become isolated in a condensed phase. The borylene complexes (BH)(PPh(3))(2) and (BH)(CO)(2) have intermediate bond strengths (D(e) =90.1 and 92.6 kcal mol(-1)). Substituted homologues with bulky groups at boron which protect the boron atom from electrophilic attack might also be stable enough to become isolated. The BDE of (BH)(N(2))(2) is much smaller (D(e) =31.9 kcal mol(-1)), but could become observable in a low-temperature matrix. The proton affinities of the borylene complexes are very large, particularly for the bulky adducts with L=PPh(3), NHC(Me), CAAC(model) and CAAC and thus, they are superbases. All (BH)L(2) molecules bind strongly AuCl either η(1) (L=N(2), PPh(3), NHC(Me), CAAC) or η(2) (L=CO, CAAC(model)). The BDEs of H(3)B-(BH)L(2) adducts which possess a hitherto unknown boron→boron donor-acceptor bond are smaller than for the AuCl complexes. The strongest bonded BH(3) adduct that might be isolable is (BH)(PPh(3))(2)-BH(3) (D(e) =36.2 kcal mol(-1)). The analysis of the bonding situation reveals that (BH)-L(2) bonding comes mainly from the orbital interactions which has three major contributions, that is, the donation from the symmetric (σ) and antisymmetric (π(||)) combination of the ligand lone-pair orbitals into the vacant MOs of BH L→(BH)←L and the L←(BH)→L π backdonation from the boron lone-pair orbital. The nitrogen cation complexes (N(+))L(2) have strongly bent L-N-L geometries, in which the calculated bending angle varies between 113.9° (L=N(2)) and 146.9° (L=CAAC). The BDEs for (N(+))L(2) are much larger than those of the borylene complexes. The carbene ligands NHC and CAAC but also the phosphane ligands PPh(3) bind very strongly between D(e) =358.4 kcal mol(-1) (L=PPh(3)) and D(e) =412.5 kcal mol(-1) (L=CAAC(model)). The proton affinities (PA) of (N(+))L(2) are much smaller and they bind AuCl and BH(3) less strongly compared with (BH)L(2). However, the PAs (N(+))L(2) for complexes with bulky ligands L are still between 139.9 kcal mol(-1) (L=CAAC(model)) and 168.5 kcal mol(-1) (L=CAAC). The analysis of the (N(+))-L(2) bonding situation reveals that the binding interactions come mainly from the L→(N(+))←L donation while L←(N(+) )→L π backdonation is rather weak.

Intramolecularly coordinated organotin tellurides: stable or unstable?

The step-wise oxidation of an organotin(I) compound with elemental tellurium gave a variety of unprecedented organotin tellurides containing tin atoms in the oxidation states +II and +IV.

Matrix infrared spectroscopic and theoretical of the difluoroamino metal fluoride molecules: F2NMF (M = Cu, Ag, Au)

The difluoroamino coinage metal fluoride molecules F(2)NMF (M = Cu, Ag, Au) have been made via spontaneous reactions of coinage metals and NF(3) in solid argon and neon matrixes during sample annealing without formation of the M(NF(3)) complexes. Comparisons between the matrix infrared spectra and the density functional frequency calculations provide strong support for identification of the F(2)NMF molecules, which are found to have doublet ground states with C(2v) or near C(2v) geometries. The F(2)NCuF molecule can isomerize to the less stable FNCuF(2) isomer upon UV-visible irradiation, while no similar reactions were observed for the silver and gold species. The M-N bonds in the F(2)NMF molecules are stronger than those in the FNMF(2) isomers with the Ag-N bond being longest and weakest in both cases.