DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Electrical conductivity measurements of aqueous sodium chloride solutions to 600°C and 300 MPa

Electrical conductance measurements of dilute (<0.1>^–1) aqueous NaCl solutions were made primarily to quantify the degree of ion association which increases with increasing temperature and decreasing solvent density. These measurements were carried out at temperatures from 100 to 600°C and pressures up to 300 MPa with a modified version of the apparatus used previously in the high temperature study in this laboratory. Particular emphasis was placed on conditions close to the critical temperaturelpressure region of water, i.e., at 5° intervals from 370 to 400°C. The results verify previous findings that the limiting equivalent conductance A_o of NaCl increases linearly with decreasing density from 0.75 to 0.3 g-cm^–1 and also with increasing temperature from 100 to 350°C. Above 350°C. A_o is virtually temperature independent. The logarithm of the molal association constant as calculated exclusively from the data400°C is represented as a function of temperature (Kelvin) and the logarithm of the density of water (g-cm^–3) as follows:

Complexation of aluminate anion by bis-tris in aqueous media at 25–50°C

Gibbsite, Al(OH)₃, solubility studies in aqueous NaCl solutions at pH 9 demonstrate that the aluminate anion forms a strong complex with the neutral Bis-tris molecule 2,2-Bis(hydroxymethyl)-2,2,2-nitrilotriethanol, at low temperatures. The logarithm of the molal concentration quotient for the reaction

Optical dephasing of molecular dimers in mixed crystals: Picosecond photon echo experiments

Picosecond photon echo experiments are used to examine optical dephasing of substitutional dimers and monomers of tetracene and pentacene in p-terphenyl host crystals. A comparison of experiments on tetracene and pentacene dimers permits the mechanism responsible for temperature-dependent optical dephasing to be determined. It is shown that excitation of librations rather than scattering between delocalized dimer states is the principal mechanism.     

Stereochemistry and bonding in N-substituted-2-phenyl-3-cyanoaziridines

A series of ten N-alkyl(aralkyl)-2-phenyl-3-cyanoaziridines has been synthesized to continue investigations of the molecular stereochemistry and bonding of functionalized aziridines. Substantial spectroscopic evidence is presented which indicates the presence of stereoselective hyperconjugation between the phenyl and nitrile groups and the aziridine ring. The ¹H and ¹³C nmr chemical shifts are rationalized in terms of the interactions of the substituents on the aziridine ring, and how these interactions vary with the steric bulk of the nitrogen substituents. Various stereoselective coupling constants (¹H-¹H and ¹³C-¹H) are also reported.     

Electronic structure and properties of isoreticular metal-organic frameworks: the case of M-IRMOF1 (M = Zn, Cd, Be, Mg, and Ca)

We investigate the possibility of tailoring the electronic properties of isoreticular metal-organic materials by replacing the metal atom in the metal-organic cluster and by doping. The electronic structure of M-IRMOF1, where IRMOF1 stands for isoreticular metal-organic framework 1 and M = Be, Mg, Ca, Zn, and Cd, was examined using density-functional theory. The results show that these materials have similar band gaps (ca. 3.5 eV) and a conduction band that is split into two bands, the lower of which has a width that varies with metal substitution. This variation prompted us to investigate whether doping with Al or Li could be used to tailor the electronic properties of the Zn-IRMOF1 and Be-IRMOF1 materials. It is shown that replacing one metal atom with Al can effectively be used to create IRMOFs with different metallic properties. On the other hand, adding Li produces structural changes that render this approach less suitable.     

Preparation and crystal structure ofexo-2,exo-6-dihydroxy-2,6-dimethyl-9-oxabicyclo[3.3.1]nonane

In a further exploration of the structural factors causing alicyclic diols such asexo-2,exo-6-dihydroxy-2,6-dimethylbicyclo[3.3.1]nonane (1) to adopt the helical tubuland inclusion host structure, the title compound (8) has been synthesized and its crystal structure determined. This 9-oxa analogue of (1) has a totally different structure [C₁₀H₁₈O₃; orthorhombic;P2₁2₁2;a 18.989(4),b 19.064(3),c 14.256(3) Å;Z 20; with finalR 0.065] due to involvement of the ether oxygen atom in the hydrogen bonding network. The structure of the diol (8) approximatesP¯42₁ c symmetry, and 16 of the 20 molecules per cell create a hostlike structure of this symmetry, which consists of tightly bound hydrogen bonded pillars parallel toc. The remaining guestlike molecules occupy inequivalent pseudo ¯4 sites separated byc/2 to form weakly bound columns parallel toc. Hydrogen bonds also occur between the pillars and columns. An ordered structure with sensible intermolecular contacts can be formed inP2₁2₁2₁ with thec axis doubled. A difference betweena andb axial lengths correlates with a difference in occupancies of pseudo-¯4-related sites for the guest-like component of the structure.     

Bis[bis­(3‐phenyl­pyrazol‐1‐yl)­(pyrazol‐1‐yl)­methane]­copper(II) bis­(per­chlor­ate) acetonitrile disolvate

The title copper(II) complex, [Cu(C₂₂H₁₈N₆)₂](ClO₄)₂·2C₂H₃N, comprises two neutral substituted tris­(pyrazol‐1‐yl)­methane ligands bonded to a central Cu^II ion, which is positioned on a crystallographic inversion center. Six Cu—N bonds are arranged in a distorted octa­hedral fashion. The unsubstituted pyrazole rings on each ligand are oriented trans with respect to each other, inter­digitated with the two 3‐phenyl­pyrazole rings of the other ligand.     

Helical tubulate inclusion compounds of ferrocene and squalene

The inclusion compounds of 2,8-dimethyltricyclo[5.3.1.1^3,9]dodecane-syn-2,syn-8-diol,3, with ferrocene and with squalene have been prepared. The crystal structures of these helical tubulate compounds: (3)₃·(ferrocene)_0.75 [P3₁21,a=b=13.7480(6),c=7.0312(5) Å,Z=1,R=0.038] and (3)₃·(squalene)_0.23 [P3₁21,a=b=13.677(1),c=7.0533(9) Å,Z=1,R=0.042] are described. Supplementary Data relating to this article are deposited with the British Library as supplementary publication No. SUP 82151 (16 pages).     

A preliminary observation of additive thermodynamic contribution of pendant arms to the complexation of calixarene derivatives with mercury(II)

An additive thermodynamic contribution of pendant arms to the complexation of calixarene derivatives with mercury(II) in acetonitrile is for the first time demonstrated.