Interaction with glycine increases stability of a mutagenic tautomer of uracil. A density functional theory study

The most stable structures for the gas-phase complexes of minor tautomers of uracil (U) with glycine (G) were characterized at the density functional B3LYP/6-31++G level of theory. These are cyclic structures stabilized by two hydrogen bonds. The relative stability of isolated tautomers of uracil was rationalized by using thermodynamic and structural arguments. The stabilization energies for complexes between the tautomers of U and G result from interplay between the stabilizing two-body interaction energies and destabilizing one-body terms. The latter are related to the energies of (i) tautomerization of the unperturbed moieties and (ii) distortions of the resulting rare tautomers in the complex. The two-body term describes the interaction energy between distorted tautomers. The two-body interaction energy term correlates with perturbations of length of the proton-donor bonds as well as with deprotonation enthalpies and proton affinities of the appropriate monomer sites. It was demonstrated that the relative instability of rare tautomers of uracil is diminished due to their interactions with glycine. In particular, the instability of the third most stable tautomer (U(III)) is decreased from 11.9 kcal/mol for non-interacting uracil to 6.7 kcal/mol for uracil in a complex with the zwitterionic tautomer of glycine. A decrease of instability by 5.2 kcal/mol could result in an increase of concentration of U(III) by almost 5 orders of magnitude. This is the tautomer with proton donor and acceptor sites matching guanine rather than adenine. Moreover, kinetic characteristics obtained for the glycine-assisted conversion of the most stable tautomer of uracil (U(I)) to U(III) indicate that the U(I)<-->U(III) thermodynamic equilibrium could be easily attained at room temperature. The resulting concentration of this tautomer falls in a mutationally significant range.     

Divergent coordination mode of magnesium and zinc alkyls supported by the bifunctional pyrrolylaldiminato ligand

The first magnesium and zinc alkyls derived from N-(iso-propyl)-pyrrolylaldimine have been synthesised and structurally characterised: both tBuM(N,N')-type compounds exist as three-coordinate monomers in benzene solution, but in the solid state the magnesium complex is a centrosymmetric dimer with Mg2(mu-N)2 bridges, whereas the zinc complex is a Zn...pi bonded dimer with a pi-coordinated pyrrole unit.     

X-ray structures and homolysis of some alkylcobalt(III) phthalocyanine complexes

The first crystallographic data for sigma-bonded alkylcobalt(III) phthalocyanine complexes are reported. A single-crystal X-ray structure of CH(3)CH(2)Co(III)Pc (Pc = dianion of phthalocyanine) reveals that the solid consists of centrosymmetric face-to-face dimers in which the CH(3)CH(2)Co(III)Pc units retain their square pyramidal geometry. The structure appears to be the first one reported for a five-coordinate RCo(III)(chelate) complex with an electron-deficient equatorial system. The Co-C bond in CH(3)CH(2)Co(III)Pc (2.031(5) A) is the longest found in five-coordinate RCo(III)(chel) complexes (R = simple primary alkyl group). Another X-ray study demonstrates that CH(3)Co(III)Pc(py) has a distorted octahedral geometry with axial bonds of very similar length to those in methylcobalamin. The axial bonds are shorter than those in its octaethylporphyrin analogue, in accordance with a weaker trans axial influence in six-coordinate complexes containing an electron-deficient phthalocyanine equatorial ligand. A different trend has been observed for five-coordinate RCo(III)(chel) complexes: electron-rich equatorial systems seem to make the Co-C axial bond shorter. Kinetic data for the homolysis of RCo(III)Pc complexes (R = Me, Et) in dimethylacetamide are also reported. Homolysis of ethyl derivatives is faster. The Co-C bond dissociation energies (BDEs) for the pyridine adducts of the methyl and the ethyl derivative are 30 +/- 1 and 29 +/- 1 kcal/mol, respectively. The BDE for CH(3)CoPc(py) is considerably lower than that for MeCbl despite the very similar lengths of the axial bonds in the two complexes. The results of this work do not support any correlation between the Co-C bond length and the bond strength as defined by BDE.     

Renormalization group and high-temperature series for the two-dimensional ising model

We employ high-temperature series to investigate a two-parameter class of renormalization group transformations for the two-dimensional Ising model on the triangular lattice. For the static case we identify an optimal organization of the high-temperature expansion and an optimal transformation matrix and thus find, in second order, =0.96 and the magnetic eigenvaluey=2-/2=1.76.From recursion relations for flip rates we find the dynamic exponent to be the same for all transformations in our two-parameter class,z=2.32.Our fixed-point flip rates do not describe a Markov process even though the corresponding master equation for the single-event probability displays no explicit memory effects. The non-Markovian nature shows up only in a violation of the Markovian detailed balance conditions.     

Deuterium isotope effects on hydrophobic interactions: the importance of dispersion interactions in the hydrophobic phase

Hydrogen/deuterium isotope effects on hydrophobic binding were examined by means of reversed-phase chromatographic separation of protiated and deuterated isotopologue pairs for a set of 10 nonpolar and low-polarity compounds with 10 stationary phases having alkyl and aryl groups bonded to the silica surface. It was found that protiated compounds bind to nonpolar moieties attached to silica more strongly than deuterated ones, demonstrating that the CH/CD bonds of the solutes are weakened or have less restricted motions when bound in the stationary phase compared with the aqueous solvent (mobile phase). The interactions responsible for binding have been further characterized by studies of the effects of changes in mobile phase composition, temperature dependence of binding, and QSRR (quantitative structure-chromatographic retention relationship) analysis, demonstrating the importance of enthalpic effects in binding and differentiation between the isotopologues. To explain our results showing the active role of the hydrophobic (stationary) phase we propose a plausible model that includes specific contributions from aromatic edge-to-face attractive interactions and attractive interactions of aliphatic groups with the pi clouds of aromatic groups present as the solute or in the stationary phase.     

Polyurethane anionomers synthesised with aromatic, aliphatic or cycloaliphatic diisocyanates, polyoxyethylene glycol and 2,2-bis-(hydroxymethyl)propionic acid. Part II. Supermolecular structure. Thermal properties

Small angle X-ray scattering and differential scanning calorimetry methods were employed to characterise the internal order of structural phases present in polyurethane coatings obtained as a result of water evaporation from anionomer dispersions. Those anionomers were produced in the reaction of aromatic, cycloaliphatic and aliphatic diisocyanates with polyoxyethylene glycol, 2,2-bis-(hydroxymethyl)propionic acid and 1,6-hexamethylenediamine. The decisive effects were found from ionic and polar structures within the rigid urethane and urea segments on the ordered arrangement degree of the supermolecular structures in the obtained anionomers. That becomes apparent in differential scanning calorimetry thermograms and contributes to improved thermal stability of the produced polyurethane coatings.     

Unimolecular photochemistry of 4-thiouracils

Unimolecular phototautomeric reactions in 4-thiouracil, 1-methyl-4-thiouracil and 6-aza-4-thiouracil were studied using the matrix-isolation technique combined with infrared absorption spectroscopy. For monomers of these compounds, isolated in solid argon at 10 K, an intramolecular proton-transfer photoreaction was observed. Upon UV (lambda > 345 nm) irradiation, the initial oxo-thione forms of 4-thiouracils were converted into the corresponding oxo-thiol tautomers. The photogenerated oxo-thiol isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-311++G(2d,p) level. Good agreement between the observed and predicted pattern of spectral bands allowed a reliable identification. This is the first report on experimental observation of isomeric forms of 4-thiouracils other than the canonical oxo-thione tautomers.     

Synthesis of hapten-phosphoramidites from 2′-deoxyuridine

A total of 11 novel phosphoramidites, 3a-d, 4a-d and 14a-c were prepared from 2′-deoxyuridine functionalized at 5 and 6-position of the pyrimidine ring with hapten reporter groups, e.g. adamantane, carbazole, dansyl and dabsyl, suitable for use in immunodetection nucleic acid testing assays.     

Crystal packing of two 5‐substituted 2‐methyl‐4‐nitro‐1H‐imidazoles

Infinite chains connected by N—H...N hydrogen bonding form the primary packing motif in two closely related 4‐nitroimidazole derivatives, viz. 5‐bromo‐2‐methyl‐4‐nitro‐1H‐imidazole, C₄H₄BrN₃O₂, (I), and 2‐methyl‐4‐nitro‐1H‐imidazole‐5‐carbonitrile, C₅H₄N₄O₂, (II). These chains are almost identical, even though in (II) there are two symmetry‐independent molecules in the asymmetric unit. The differences appear in the interactions between the chains; in (I), there are strong C—Br...O halogen bonds, which connect the chains into a two‐dimensional grid, while in (II), the cyano group does not participate in specific interactions and the chains are only loosely connected into a three‐dimensional structure.     

Stabilization of very rare tautomers of 1-methylcytosine by an excess electron

We characterized valence anionic states of 1-methylcytosine using various electronic structure methods. We found that the most stable valence anion is related to neither the canonical amino-oxo nor a rare imino-oxo tautomer, in which a proton is transferred from the N4 to N3 atom. Instead, it is related to an imino-oxo tautomer, in which the C5 atom is protonated. This anion is characterized by an electron vertical detachment energy (VDE) of 2.12 eV and it is more stable than the anion based on the canonical tautomer by 1.0 kcal/mol. The latter is characterized by a VDE of 0.31 eV. Another unusual low-lying imino-oxo tautomer with a VDE of 3.60 eV has the C6 atom protonated and is 3.6 kcal/mol less stable than the anion of the canonical tautomer. All these anionic states are adiabatically unbound with respect to the canonical amino-oxo neutral, with the instability of 5.8 kcal/mol for the most stable valence anion. The mechanism of formation of anionic tautomers with carbon atoms protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to the C5 or C6 atom. The six-member ring structure of anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Indeed the neutral systems collapse without a barrier to a linear or a bicyclo structure, which might be viewed as lesions to DNA or RNA. Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated.