Biomedical subjects

Paulina M Dominiak

Publications and source records attributed to Paulina M Dominiak.

9 recordsLinked to original sources

PubMed2006

Effect of the environment on molecular properties: synthesis, structure, and photoluminescence of Cu(I) bis(2,9-dimethyl-1,10-phenanthroline) nanoclusters in eight different supramolecular frameworks.

By selection of different charge-balancing anionic frameworks and different host-to-guest ratios, the photosensitizer-dye cation [Cu(dmp)2]+ (dmp = 2,9-dimethyl-1,10-phenanthroline) has been embedded in a series of three-dimensional host structures. It occurs with variable geometry in different states of aggregation, including weakly interacting monomers, isolated dimers, columns, and layers. A large variation in its emission lifetime is correlated with the relative energy level spacings of the guest- and host-framework components. In a fully saturated host framework, the lifetime exceeds values reported for a series of conventional Cu(dmp)2 salts.

Journal Article↗

PubMed2006

Investigation into factors influencing stereoselectivity in the reactions of heterocycles with donor-acceptor-substituted rhodium carbenoids.

Rhodium-catalyzed decomposition of aryldiazoacetates in the presence of pyrroles or furans results in mono- or biscyclopropanation of the heterocycle, but with opposite enantioinduction. In the absence of sterically encumbering groups, the cyclopropanation of furan occurs with initial bond formation at the 2-position. If this pathway is sterically blocked, cyclopropanation can occur with initial bond formation at the 3-position of the furan ring; in this case, the cyclopropanation reaction takes place on the opposite face of the heterocycle, and the opposite enantioinduction is observed. Upon extension of this methodology to benzofurans, a highly enantioselective monocyclopropanation reaction occurs to furnish a product derived from initial bond formation at the 2-position of the benzofuran. When this reaction pathway is inhibited by sterically encumbering substituents on the benzofuran, no cyclopropanation of the furan ring is observed, and instead, double cyclopropanation of the benzene ring occurs. Double cyclopropanation of the benzene ring was also observed in reactions with indoles.

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PubMed2006

Finding optimal radial-function parameters for S atoms in the Hansen-Coppens multipole model through refinement of theoretical densities.

The multipolar model of the valence-electron-density distribution for S atoms has been optimized based on theoretical structure factors for six organic molecules. The evaluation of different sets of radial function parameters shows that: (a) the ratio of the n(l) values for different l is more important than their absolute values, as parallel changes in all n(l) for a given atom are compensated for by a change in the refined value of the kappa' parameter, and (b) the (2,4,6,8) set of n(l) with kappa' refined as a single value is an optimal choice of radial function parameters for S atoms.

Journal Article↗

PubMed2006

Continua of interactions between pairs of atoms in molecular crystals.

The electron density distributions in crystals of five previously studied DMAN complexes and five Schiff bases (two new ones) have been analysed in terms of various properties of bond critical points (BCPs) found in the pair-wise interactions in their lattices. We analysed the continua of interactions including covalent/ionic bonds as well as hydrogen bonds and all other types of weak interactions for all pairs of interacting atoms. The charge density at BCPs and local kinetic and potential energy densities vary exponentially with internuclear distance (or other measures of separation). The parameters of the dependences appear to be characteristics of particular pairs of atom types. The Laplacian and the total (sum of kinetic and potential) energy density at BCPs show similar behaviour with the dependence being of the Morse type. The components lambda1, lambda2, lambda3 of the Laplacian at BCPs vary systematically with internuclear distance according to the type of atom pair. For lambda1 and lambda2 the distribution is of the exponential type, whereas lambda3 does not seem to follow any simple functional form, consistent with previous theoretical findings. Analytical nonlinear dependences of Laplacian on charge density have been found. They agree reasonably well with those obtained by least square fit of the Laplacian to charge density data. There are four distinct regions of the [symbol: see text]2rho(BCP)/rho(BCP) space, generated by E(BCP) = 0 and G(BCP)/rho(BCP) = 1 conditions. Two regions clearly correspond to the shared-shell and closed-shell interactions and the other two to some intermediate situation.

Algorithms↗

PubMed2005

Carbon monoxide-promoted carbene insertion into the aryl substituent of an N-heterocyclic carbene ligand: Buchner reaction in a ruthenium carbene complex.

In the presence of carbon monoxide, ruthenium carbenes give a net insertion/ring expansion (Buchner reaction) into one of the aromatic rings of the N-heterocyclic carbene ligand. In alkene metathesis applications, the N-heterocyclic carbene ligand is both robust and typically inert to reactions with the metal-bound carbene. This unique reaction is completely regioselective. The complexes obtained through ring expansion were fully characterized in the solid state using X-ray crystallography and in solution using NMR and IR spectroscopy.

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PubMed2005

Factor analysis of deuterium isotope effects on 13C NMR chemical shifts in Schiff bases.

We have analyzed deuterium isotope effects on (13)C chemical shifts in a series of o-hydroxy Schiff bases by applying factor analysis. Two orthogonal factors were obtained that explain about 80 and 10 % of the variance of the data. The numerical values of these factors can be related to 1H NMR chemical shifts of the proton involved in the intramolecular bonds delta(XH) (X = O or N). Such a relation allows one to identify clusters of compounds with different tautomeric forms of hydrogen bonding. Application of a similar approach to solution 13C NMR chemical shifts produces three important factors, which have a different structure to factors describing isotope effects. This illustrates well the different nature of chemical shifts and isotope effects. The three factors explain about 54, 15, and 13 % of variance. They can be rationalized and are strongly related to the electronic properties and location of substituents.

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PubMed2003

Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase.

The derivative of vitamin B1, thiamin pyrophosphate, is a cofactor of enzymes performing catalysis in pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, this cofactor is used to cleave the Calpha-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites has not yet been understood. To understand the mechanism of action of this enzyme, we determined the crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95-A resolution. We propose a model for the flip-flop action of this enzyme through a concerted approximately 2-A shuttle-like motion of its heterodimers. Similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase with functionally related enzymes suggests that this newly defined shuttle-like motion of domains is common to the family of thiamin pyrophosphate-dependent enzymes.

Amino Acid Sequence↗

PubMed2003

H-bonding dependent structures of (NH4+)3H+(SO4 2-)2. Mechanisms of phase transitions.

The role of different H-bonds in phases II, III, IV, and V of triammonium hydrogen disulfate, (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), has been studied by X-ray diffraction and (1)H solid-state MAS NMR. The proper space group for phase II is C2/c, for phases III and IV is P2/n, and for phase V is P onemacr;. The structures of phases III and IV seem to be the same. The hydrogen atom participating in the O(-)-H(+).O(-) H-bond in phase II of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) at room temperature is split at two positions around the center of the crucial O(-)-H(+).O(-) H-bonding, joining two SO(4)(2)(-) tetrahedra. With decreasing temperature, it becomes localized at one of the oxygen atoms. Further cooling causes additional differentiation of possibly equivalent sulfate dimers. The NH(4)(+) ions participate mainly in bifurcated H-bonds with two oxygen atoms from sulfate anions. On cooling, the major contribution of the bifurcated H-bond becomes stronger, whereas the minor one becomes weaker. This is coupled with rotation of sulfate ions. In all the phases of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), some additional, weak but significant, reflections are observed. They are located between the layers of the reciprocal lattice, suggesting possible modulation of the host (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) structure(s). According to (1)H MAS NMR obtained for phases II and III, the nature of the acidic proton disorder is dynamic, and localization of the proton takes place in a broader range of temperatures, as can be expected from the X-ray diffraction data.

Journal Article↗

PubMed2003

Neutral and ionic hydrogen bonding in Schiff bases.

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.

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