Modulating the rate of a native ligation coupling between tripyrrole derivatives by using specific dsDNA sequences

The intrinsic recognition code associated with dsDNA allows either accelerating or retarding of a native chemical ligation reaction between tripyrrole ligands. The rate changes most probably stem from the sequence-dependent characteristics of the dsDNA-ligand complexes.     

Do the neighboring residues in a polypeptide affect the electron distribution of an amino acid significantly? A quantitative study using the quantum theory of atoms in molecules (QTAIM)

Geometries, as well as bond and atomic properties obtained with the atoms-in-molecules theory applied on B3LYP/6-31++G//B3LYP/6-31G charge densities, of the N-formyl amides of the nine tripeptides obtained by combining glycine, alanine, and serine around a central glycine residue were analyzed to check how the properties of the central residue are modified by other amino acids bonded to it. All of the molecules were optimized from an alpha-helix conformation that was also displayed by the optimized structure. Significant variations of the geometry (especially remarkable for dihedral angles) and atomic properties of the central glycine residue are observed when it is attached to a serine residue whose side chain is involved in a hydrogen bond.     

Trapping unstable terminal M-O multiple bonds of monocyclopentadienyl niobium and tantalum complexes with Lewis acids

Hydrolysis of [NbCp'Cl(4)] (Cp' = η(5)-C(5)H(4)SiMe(3)) with the water adduct H(2)O·B(C(6)F(5))(3) afforded the oxo-borane compound [NbCp'Cl(2){O·B(C(6)F(5))(3)}] (2a). This compound reacted with [MgBz(2)(THF)(2)] giving [NbCp'Bz(2){O·B(C(6)F(5))(3)}] (2b), whereas [NbCp'Me(2){O·B(C(6)F(5))(3)}] (2c) was obtained from the reaction of [NbCp'Me(4)] with H(2)O·B(C(6)F(5))(3). Addition of Al(C(6)F(5))(3) to solutions containing the oxo-borane compounds [MCp(R)X(2){O·B(C(6)F(5))(3)}] (M = Ta, Cp(R) = η(5)-C(5)Me(5) (Cp*), X = Cl 1a, Bz 1b, Me 1c; M = Nb, Cp(R) = Cp', X = Cl 2a) afforded the oxo-alane complexes [MCp(R)X(2){O·Al(C(6)F(5))(3)}] (M = Ta, Cp(R) = Cp*, X = Cl 3a, Bz 3b, Me 3c; M = Nb, Cp(R) = Cp', X = Cl 4a), releasing B(C(6)F(5))(3). Compound 3a was also obtained by addition of Al(C(6)F(5))(3) to the dinuclear μ-oxo compound [TaCp*Cl(2)(μ-O)](2), meanwhile addition of the water adduct H(2)O·Al(C(6)F(5))(3) to [TaCp*Me(4)] gave complex 3c. The structure of 2a and 3a was obtained by X-ray diffraction studies. Density functional theory (DFT) calculations were carried out to further understand these types of oxo compounds.     

Kinetic studies on the formation of N-nitroso compounds

Acetic acid/acetate ion buffer acts catalytically upon the nitrosation of amines under conditions in which the only nitrosating agents are N₂O₃ and NOBr, but inhibits nitrosation by H₂NO ₂ ⁺ . The kinetic characteristics of these phenomena have been analysed quantitatively and compared with similar effects caused by the solventsTHF, DMSO and dioxane. The experimental results show that this behaviour is an effect of the medium.

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Kinetische Untersuchungen zur Bildung von N-Nitroso-Verbindungen, 8. Mitt.: Nachweis eines Medium-Effekts von Essigsäure/Acetat-Puffer auf die Geschwindigkeitskonstante der Nitrosierung

Zusammenfassung Essigsäure/Acetat-Puffer wirkt bei der Nitrosierung von Aminen katalytisch, unter Bedingungen, wo die alleinigen nitrosierenden Agentien N₂O₃ und NOBr sind; andererseits wird die Nitrosierung durch H₂NO ₂ ⁺ unterbunden. Die kinetischen Charakteristika dieses Phänomens wurden quantitativ analysiert und mit ähnlichen Effekten der LösungsmittelTHF, DMSO und Dioxan verglichen. Die experimentellen Ergebnisse zeigen, daß dieses Verhalten auf einen Mediumeffekt zurückzuführen ist.

     

Human serum albumin unfolding pathway upon drug binding: A thermodynamic and spectroscopic description

The interest on phenothiazine drugs has been increased during last years due to their proved utility in the treatment of several diseases and biomolecular processes. In the present work, the binding of the amphiphilic phenothiazines promazine and thioridazine hydrochlorides to the carrier protein human serum albumin (HSA) has been examined by ζ-potential, isothermal titration calorimetry (ITC), fluorescence and circular dichorism (CD) spectroscopies, and dynamic light scattering (DLS) at physiological pH with the aim of analyzing the role of the different interactions in the drug complexation process with this protein. The ζ-potential results were used to check the existence of complexation. This is confirmed by a progressive screening of the protein charge up to a reversal point as a consequence of drug binding. On the other hand, binding causes alterations on the tertiary and secondary structures of the protein, which were observed by fluorescence and CD spectroscopies, involving a two-step, three-state transition. The thermodynamics of the binding process was derived from ITC results. The binding enthalpies were negative, which reveal the existence of electrostatic interactions between protein and drug molecules. In addition, increases in entropy are consistent with the predominance of hydrophobic interactions. Two different classes of binding sites were detected, viz. Binding to the first class of binding sites is dominated by an enthalpic contribution due to electrostatic interactions whereas binding to a second class of binding sites is dominated by hydrophobic bonding. In the light of these results, protein conformational change resembles the acid-induced denaturation of HSA with accumulation of an intermediate state. Binding isotherms were derived from microcalorimetric results by using a theoretical model based on the Langmuir isotherm. On the other hand, the population distribution of the different species in solution and their sizes were determined through dynamic light scattering (DLS). Aggregation of drug/protein complexes was found as a result of a possible expansion of protein structure induced at high drug concentrations. In addition, the presence of free drug aggregates at concentrations below the drug critical micelle concentration was also detected.     

Surface and bulk properties of two anionic amphiphilic penicillins in a selective solvent

The surface physicochemical properties of two anionic penicillins-cloxacillin and dicloxacillin-in mixed ethanol-water solvent were investigated by surface tension and dynamic light scattering (DLS). The data were analyzed according to the treatment of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to study the stability of the systems. The aim of the study is to obtain information about the effects of ethanol on the surface activity, bulk properties, and aggregate stability of these amphiphilic drugs, keeping in mind that both penicillins have the same counterion, and the difference in their structures is only a Cl atom in the phenyl ring that makes dicloxacillin more hydrophobic. The surface tension data show a minimum area per molecule increment with ethanol concentration that is related to the variation of the dielectric constant with the alcohol. Dicloxacillin has lower values of the standard Gibbs energies of adsorption than does cloxacillin, which gives this drug a more marked escaping tendency from the aqueous environment to the air-water monolayer. DLS data was fitted to an exponential function for cloxacillin at any drug or alcohol concentration in the range of concentrations studied that indicates that the system can be modeled as an ergodic system of dilute diffusing monodisperse particles. Dicloxacillin DLS data at an ethanol concentration of 5% (v/v) had to be fitted at a sum of an exponential and a stretched exponential function, which indicates that, besides the drug aggregates, a small population of penicillin clusters with longer relaxation times is present. The stability curves predicted by the DLVO theory, for both penicillins, indicate the predominance of electrostatic repulsion, leading to a stable system over the drug-ethanol concentration range studied, but the height of the reduced pair interaction potential energy barrier decreases with ethanol concentration, thus it is expected to undergo a transition from a stable dispersion to a coagulated one.     

Quantum theory of atoms in molecules analysis on the conformational preferences of vinyl alcohol and related ethers

Vinyl alcohol, methyl vinyl ether, and tert-butyl vinyl ether were studied within the framework of the quantum theory of atoms in molecules at the B3LYP/6-311++G(2d,2p) level. Local and integrated properties of the charge density indicate that the anti conformational preference of the tert-butyl derivative is not due to a differing resonance contribution with regard to the less bulky vinyl ethers but to steric effects. There is a small delocalization of charge density, either total or pi, between oxygen and the terminal vinyl carbon, which does not support the resonance picture of vinyl compounds.     

On the applicability of resonance forms in pyrimidinic bases. II. QTAIM interpretation of the sequence of protonation affinities

The atomic properties of neutral and protonated forms of uracil and some model compounds, computed from B3LYP/6-31++G//B3LYP/6-31G charge densities with the QTAIM theory, indicate that sigma electron reorganization plays a significant role in the protonation processes. This reorganization is substantially different for O=C-C=C and O=C-C-X (X = N, O) units, involving transfers of electron population between all atoms in the first case but not across the C-X bond in the second unit. O-Protonation is basically favored over the N-protonation because of the lower electron population transferred to the proton. The stability sequence of N-protonated forms can be rationalized in terms of the closer position of the proton, when attached to N3, to regions of larger electron population (carbonyl groups).