Review: Bilirubin pKa studies; new models and theories indicate high pKa values in water,dimethylformamide and DMSO

Background  

Unconjugated bilirubin (UCB) is an unstable substance with very low aqueous solubility. Its aqueous pKa values affect many of its interactions, particularly their pH-dependence. A companion paper shows that only our prior solvent partition studies, leading to pKa values of 8.12 and 8.44, met all essential requirements for valid pKa determinations. Other published values, generally lower, some below 5.0, were shown to be invalid. The present work was designed to derive suitable models for interpreting published data on the pH-dependent binding of UCB with four agents, mentioned below, chosen because they are not, themselves, sensitive to changes in the pH range 4-10, and the data, mainly spectrometric, were of reasonable quality.     

Interactions of unconjugated bilirubin with vesicles,cyclodextrins and micelles: New modeling and the role of high pKa values

Background

Unconjugated bilirubin (UCB) is an unstable substance with very low aqueous solubility. Its aqueous pKa values affect many of its interactions, particularly their pH-dependence. A companion paper shows that only our prior solvent partition studies, leading to pKa values of 8.12 and 8.44, met all essential requirements for valid pKa determinations. Other published values, generally lower, some below 5.0, were shown to be invalid. The present work was designed to derive suitable models for interpreting published data on the pH-dependent binding of UCB with four agents, mentioned below, chosen because they are not, themselves, sensitive to changes in the pH range 4-10, and the data, mainly spectrometric, were of reasonable quality.

Results

These analyses indicated that the high pKa values, dianion dimerization constant and solubilities of UCB at various pH values, derived from our partition studies, along with literature-derived pH- and time-dependent supersaturation effects, were essential for constructing useful models that showed good qualitative, and sometimes quantitative, fits with the data. In contrast, published pKa values below 5.0 were highly incompatible with the data for all systems considered. The primary species of bound UCB in our models were: undissociated diacid for phosphatidylcholine, dianion for dodecyl maltoside micelles and cyclodextrins, and both monoanions and dianion for sodium taurocholate. The resulting binding versus pH profiles differed strikingly from each other.

Conclusions

The insights derived from these analyses should be helpful to explore and interpret UCB binding to more complex, pH-sensitive, physiological moieties, such as proteins or membranes, in order to understand its functions.

     

Deprotonation of calixarenes in acetonitrile

[Structure: see text]. The pKa values for calixarenes in MeCN have been determined by selective titration with bases using a spectroscopic method. These values are as follows: calix[4]arene pKa(1) = 19.06 +/- 0.22, pKa(2) > 33; calix[6]arene pKa(1) = 15.59 +/- 0.06, pKa(2) = 23.85 +/- 0.35, pKa(3) > 33; calix[8]arene pKa(1) = 17.20 +/- 0.20, pKa(2) = 20.32 +/- 0.31, pKa(3) > 33. The trends in acidity are rationalized using structures generated by a DFT model. For mono-deprotonation, the degree and nature of hydrogen bonding in the anion is the dominant factor; for di-deprotonation, spatial separation of the anionic charges becomes important.     

Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components

Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3, 5-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA data and to detect possible outliers in the data set. PLS is applied to correlate the CoMFA data with either calculated AM1 proton affinities or with experimental pKa values. The possibility of making a prediction of pKa values directly from 3D structures of the monomers for polynucleotides is also shown. The influence of the superposition criteria and of conformational changes along the glycosidic bond on the pKa prediction are studied as well.     

Electrochemical study of gallium(III) with <Emphasis Type="SmallCaps">l</Emphasis>-glutamine at the dropping mercury electrode

Abstract  

Gallium complexes of l-glutamine have been studied polarographically in aqueous media. The reduction was found to be irreversible and diffusion controlled in the presence of 0.1 M KNO₃ and 0.002% Triton-x-100. The values of kinetic parameters, transfer coefficient (α _n), and formal rate constant ( k_{\textf,\texth}⁰ k_{{{\text{f}},{\text{h}}}}^{0} ) of the electrode reactions were calculated by Koutecky's method. The stability constants and composition of the gallium(III)-l-glutamine complexes were evaluated with the help of the Deford-Hume method. The values of stability constants of 1:1, 1:2, and 1:3 gallium(III)-l-glutamine complexes are 1.35, 6.5, and 1,350 at 30 °C, respectively. The values of thermodynamic parameters, the free energy of activation, the enthalpy of activation, and the entropy of activation have been determined at 30 °C. The formation of the metal complexes has been found to be non-spontaneous, endothermic in nature, and entropically favorable at higher temperature.     

Ab initio and DFT conformational study on nitrosamine (H<Subscript>2</Subscript>N–N=O) and <Emphasis Type="Italic">N</Emphasis>-Nitrosodimethylamine [(CH<Subscript>3</Subscript>)<Subscript>2</Subscript>N–N=O]

Abstract  

Ab initio and DFT calculations have been performed to characterize some ground state structures of the title molecules. Relative energies, rotational barriers, NBO charges, and dipole moments (μ) have been calculated and analyzed. It has been confirmed that only highly correlated methods (e.g., CCSD) are able to yield the non-planar structure as a minimum, for the H₂NNO molecule. On the other hand, all computational levels here employed are able to yield a planar C₂NNO frame for the (CH₃)₂NNO as a minimum. Important correlations between atomic charges and bond distances are discussed. Replacement of H by methyl group increases the rotational barrier and μ values by at least 3 kcal/mol and 0.4 D, respectively. The largest μ values are obtained for the structures in which the nitrogen lone pair is parallel to the NO group π system, and are consistent with a larger contribution of a dipolar resonance structure.     

Accurate pKa determination for a heterogeneous group of organic molecules.

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.     

Monitoring compartment-specific substrate cleavage by cathepsins B, K, L, and S at physiological pH and redox conditions

Background  

Cysteine cathepsins are known to primarily cleave their substrates at reducing and acidic conditions within endo-lysosomes. Nevertheless, they have also been linked to extracellular proteolysis, that is, in oxidizing and neutral environments. Although the impact of reducing or oxidizing conditions on proteolytic activity is a key to understand physiological protease functions, redox conditions have only rarely been considered in routine enzyme activity assays. Therefore we developed an assay to test for proteolytic processing of a natural substrate by cysteine cathepsins which accounts for redox potentials and pH values corresponding to the conditions in the extracellular space in comparison to those within endo-lysosomes of mammalian cells.     

Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins

Background  

Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families.     

A one-pot synthesis of alkyl acylcarbamodithioates from acid chlorides, thiols, and ammonium thiocyanate

Abstract  

An efficient synthesis of alkyl acylcarbamodithioates by reaction of acid chlorides with ammonium thiocyanate in the presence of thiols is described. The unusually large values of ⁵ J _FH = 12–15 Hz, observed for alkyl (2-fluorobenzoyl)carbamodithioates provide information about Ar–C–N–H torsion in these compounds.     

QSAR of α-campholenic derivatives with sandalwood odor, and molecular design

Abstract  

Quantitative structure–activity relationship (QSAR) studies have been carried out in a series of α-campholenic derivatives with sandalwood odor based on quantum-chemical data derived by use of the Hartree–Fock (HF) method. To build QSAR models, a multiple linear regression method was used. The models obtained have good predictive ability and are of high statistical significance, with good correlation coefficients, and p values less than 0.05. The models contribute also to identification of important quantum-chemical aspects of the sandalwood odor. On the basis of the QSAR models built, several new sandalwood compounds were designed and the best candidate for experimental synthesis was suggested.     

pKa calculations of aliphatic amines, diamines, and aminoamides via density functional theory with a Poisson-Boltzmann continuum solvent model

In order to make reliable predictions of the acid-base properties of macroligands with a large number of ionizable sites such as dendrimers, one needs to develop and validate computational methods that accurately estimate the acidity constants (pKa) of their chemical building blocks. In this article, we couple density functional theory (B3LYP) with a Poisson-Boltzmann continuum solvent model to calculate the aqueous pKa of aliphatic amines, diamines, and aminoamides, which are building blocks for several classes of dendrimers. No empirical correction terms were employed in the calculations except for the free energy of solvation of the proton (H+) adjusted to give the best match with experimental data. The use of solution-phase optimized geometries gives calculated pKa values in excellent agreement with experimental measurements. The mean absolute error is <0.5 pKa unit in all cases. Conversely, calculations for diamines and aminoamides based on gas-phase geometries lead to a mean absolute error >0.5 pKa unit compared to experimental measurements. We find that geometry optimization in solution is essential for making accurate pKa predictions for systems possessing intramolecular hydrogen bonds.     

Benchmarking pKaprediction

Background  

pK_avalues are a measure of the protonation of ionizable groups in proteins. Ionizable groups are involved in intra-protein, protein-solvent and protein-ligand interactions as well as solubility, protein folding and catalytic activity. The pK_ashift of a group from its intrinsic value is determined by the perturbation of the residue by the environment and can be calculated from three-dimensional structural data.     

Kinetic study of the tocopherol regeneration reaction by biological hydroquinones in micellar solution

The rate constants (kr) of the regeneration reaction of 7-t-butyl-5-isopropyltocopheroxyl with ubiquinol-10 (UQ10H2), ubiquinol-0 (UQ0H2), alpha-, beta-, and gamma-tocopherolhydroquinones (alpha-, beta-, gamma-TQH2), 2,3,5-trimethyl-1,4-hydroquinone (TMQH2), vitamin K3 hydroquinone (VK3H2), and vitamin C (Vit C) have been measured in 2-propanol/water and micellar solutions by a stopped-flow spectrophotometer. The kr values of these hydroquinones (HQs) in micellar solution remained constant at pHs of 6-9 and increased rapidly by increasing the pH value. The kr values decreased in the order of VK3H2 > gamma-TQH2 > or = alpha-TQH2 > beta-TQH2 > or = UQ10H2 > or = TMQH2 > UQ0H2 > Vit C at pHs of 6-9. These HQs are dibasic acids and can exist in three different molecular forms, depending on pH. By comparing the kr values with the mole fraction of each molecular form of the HQs, the reaction rate kr1 for the undissociated form, kr2 for the monoanion, and kr3 for the dianion and the pKa1 and pKa2 values were determined. It has been found that the kr values of UQ10H2, alpha-TQH2, beta-TQH2, and gamma-TQH2 (plastoquinol model) are 460, 1430, 494, and 1530 times larger than that of Vit C at pH 7.0, respectively, although the values are similar to that of Vit C in 2-propanol/water. The biological HQs and Vit C coexist in many tissues of animals and plants, and thus, the relative antioxidant activities of HQs and Vit C have been tentatively discussed based on the products of kr values by concentrations in several tissues. The results suggest that these HQs show high activity for the tocopherol regeneration in biological systems.     

Identification and characterization of endonuclein binding proteins: evidence of modulatory effects on signal transduction and chaperone activity

Background  

We have previously identified endonuclein as a cell cycle regulated WD-repeat protein that is up-regulated in adenocarcinoma of the pancreas. Now, we aim to investigate its biomedical functions.     

Synthesis,characterization and biological activity studies of octahedral nickel(II) complexes

Abstract  

Three nickel(II) complexes, namely [Ni(BH)₃](H₂O)(NO₃)(ClO₄) 1, [Ni(BH)₂(NO₃)₂] 2 and [Ni(BH)(Tren)](ClO₄)₂ 3 (BH = Benzoylhydrazine, Tren = Tris(2-aminoethyl)amine) have been synthesized and characterized by physico-chemical techniques. X-ray crystallographic analysis shows the nickel to be six-coordinated in these complexes. The complexes are efficient catalysts for the dismutation of superoxide in alkaline DMSO-NBT assays. The IC₅₀ values are 74,108 and 105 μM for 1, 2 and 3, respectively.     

Synthesis of 5-spirocyclohexyl-2,4-dithiohydantoin derivatives: a potential anti-leishmaniasis agent

Abstract  

A series of spiro-dithiohydantoins were synthesized by heating a mixture of 5-spirocyclohexyl-2,4-dithiohydantoin potassium salt and 3-chloropropanoyl chloride. These compounds were synthesized and evaluated for their activity against five Leishmanial strains in the promastigote stage in vitro. Seventy-two hours inoculation of a variety of products gave an IC ₁₀₀ and average IC ₅₀ values of 1.25 and 0.376 mg/cm³ against all Leishmanial strains tested.     

The density and surface tension of In–Sn and Cu–In–Sn alloys

Abstract  

The density and surface tension of binary In–Sn and ternary Cu–In–Sn alloys have been measured by a sessile-drop method. Decrease of the density and of the surface tension was observed with rising temperature. With increased Sn content in the alloys, the density increased while the surface tension reduced slightly. Addition of Cu could significantly increase the density and surface tension in the Cu–In–Sn system. The surface tension of the Cu–In–Sn alloys was also calculated by means of Butler’s equation, and compared with experimental values, showing good agreement.     

Supramolecular assembled of hexameric water clusters into a 1D chain containing (H<Subscript>2</Subscript>O)<Subscript>6</Subscript> and [(H<Subscript>2</Subscript>O)<Subscript>4</Subscript>O<Subscript>2</Subscript>] stabilized by hydrogen bonding in a copper complex

Background  

Various water clusters including hexamers, heptamers, octamers, decamers and 1D or 2D infinite water chains in a number of organic and inorganic-organic hybrid hosts, have been reported.     

Study on the influence of methyl groups and their location on properties of triphenylamino-based charge transporting hydrazones

Abstract  

Methyl substituent effects on the HOMO and LUMO energy levels, and the ability to transport charge and form stable molecular glasses of 4-(diphenylamino)benzaldehyde phenylhydrazones were investigated. Thermal properties, HOMO and LUMO energy levels, and hole mobility values are dependent on the number of methyl substituents and their position in the investigated transporting materials. Surprisingly, however, the presence of methyl groups at any position negatively affects the hole drift mobility of the molecularly doped polymers containing those hydrazones.