Potentiometric saccharide detection based on the pK(a) changes of poly(aniline boronic acid)

A novel approach for the potentiometric detection of saccharides using poly(aniline boronic acid) is presented. A model is described in which the electrochemical potential is sensitive to the change in the pK(a) of the conducting polymer as a result of boronic acid-diol complexation. In this system, boronic acid complexation is the mode of transduction and it is manifested as changes in the electrochemical potential of the polymer with remarkable selectivity. Characteristics of both transient and steady-state response associated with the complexation are discussed. The presence of Nafion and fluoride during the electrochemical polymerization of 3-aminophenylboronic acid are shown to impact the sensitivity and the stability of the electrode response. The sensor sensitivity is improved significantly by increasing the concentration of sodium fluoride during the polymerization. Finally, the nature of the selectivity of the boronic acid-diol reaction under these conditions is explored by using molecular orbital calculations.     

pK(a) values and geometries of secondary and tertiary amines complexed to boronic acids-implications for sensor design

[structure in text] The pK(a) values and the geometries of secondary and tertiary amines adjacent to boronic acids were determined using potentiometric and (11)B NMR titrations. The studies showed that the secondary ammonium ion has a pK(a) similar to that of the tertiary ammonium species, which leads to the formation of tetrahedral boron centers at pH values above approximately 5.5. Therefore, secondary amines as well as tertiary amines, when placed proximal to boron centers, can be used to create tetrahedral boronic acids at neutral pH for diol complexation.     

A perturbed pK(a) at the binding site of the nicotinic acetylcholine receptor: implications for nicotine binding

A series of tethered quaternary ammonium derivatives of Tyr have been incorporated into the binding site of the nicotinic acetylcholine receptor (nAChR) using the in vivo nonsense suppression method, producing constitutively active (self-gating) receptors. We have incorporated primary, secondary, and tertiary amine tethered agonists to give receptors whose constitutive activity can be modulated by pH. Lowering the pH protonates the tethered amine, giving it a positive charge and allowing it to reversibly activate the receptor. Tertiary and secondary tethered amines, TyrO3T and TyrO3S, have been successfully incorporated at alpha149 in the nAChR. Constitutive currents at pH 5.5 are 6 times those at pH 9.0. The pKa of TyrO3T in the binding site appears to be 6 or lower, differing substantially from its pKa in solution ( approximately 9.3). This local pKa perturbation has substantial implications for pharmacological research on the nAChR: of the tertiary agonists considered, noracetylcholine experiences this pKa perturbation, while nicotine does not.     

Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA

Phosphorothioates were substituted into double-stranded DNA to study protonated Class I A+.C basepairs by 31P NMR. The method was effective in reporting the A+.C pKa. pKa values near 7.0 were found with optimal nearest-neighbor partners. Such pKa values could expand the catalytic repertoire of nucleic acids.     

Thermodynamic analysis of receptors based on guanidinium/boronic acid groups for the complexation of carboxylates, alpha-hydroxycarboxylates, and diols: driving force for binding and cooperativity

The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.     

The pK(a), values of the conjugate acid of imidazole in water-ethanol mixtures

The pK(a) values of protonated imidazole in 10 different water-ethanol mixtures were determined at 25 degrees by potentiometric titration in a cell without liquid junction (glass and silver-silver bromide electrodes). The pK(a) values can be used in a standardization procedure that allows determination of pK(a) values for protonated organic nitrogen bases in aqueous ethanol.     

Comments on the article "Evaluation of pK(a) estimation methods on 211 druglike compounds"

The recent article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds" ( Manchester, J.; et al. J. Chem Inf. Model. 2010, 50, 565-571 ) reports poor results for the program Epik. Here, we highlight likely sources for the poor performance and describe work done to improve the performance. Running Epik in the mode intended to calculate pK(a) values for sequentially adding/removing protons, as needed to reproduce the experimental conditions, improves the root mean squared error (RMSE) from 3.0 to 2.18 for the 85 public compounds available from the paper. Despite this improvement, there are still other programs in the Manchester paper that outperform Epik. The primary reason is that the public portion of the data set is not diverse and Epik is missing a few key functional groups in this data set that are heavily represented. We show that incorporation of these missing functional groups into the Epik training set improves the RMSE for the public compounds to 1.04. Furthermore, these enhancements help improve the overall performance of Epik on a large druglike test set.     

The synthesis,spectroscopic and thermal study of oxamic acid compounds of some metal(II) ions

Summary The preparation of oxamic acid complexes of general formula M(H₂NCOCOO)₂·xH₂O (M = Mn^II, Co^II, Ni^II, Cu^II or Zn^II; x = 1 for Cu^II, x = 2 for the other metals) is reported. The i.r. and Raman spectra are discussed considering a trans-octahedral structure, formed by five-membered chelate rings with the amide oxygen and one carboxylic oxygen as donor atoms. The apical positions are occupied by water molecules. The thermal degradation process is very similar for the different complexes, first losing H₂O in one or different steps, then the fragments of the organic ligand to give the metal oxide as residue. The thermal degradation of the Cu^II and Zn^II compounds results in the formation of a new polymeric compound by deprotonation of the primary amide function in an endothermic process, the polymer further decomposes to form the metal oxide.     

On the perturbation of the intramolecular H-bond in diols by supercritical CO2: a theoretical and spectroscopic study

The role played by supercritical carbon dioxide used as a dispersant medium in the synthesis of polyurethane particles has been investigated. High-temperature-high-pressure in situ infrared spectroscopic measurements combined with ab initio calculations were performed to investigate the hydroxyl stretching vibrations of ethylene glycol (EG) and 1,4-butanediol (BD), two monomers commonly used in the field of step growth polymerization. Specific interactions between the diols and CO2 have been put in evidence. While the structural characteristics of EG and BD are very similar--both diols have a gauche conformation due to an internal H-bond between the two hydroxyl functions--they behave differently in the presence of dense CO2. In the case of EG, this internal H-bond is broken, allowing the diol and CO2 to form a complex through the conjunction of a Lewis acid-Lewis base (LA-LB) interaction and a new H-bond. When BD complexes to CO2, this internal H-bond remains and is even reinforced indirectly by the LA-LB interaction occurring between the two moieties. In both cases, such a complex formation induces a polarization of the hydroxyl groups and consequently an increase of their nucleophilicity.     

Enhancing effect of phenylboronic acid compounds and their interactions with the diol groups of saccharides in a capillary electrophoresis-chemiluminescence detection system.

In our previous study, we proposed molecular recognition of mono- and disaccharides making use of the interaction between their diol groups and p-iodophenylboronic acid in capillary electrophoresis with a chemiluminescence detection system. Here, to extend our knowledge of molecular recognition, we first examined the enhancing effects of four phenylboronic acid compounds other than p-iodophenylboronic acid i.e., 4-biphenylboronic acid, 4-octyloxyphenyl-boronic acid, 3-octyloxyphenylboronic acid, and 4-dodecyloxyphenylboronic acid, for luminol-hydrogen peroxide-horseradish peroxidase reaction in the capillary electrophoresis-chemiluminescence detection system. Only 4-biphenylboronic acid showed an enhancing effect similar to that of p-iodophenylboronic acid; the effect was determined over the range of 0.5-10 microM in this system. Second, we estimated the apparent stability constants between the diol groups of saccharides (1-methyl-D-glucoside, D-saccharose, and D-fructose) and the boronic acid moieties of the two enhancers, p-iodophenylboronic acid and 4-biphenylboronic acid. The apparent binding constants obtained here provided insight to confirm the principle of molecular recognition for the saccharides examined here.     

Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis

Knowledge of the pK(a) of phosphoranes is important for the interpretation of phosphate ester hydrolysis. Calculated pK(a)'s of the model phosphorane, ethylene phosphorane, are reported. The method of calculation is based on the use of dimethyl phosphate as a reference state for evaluating relative pK(a) values, and on the optimization of the oxygen and acidic hydrogen van der Waals radii to give reasonable pK(1)(a), pK(2)(a), and pK(3)(a) for phosphoric acid in solution. Density functional theory is employed to calculate the gas-phase protonation energies, and continuum dielectric methods are used to determine the solvation corrections. The calculated pK(1)(a) and p(2)(a) for the model phosphorane are 7.9 and 14.3, respectively. These values are within the range of proposed experimental values, 6.5-11.0 for pK(1)(a), and 11.3-15.0 for pK(2)(a). The mechanistic implications of the calculated pK(a)'s are discussed.     

The copigmentation effect of sinapic acid on malvin: a spectroscopic investigation on colour enhancement

The present paper reports on spectroscopic investigation of copigmentation effect of sinapic acid on the malvin molecule. A reaction of copigmentation was investigated by the use of UV-Vis absorption spectra in the whole range of acidic and moderately acidic buffered aqueous solutions (pH range 1.0-6.0). It was observed that the ratio (A-A0)/A0, as a good measure of the copigment effect, has its maximum value at pH 3.6. The influences of the pH of the medium, molecular concentration, and temperature were investigated. The reaction was thermodynamically defined in terms of deltaH0, deltaG0 and deltaS0 values.     

Copper(II) binding modes in the prion octapeptide PHGGGWGQ: a spectroscopic and voltammetric study

The N-terminal octapeptide repeat region of human prion protein (PrPc) is known to bind Cu(II). To investigate the binding modes of copper in PrPc, an octapeptide Ac-PHGGGWGQ-NH2 (1), which corresponds to an octa-repeat sequence, and a tetrapeptide Ac-HGGG-NH2 (2) have been synthesised. The copper(II) complexes formed with 1 and 2 have been studied by circular dichroism (CD) and electron spin resonance (ESR) spectroscopy. Both peptides form 1:1 complexes with Cu(II) at neutral and basic pH. CD, ESR and visible absorption spectra suggest a similar co-ordination sphere of the metal ion in both peptides, which at neutral pH consists of a square pyramidal geometry with three peptidic nitrogens and the imidazole nitrogen as donor atoms. Cyclic voltammetric measurements were used to confirm the geometrical features of these copper(II) complexes: the observation of negative redox potentials are in good agreement with the inferred geometry. All these results taken together suggest that peptide 1 provides a single metal binding site to which copper(II) binds strongly at neutral and basic pH and that the binding of the metal induces the formation of a stiffened structure in the HGGG peptide fragment.     

On the mechanism of Re(I)-carboxylate bond cleavage by perchloric acid: a kinetic and spectroscopic study

We have studied the reaction between pz-CO(2)-Re(CO)(3)(bpy) and perchloric acid in acetonitrile by following the UV-vis and IR spectral changes in the reaction mixture. A fast equilibrium was found to be established between solvated protons, pz-CO(2)-Re(CO)(3)(bpy), and the protonated intermediate [pz-C(OH)O-Re(CO)(3)(bpy)](+) which finally yields pz-COOH and Re(CO)(3)(bpy)(CH(3)CN)(+) as reaction products. This intermediate has been characterized by UV-vis and IR spectroscopies and by DFT calculations. The fully optimized DFT/CPCM structures for pz-CO(2)-Re(CO)(3)(bpy) and [pz-C(OH)O-Re(CO)(3)(bpy)](+) were compared with the X-ray structure of pz-CO(2)-Re(CO)(3)(bpy). The structural parameters associated with the carboxyl group in the protonated intermediate are between those of pz-CO(2)-Re(CO)(3)(bpy) and pz-COOH. Multivariate curve resolution methods were employed to obtain the spectrum of the protonated intermediate and the concentration profiles from the full matrix of time-resolved UV-vis spectra. The proposed mechanism was numerically simulated by using Runge-Kutta methods. Model parameters were estimated by nonlinear regression fitting of the concentration profiles, yielding values of log(K) = 4.9 ± 0.3 and k = 0.16 ± 0.03 min(-1) for the formation equilibrium constant and the decay rate constant of the protonated intermediate, respectively.     

The effect of ionic environment and mercury(II) binding on the alternative structures of DNA. An infrared spectroscopic study

Infrared spectroscopy was used to measure the effects of NaCl, NaNO₃ and HgCl₂ on the structure and structural transitions of DNA in hydrated films. The following conclusions are supported by the data. (1) The transition from the B- to the A-structural form in films of salt-free, calf-thymus DNA occurs between 86 and 75% r.h. Previous failures to obtain this transition in salt-free films and the finding that ca 4% (w/w) NaCl is needed to observe the B to A transition in films of DNA appear to be anomalies produced by the very slow kinetics for this transition. (2) The addition of NaCl to DNA increases the quantity of water absorbed at a given r.h. value and shifts the B to A transition to lower r.h. values. (3) Highly hydrated DNA (100% r.h.) with or without added NaCl exists in the B-helical structure for all samples examined. (4) DNA films containing one NaNO₃ per 6.7 nucleotide residues remained in the B-helical form to very low values of hydration. (5) The interaction of HgCl₂ with DNA to form the type I complex prevents the transition of DNA from the B- to the A-helical form but a conformational variation within the B family of structures was observed to occur between 94 and 75% r.h. (6) The primary sites of binding of Hg²⁺ in the type-1 complex with the DNA are the AT base pairs. Hg²⁺ binds to the N3 atom of thymine. Binding of Hg²⁺ to AT pairs perturbs the CG pairs but has only a minor effect on the sugar—phosphate conformation.     

From chain collapse to new structures: spectroscopic properties of poly(3-thiophene acetic acid) upon binding by alkyl trimethylammonium bromide surfactants

The binding of cationic surfactants with varying alkyl chain length to a regiorandom conjugated polyanion, poly(3-thiophene acetic acid) (PTAA), is studied in an aqueous buffer by using absorption and emission spectroscopies, photon correlation spectroscopy, isothermal titration calorimetry, and cryogenic transmission electron microscopy. We study the mixed solutions as a function of composition ratio R of surfactant molecules to monomer units molar concentrations, at low polymer concentration and in a very wide composition range (10(-6) < R < 10(2)) below the critical micellar concentration. Upon surfactant binding, the molecularly dispersed chains first collapse progressively and then form new structures as the mixed aggregates get enriched in surfactant. The collapse leads to a strong decrease of the conjugation length and to a blue shift of the absorption spectra by 30 to 50 nm. The new structures are responsible for a new intense emission band at about 600 nm, red-shifted by nearly 130 nm from the initial emission maximum of the polymer (~472 nm). As the surfactant tail becomes shorter, the blue shift of the absorption spectra and the intensity raise of the new emission are delayed to larger composition ratios while their variations become smoother functions of the surfactant concentration. These particular spectroscopic properties of PTAA seem related to its unique combination of a strongly hydrophobic backbone, a large ratio of contour length to persistence length, and an overall good aqueous solubility. Our results show that such features are well suited to design a colorimetric biosensor at small composition ratio, and a fluorescent biomarker at large composition ratio.     

Molecular design of lipophilic disalicylic acid compounds with varying spacers for selective lead(II) extraction

Lipophilic disalicylic acids 5,5'-decyl-2,2'-[1,2-ethanediylbis(oxy)]bisbenzoic acid (1), 5,5'-decyl-2,2'-[1,3-propanediylbis(oxy)]bisbenzoic acid (2), 5,5'-decyl-2,2'-[oxybis(1,2-ethanediyl-oxy)]bisbenzoic acid (3), 3,5-bis[2'-(2'-carboxyphenoxy)ethyl]-4-oxahexacyclo-[5.4.1.0(2,6).0(3,10).0(5,9).0(8,11)]dodecane (4), and 1,3-bis[2'-(2'-carboxyphenoxy)ethyl]adamantane (5) are evaluated as selective Pb(II) extractants. The solvent extraction of Pb(II) and of Cu(II) from buffered aqueous solutions of varying pH into chloroform by ligands 1-5 is examined in relation to the molecular structure of the dicarboxylic acid extractant. Ligand 1, with an ethylene spacer between two lipophilic salicylic acid units, exhibits excellent extraction selectivity for Pb(II) over Cu(II). Lengthening the spacer in ligands 2 and 3 diminishes both the extraction efficiency and selectivity. Ligands 4 and 5, with rigid spacer units, show significant reductions in both Pb(II) and Cu(II) extraction. Slope analysis reveals that ligand 1 reacts in a 2:1 stoichiometry with Pb(II) in extraction, which differs from the 1:1 stoichiometries for 2 and 3. The differences in the half extraction pH (DeltapH(1/2)) values for Pb(II) and Cu(II) extraction are 1.29, 0.49, and 0.48 for 1-3, respectively.     

Cyanation: providing a three-in-one advantage for the design of n-type organic field-effect transistors

The theoretical work presented here demonstrates that, when substitution takes place at appropriate positions, cyanation could be a useful tool for reducing the internal reorganization energy of molecules. A molecular-orbital-based explanation is given for this fundamentally important phenomenon. Some of the cyanated pentacene derivatives (nCN-PENT-n) not only have internal reorganization energies for electron transfer (lambda(-)) smaller than that of pentacene, but the lambda(-) values are even of the same magnitude as the internal reorganization energy for hole transfer (lambda(+)) of pentacene, a small value that few organic compounds have surpassed. In addition, cyanation raises the electron affinity of the parent compound and may afford good electronic couplings between neighboring molecules, because of its ability in promoting pi-stacking. For the design of high performance n-Type Organic field-effect transistors, high electron affinities, large intermolecular electronic couplings, and small reorganization energies are necessary. Cyanation may help in all three aspects. Two cyanated trialkylsilylethynyl pentacene derivatives with known pi-stacking structures are predicted to provide reasonably small internal reorganization energies, large electronic couplings, and high electron affinities. They have the potential to outperform N-fluoroalkylated dicyanoperylene-3,4:9,10-bis(dicarboximides) (PDI-FCN(2)) in terms of electron mobility.     

Novel sequential sigmatropic rearrangements of allylic diols: application to the total synthesis of (-)-kainic acid

Sequential sigmatropic rearrangements (Claisen/Claisen and Claisen/Overman) of enantiopure allylic diols are described. The reactions proceeded in complete diastereoselectivity without protecting group manipulations. The sequential Claisen/Overman rearrangement was successfully applied to the total synthesis of (-)-kainic acid.