Thermodynamic Dissociation Constants Research Articles

Monitoring Inhibitor-Induced Conformational Population Shifts in HIV-1 Protease by Pulsed EPR Spectroscopy

Double electron-electron resonance (DEER), a pulsed electron paramagnetic resonance (EPR) spectroscopy technique, was utilized to characterize conformational population shifts in HIV-1 protease (HIV-1PR) upon interaction with various inhibitors. Distances between spin-labeled sites in the flap region of HIV-1PR were determined, and detailed analyses provide population percentages for the ensemble flap conformations upon interaction with inhibitor or substrate. Comparisons are made between the percentage of the closed conformer seen with DEER and enzymatic inhibition constants, thermodynamic dissociation constants, and the number of hydrogen bonds identified in crystallographic complexes.

Application of Davis method to estimation of ions activity coefficients at the evaluation of dissociation constants of aromatic dicarboxylic acids in organic solvents

Validity of the Davis method for the estimation of activity coefficients of the ions forming in an acid-base system at the evaluation of thermodynamic dissociation constants of aromatic acids in dimethylformamide medium is evidenced.

Acid-base equilibriums in solutions of polybases (model and experiment): II. Thermodynamic dissociation constants of protonated trifunctional bases

A procedure for estimation of dissociation constants of protonated tribasic species is developed distinguished by a new approach to evaluation of concentrations of all moieties in the equilibrium and accounting for it in the calculation of the solution ionic strength.

Impact of dissociation equilibrium shift on bacterial spore inactivation by heat and pressure

The shift of the dissociation equilibrium under pressure and temperature plays a decisive role in the inactivation of bacterial spores. To obtain the dissociation equilibrium shift in water and buffer systems, the thermodynamic dissociation constants in a wide range of pressure and temperature were modelled. Heat and pressure inactivation of Geobacillus stearothermophilus spores at different initial pH-values in ACES and phosphate buffer confirmed the modelled data. Thermal inactivation in both buffers at 114, 122 and 127 °C resulted in higher logarithmic reductions with ACES. Contrary, after pressure treatment at 500, 600 and 900 MPa with 80 °C phosphate buffer showed higher inactivation. These results indicated the different dissociation equilibrium shifts in buffer systems by heat and pressure.

Determination of the Dissociation Constants of Urocanic Acid Isomers in Aqueous Solutions

Summary. (E)- and (Z)-Urocanic acids are endogenous chemicals in the normal mammalian skin. The first and the second thermodynamic dissociation constants (pKa1 and pKa2) of urocanic acid isomers were determined using UV spectrophotometry in aqueous solutions. The values with standard deviation (pKa1 ¼ 3.43 � 0.12 and pKa2 ¼ 5.80 � 0.04) and (pKa1 ¼ 2.7 � 0.3 and pKa2 ¼ 6.65 � 0.04) were obtained to (E)- and (Z)-urocanic acids, respectively. The second dissociations were studied also by potentiometric titration in aqueous sodium chloride solutions up to the isotonic salt concentration (0.154 mol dm � 3 ), and the second thermodynamic dissociation constants as well as activity parameters for both isomers were determined at temperature 25 � Ca nd for (E)urocanic acid also at 37 � C. The obtained pKa2 values were close to those found by UV spectrophotometry. The equations for the calculation of the second stoichiometric dissociation constants of urocanic acid isomers on molality and molarity scale in aqueous sodium chloride solutions were derived. The obtained pKa1 and pKa2 values for (Z)-urocanic acid appear to be essentially lower than some previously reported values in literature.

The thermodynamic dissociation constants of four non-steroidal anti-inflammatory drugs by the least-squares nonlinear regression of multiwavelength spectrophotometric pH-titration data

The mixed dissociation constants of four non-steroidal anti-inflammatory drugs (NSAIDs) ibuprofen, diclofenac sodium, flurbiprofen and ketoprofen at various ionic strengths I of range 0.003–0.155, and at temperatures of 25 °C and 37 °C, were determined with the use of two different multiwavelength and multivariate treatments of spectral data, SPECFIT/32 and SQUAD(84) nonlinear regression analyses and INDICES factor analysis. The factor analysis in the INDICES program predicts the correct number of components, and even the presence of minor ones, when the data quality is high and the instrumental error is known. The thermodynamic dissociation constant p K a T was estimated by nonlinear regression of (p K a, I) data at 25 °C and 37 °C. Goodness-of-fit tests for various regression diagnostics enabled the reliability of the parameter estimates found to be proven. PALLAS, MARVIN, SPARC, ACD/p K a and Pharma Algorithms predict p K a being based on the structural formulae of drug compounds in agreement with the experimental value. The best agreement seems to be between the ACD/p K a program and experimentally found values and with SPARC. PALLAS and MARVIN predicted p K a,pred values with larger bias errors in comparison with the experimental value for all four drugs.

Acid-base equilibria in solutions of polyacid bases (Model and experiment): II. Thermodynamic dissociation constants of tribasic acids

A model is developed for estimating thermodynamic dissociation constants of tribasic acids in organic solvents, with an example of ethanol solution of citric acid in which the functional groups are neutralized jointly.

The dissociation of ethylenedithiodiacetic acid in aqueous solution

The dissociation of ethylenedithiodiacetic acid (H2Edtda) was studied by potentiometric titration at 298.15 K and ionic strength values of 0.5, 1.0, and 1.5 against the background of sodium and lithium nitrates. The concentration and thermodynamic dissociation constants were determined.

The Effect of a Hydrogen Bonding Environment (Dimethyl Sulfoxide) on the Ionisation and Redox Properties of the Thiol Group in Cysteine and a Protein Disulfide Isomerase Mimic (Vectrase)

Increasing enrichment of dimethyl sulfoxide, DMSO, in DMSO-water mixtures causes a reversal in the thermodynamic dissociation constants, pK as, and has a marked effect on the redox potentails of the thiolic and amino groups in cysteine and the protein disulfide isomerase (PDI) mimic BMC, Vectrase. This paper illustrates the effect of a hydrogen-bonding environment on the ionisation and redox properties of thiol groups in amino acids. A combination of potentiometry and Raman spectroscopy was applied to rationalise the observations. Intracellular environments are full of hydrophobic, hydrogen-bonding environments. The results illustrate the profound effects of the local environment on the thiol group.

Molecular Basis of RNA Recognition by the Embryonic Polarity Determinant MEX-5

Embryonic development requires maternal proteins and RNA. In Caenorhabditis elegans, a gradient of CCCH tandem zinc finger (TZF) proteins coordinates axis polarization and germline differentiation. These proteins govern expression from maternal mRNAs by an unknown mechanism. Here we show that the TZF protein MEX-5, a primary anterior determinant, is an RNA-binding protein that recognizes linear RNA sequences with high affinity but low specificity. The minimal binding site is a tract of six or more uridines within a 9-13-nucleotide window. This sequence is remarkably abundant in the 3'-untranslated region of C. elegans transcripts, demonstrating that MEX-5 alone cannot specify mRNA target selection. In contrast, human TZF homologs tristetraprolin and ERF-2 bind with high specificity to UUAUUUAUU elements. We show that mutation of a single amino acid in each MEX-5 zinc finger confers tristetraprolin-like specificity to this protein. We propose that divergence of this discriminator residue modulates the RNA-binding specificity in this protein class. This residue is variable in nematode TZF proteins, but is invariant in other metazoans. Therefore, the divergence of TZF proteins and their critical role in early development is likely a nematode-specific adaptation.

The thermodynamic dissociation constants of the anticancer drugs camptothecine, 7-ethyl-10-hydroxycamptothecine, 10-hydroxycamptothecine and 7-ethylcamptothecine by the least-squares nonlinear regression of multiwavelength spectrophotometric pH-titration data

The mixed dissociation constants of four anticancer drugs – camptothecine, 7-ethyl-10-hydroxycamptothecine, 10-hydroxycamptothecine and 7-ethylcamptothecine, including diprotic and triprotic molecules at various ionic strengths I of range 0.01 and 0.4, and at temperatures of 25 and 37 °C – were determined with the use of two different multiwavelength and multivariate treatments of spectral data, SPECFIT32 and SQUAD(84) nonlinear regression analyses and INDICES factor analysis. A proposed strategy for dissociation constants determination is presented on the acid–base equilibria of camptothecine. Indices of precise modifications of the factor analysis in the program INDICES predict the correct number of components, and even the presence of minor ones, when the data quality is high and the instrumental error is known. The thermodynamic dissociation constant p K a T was estimated by nonlinear regression of {p K a, I} data at 25 and 37 °C: for camptothecine p K a , 1 T = 2.90 ( 7 ) and 3.02(8), p K a , 2 T = 10.18 ( 30 ) and 10.23(8); for 7-ethyl-10-hydroxycamptothecine, p K a , 1 T = 3.11 ( 2 ) and 2.46(6), p K a , 2 T = 8.91 ( 4 ) and 8.74(3), p K a , 3 T = 9.70 ( 3 ) and 9.47(8); for 10-hydroxycamptothecine p K a , 1 T = 2.93 ( 4 ) and 2.84(5), p K a , 2 T = 8.93 ( 2 ) and 8.92(2), p K a , 3 T = 9.45 ( 10 ) and 9.98(4); and for 7-ethylcamptothecine p K a , 1 T = 3.10 ( 4 ) and 3.30(16), p K a , 2 T = 9.94 ( 9 ) and 10.98(18). Goodness-of-fit tests for various regression diagnostics enabled the reliability of the parameter estimates found to be proven. Pallas and Marvin predict p K a being based on the structural formulae of drug compounds in agreement with the experimental value.

Acid-base equilibria in solutions of polyacid bases (model and experiment): I. Thermodynamic dissociation constants of protonated mono- and diacid bases

A procedure was developed for determining the dissociation constants of protonated mono-and diacid bases. The procedure is based on a new approach to estimating and taking into account the concentrations of all the equilibrium species forming in the course of titration with a strong acid, with the aim to calculate the ionic strength of the solution and the activity coefficients.

Re-evaluation of the First and Second Stoichiometric Dissociation Constants of Phthalic Acid at Temperatures from (0 to 60) °C in Aqueous Phthalate Buffer Solutions with or without Potassium Chloride. 2. Estimation of Parameters for the Model for the First Dissociation Constant and Tests and Use of the Resulting Activity Coefficient Equations

Previously (in Part 1, J. Chem. Eng. Data 2006, 51, 777−784), equations were determined for the calculation of the second stoichiometric (molality scale) dissociation constant (Km2) of phthalic acid in buffer solutions containing potassium hydrogen phthalate (KHPh), dipotassium phthalate, and potassium chloride from the determined thermodynamic values of this dissociation constant (Ka2) and the molalities of the components in the solutions. These equations apply at temperatures from (0 to 60) °C up to ionic strengths of about 0.5 mol·kg-1, and they were based on the single-ion activity coefficient equations of the Huckel type. The parameters of phthalate species for these equations and the second thermodynamic dissociation constant of this acid at various temperatures were determined from Harned cell data of Hamer and Acree (J. Res. Natl. Bur. Stand. 1945, 35, 381−416), and the resulting parameter values were also tested with these data. In the present study, the corresponding equations were determined fr...

Determination of limiting mobilities and dissociation constants of 21 amino acids by capillary zone electrophoresis at very low pH

The dependence of the effective electrophoretic mobility on pH of the background electrolyte was experimentally determined by capillary zone electrophoresis (CZE) for cationic forms of amino acids. The pH of the background electrolytes was in the highly acidic range, 1.6-2.6 pH units, to ensure a high degree of protonation of the amino acids. Poly(vinyl alcohol) was added to the background electrolytes to avoid possible adsorption of the analytes at the inner capillary wall. Non-linear regression of the experimental data was applied to obtain the parameters of the relevant regression functions--the actual mobilities and mixed dissociation constants corresponding to the actual ionic strength. The extended Onsager and Debye-Hückel law was used to calculate the limiting mobilities and thermodynamic dissociation constants. The comparison of the experimental electropherogram with the computer prediction by PeakMaster using the determined data is presented for the selected sample of amino acids.

Determination of Stoichiometric Dissociation Constant of Ammonium Ion in Aqueous Potassium Chloride Solutions at 298.15 K

Equations were developed for the calculation of the stoichiometric (molality scale) dissociation constants, K m , of ammonium ion in aqueous KCl solutions at 298.15 K from the thermodynamic dissociation constant, K a , of this acid and the ionic strength, I m , of the solutions. Excess KCl was used in the solutions considered so that this salt in practice determined the ionic strength of these solutions. Equations for K m were based on the single-ion activity coefficient equations of the Hückel type. Potentiometric titration data measured with a glass electrode cell were used in the estimation of the parameters for the Hückel equations. By means of the calculation method suggested in this study, K m can be obtained almost within experimental error up to I m of 1.0 mol kg −1 for KCl solutions. The K m values obtained by this method were compared to the literature results obtained from the Harned cell data of Bates and Pinching (1949) and from the concentration cell data of Everett and Wynne-Jones (1938) measured with hydrogen electrodes on cells containing two liquid junctions.

Pressure dependence of the dissociation of acetic, benzoic, mandelic and succinic acids at 298.15 K

Dissociation constants for acetic, benzoic, mandelic and succinic acids have been measured at 298.15 K as a function of pressure up to 138.8 MPa. The spectrophotometric technique using Bromocresol Green as the optical indicator was employed up to ionic strength of 0.03 mol kg −1 in aqueous solution. Thermodynamic dissociation constants were calculated with the Davies activity coefficient equation. The pressure dependences of the ionization constants for the weak acids can be described by the equation of Lown, Thirsk and Wynne-Jones, application of which leads to accurate partial molal volume change on ionization, Δ V ¯ 0 and compressibility change, Δ κ ¯ 0 at 0.1 MPa.

Transport of Contaminants with Boiler Water Steam

A method for determining coefficients of distribution of contaminants between boiler water and steam generated in boilers and steam generators of nuclear power plants, which is based on standard thermodynamic dissociation constants, is presented. Appropriate analytical dependences are given for hydroxides of metals used in the power industry for pressures of 40, 87.5, and 155 kgf/cm2 (3.9, 8.6, and 15.2 MPa).

Thermodynamic constants of N-[tris(hydroxymethyl)methyl-3-amino]propanesulfonic acid (Taps) from the temperatures 278.15 K to 328.15 K

Values of the second thermodynamic dissociation constant p K 2 of N-[tris(hydroxymethyl)methyl-3-amino]propanesulfonic acid (Taps) have been determined at twelve temperatures from 278.15 K to 328.15 K including 310.15 K by measurements of the electromotive-force for cells without liquid junction of the type: Pt|H 2 (g, p ∘ = 101.325 kPa)|Taps ( m 1), NaTapsate ( m 2), NaCl ( m 3)|AgCl|Ag, where m denotes molality. The p K 2 values for the dissociation of Taps are represented by the equation: p K 2 = 2969.61 · (K/ T) – 17.05052 + 2.73697 · ln( T/K). The values of p K 2 for Taps were found to be (8.502 ± 0.0007) at T = 298.15 K and (8.225 ± 0.0009) at T = 310.15 K, respectively, indicating thereby to be useful as buffer solutions for pH control in the region 7.4 to 8.5. The thermodynamic quantities, Δ G ∘, Δ H ∘, Δ S ∘, and Δ C p ∘ dissociation process of Taps have been derived from the temperature coefficients of the p K 2.

Acid-Base Properties of Cefalotin, Cefazoline, and Cefalexin

The acid-base properties of cefalosporines, such as cefalotin, cefazoline, and cefalexin, were studied. The concentration constants of their acid dissociation at 20°C on the background of 0.1, 0.4, 0.7, and 1.0 M solutions of KCl and KNO3 were determined. Thermodynamic dissociation constants were calculated. The semiempirical PM3 quantum-chemical method was used to calculate the size of the ionic forms of the cefalosporines in the energetically preferred conformations.

Acid-Base Properties of Amoxycillin

Acid-base properties were studied by means of pH-metry. The concentration acid dissociation constants of the carboxy, ammonium, and phenolic groups (20°C, on the background of 0.1, 0.4, 0.7, and 1.0 M solutions of KCl and KNO3) were determined. Semiempirical quanum-chemical calculations by the PM3 method were used to calculate the sizes of ionic forms of amoxycillin in energetically favorable conformations. Thermodynamic dissociation constants were obtained by extrapolation of the concentration constants to zero ionic strength according to the Huckel equation with inclusion of the calculated ionic sizes.