Estimation of uncertainty in p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values determined by potentiometric titration

A procedure is presented for estimation of uncertainty in measurement of the pK(a) of a weak acid by potentiometric titration. The procedure is based on the ISO GUM. The core of the procedure is a mathematical model that involves 40 input parameters. A novel approach is used for taking into account the purity of the acid, the impurities are not treated as inert compounds only, their possible acidic dissociation is also taken into account. Application to an example of practical pK(a) determination is presented. Altogether 67 different sources of uncertainty are identified and quantified within the example. The relative importance of different uncertainty sources is discussed. The most important source of uncertainty (with the experimental set-up of the example) is the uncertainty of pH measurement followed by the accuracy of the burette and the uncertainty of weighing. The procedure gives uncertainty separately for each point of the titration curve. The uncertainty depends on the amount of titrant added, being lowest in the central part of the titration curve. The possibilities of reducing the uncertainty and interpreting the drift of the pK(a) values obtained from the same curve are discussed.     

The unsubstituted <Emphasis Type="Italic">ortho</Emphasis>-amidino benzoic acid: crystal structure,characterization and p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> determination

The simplest o-amidino benzoic acid—2-(amino(imino)methyl)benzoic acid—has been isolated in 23 % yield as a side product of the reaction of phthalonitrile and ammonia along with desired 1-imino-1H-isoindol-3-amine. This amidino acid was fully characterized by nuclear magnetic resonance, IR spectroscopy, mass spectrometry; pK_a values were also determined. X-ray diffraction study and quantum chemical calculations revealed that in the solid state it exists as a zwitterion that is stabilized by intermolecular hydrogen bonds.     

Interactions of Puerarin with Micelles: p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> Shifts and Thermodynamics

In this paper, the effect of varying hydrophobic chain lengths on the acid-base equilibrium of an isoflavone, puerarin, in cationic micelles has been studied. The interaction of puerarin with three types of micelles of identical positively charged head groups and varying tail lengths, viz., DTAB, TTAB and CTAB, shows that there is a shift in the apparent pK _a in the direction that favors the displacement of the acid-base equilibrium of puerarin towards the base form. The relative location depth of puerarin in micelles is determined according to their dielectric values (D) taking into account that lower D values correspond to deeper location. It is evident that the reduction of polarity favors the deprotonation of puerarin. The isothermal titration calorimetry measurements show that the effect of puerarin on the thermodynamic properties of micellization is enhanced in the order CTAB>TTAB>DTAB and the results illustrate that puerarin has more affinity for micelles with greater chain length.     

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> corrections

The computation of distribution coefficients between polar and apolar phases requires both an accurate characterization of transfer free energies between phases and proper accounting of ionization and protomerization. We present a protocol for accurately predicting partition coefficients between two immiscible phases, and then apply it to 53 drug-like molecules in the SAMPL5 blind prediction challenge. Our results combine implicit solvent QM calculations with classical MD simulations using the non-Boltzmann Bennett free energy estimator. The OLYP/DZP/SMD method yields predictions that have a small deviation from experiment (RMSD = 2.3 \(\log\) D units), relative to other participants in the challenge. Our free energy corrections based on QM protomer and \({\text{p}}K_{\text{a}}\) calculations increase the correlation between predicted and experimental distribution coefficients, for all methods used. Unfortunately, these corrections are overly hydrophilic, and fail to account for additional effects such as aggregation, water dragging and the presence of polar impurities in the apolar phase. We show that, although expensive, QM-NBB free energy calculations offer an accurate and robust method that is superior to standard MM and QM techniques alone.     

The SAMPL6 challenge on predicting aqueous p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from EC-RISM theory

The “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is applied to the problem of predicting aqueous pK_a values for drug-like molecules based on an ensemble of tautomers. EC-RISM is based on self-consistent calculations of a solute’s electronic structure and the distribution function of surrounding water. Following-up on the workflow developed after the SAMPL5 challenge on cyclohexane-water distribution coefficients we extended and improved the methodology by taking into account exact electrostatic solute–solvent interactions taken from the wave function in solution. As before, the model is calibrated against Gibbs energies of hydration from the “Minnesota Solvation Database” and a public dataset of acidity constants of organic acids and bases by adjusting in total 4 parameters, among which only 3 are relevant for predicting pK_a values. While the best-performing training model yields a root-mean-square error (RMSE) of 1 pK unit, the corresponding test set prediction on the full SAMPL6 dataset of macroscopic pK_a values using the same level of theory exhibits slightly larger error (1.7 pK units) than the best test set model submitted (1.7 pK units for corresponding training set vs. test set performance of 1.6). Post-submission analysis revealed a number of physical optimization options regarding the numerical treatment of electrostatic interactions and conformational sampling. While the experimental test set data revealed after submission was not used for reparametrizing the methodology, the best physically optimized models consequentially result in RMSEs of 1.5 if only improved electrostatic interactions are considered and of 1.1 if, in addition, conformational sampling accounts for quantum-chemically derived rankings. We conclude that these numbers are probably near the ultimate accuracy achievable with the simple 3-parameter model using a single or the two best-ranking conformations per tautomer or microstate. Finally, relations of the present macrostate approach to microstate pK_a results are discussed and some illustrative results for microstate populations are presented.     

Femtosecond absorption spectroscopy of cytochrome <Emphasis Type="Italic">c</Emphasis> oxidase: Excited electronic states and relaxation processes in heme <Emphasis Type="Italic">a</Emphasis> and heme <Emphasis Type="Italic">a</Emphasis><Subscript>3</Subscript> centers

Cytochrome c oxidase, the key bioenergetic protein, was studied by femtosecond absorption spectroscopy. Time-resolved spectral characteristics of the difference spectra recorded in the timescale from 80 fs to 20 ps were analyzed. Electronic relaxation of the excitation energy in heme a occurs in three successive steps. After completion of these steps, heme a is in the excited vibrational state of the ground state. Vibrational relaxation, cooling of the heme, occurs for several picoseconds.     

Absolute and relative p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> predictions via a DFT approach applied to the SAMPL6 blind challenge

In this work, quantum mechanical methods were used to predict the microscopic and macroscopic pK_a values for a set of 24 molecules as a part of the SAMPL6 blind challenge. The SMD solvation model was employed with M06-2X and different basis sets to evaluate three pK_a calculation schemes (direct, vertical, and adiabatic). The adiabatic scheme is the most accurate approach (RMSE?=?1.40 pK_a units) and has high correlation (R²?=?0.93), with respect to experiment. This approach can be improved by applying a linear correction to yield an RMSE of 0.73 pK_a units. Additionally, we consider including explicit solvent representation and multiple lower-energy conformations to improve the predictions for outliers. Adding three water molecules explicitly can reduce the error by 2–4 pK_a units, with respect to experiment, whereas including multiple local minima conformations does not necessarily improve the pK_a prediction.     

Nickel catalysis for hydrogenation of <Emphasis Type="Italic">p</Emphasis>-dinitrobenzene to <Emphasis Type="Italic">p</Emphasis>-phenylenediamine

The activity of supported nickel catalysts (5–20% Ni) in the hydrogenation of p-dinitrobenzene to p-phenylenediamine was investigated. The catalysts were obtained by ureainduced precipitation. Activated carbon, alumina, titania, and silica gel were evaluated as supports. The most active catalysts, 5%Ni/TiO₂ and 20%Ni/SiO₂, provided 50–54% yields of p-phenylenediamine at complete dinitrobenzene conversion.     

New correlation between metal-hydrolysis p<Emphasis Type="Italic">K</Emphasis> and sorbent-ionization p<Emphasis Type="Italic">K</Emphasis> for prediction of the pH of 50% metal-cation sorption on a chelating polymer sorbent

Metal sorption on chelating polymer sorbents (CPSs) is studied. A correlation is found between the 50%-sorption pH and the metal-hydrolysis pK, and pH₅₀ is predicted.     

4<Emphasis Type="Italic">p</Emphasis><Superscript>2</Superscript> resonances in photoionization from 4<Emphasis Type="Italic">s</Emphasis>4<Emphasis Type="Italic">p</Emphasis> levels in neutral zinc

In neutral zinc the 4p ² configuration lies above the 3d ¹⁰4s ionization limit and its levels become perturbers in the continuum. Lines have been identified in the Zn I spectrum for the multiplet, whereas no lines have been found for transitions to 4p ^{2 1} D or ¹ S. In this paper, cross sections for photoionization from 4s4p levels are reported that reveal the positions and widths of the 4p ² resonances. Calculations were performed using the multiconfiguration Hartree-Fock (MCHF) and B-spline R-matrix (BSR) method. Results from Breit–Pauli calculations that ignore the background continua are also presented. Included in the latter are energies for the levels and transition data (transition energies, line strengths, f-values, and A-rates) for all E1 transitions between these levels. Transition energies and the agreement in the length and velocity values, particularly for allowed transitions, indicate the accuracy of the computational model. Line widths are compared with other estimates. Contribution to the Serafin Fraga Memorial Issue.     

Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

SAMPL6: calculation of macroscopic p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from ab initio quantum mechanical free energies

Macroscopic pK_a values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pK_a values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pK_as with a maximum likelihood estimator and appropriately summed to yield macroscopic pK_a values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pK_as: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pK_a. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pK_a units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pK_a values for novel compounds with reasonable accuracy.     

Conducting materials prepared by the oxidation of <Emphasis Type="Italic">p</Emphasis>-phenylenediamine with <Emphasis Type="Italic">p</Emphasis>-benzoquinone

p-Phenylenediamine was oxidized with p-benzoquinone in the aqueous solutions of methanesulfonic acid (MSA). The conductivity of the products increased with increasing concentration of MSA from 1.5?×?10^?12 S cm^?1 in 0.1 M MSA up to 3.4?×?10^?4 S cm^?1 in 5 M MSA. The low-molecular-weight products are basically composed of one p-benzoquinone and two p-phenylenediamine molecules. Their molecular structure is discussed on the basis of mass, Fourier-transform infrared, Raman, NMR and electron paramagnetic resonance (EPR) spectroscopies. The formation of 2,5-di(p-phenylenediamine)-p-benzoquinone protonated with methanesulfonic acid best complies with the information provided by spectroscopic techniques. Its conversion to hydroquinone tautomer explains the formation of unpaired spins observed by EPR and their potential contribution to the conduction.     

Photolysis of <Emphasis Type="Italic">p</Emphasis>-benzoquinone and <Emphasis Type="Italic">p</Emphasis>-chloranil in aqueous sodium sulfite solution

Photosubstitution of the sulfo group for hydrogen (chlorine in chloranil) is observed under irradiation of sulfonated derivatives of hydroquinone formed upon dissolving of p-benzoquinone and p-chloranil in aqueous solutions of sodium sulfite. The quantum yield of the photochemical reaction is 0.18 ± 0.02 for p-benzoquinone. The rate constant of the thermal reaction of substitution is 5.5 × 10⁻⁴ l mol⁻¹ s⁻¹. The substitution reaction is sensitized by eosin upon irradiation with visible light. During the course of irradiation of sulfohydroquinones, the formation of a product with an absorption maximum at 235 nm was found. The product decays with a rate constant of 0.005 s⁻¹.     

Oxidation of <Emphasis Type="Italic">p</Emphasis>-Xylene

The review discusses the main procedures for producing terephthalic acid from p-xylene (primarily the Amoco process with the participation of Co, Mn, and Br salts), the oxidation mechanisms, alternative processes, and perspectives.     

Molecular structure of <Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">o</Emphasis>-and <Emphasis Type="Italic">p</Emphasis>-hydroxybenzyl)cytisine

The molecular structures of N-(o-and p-hydroxybenzyl)cytisine were investigated by NMR spectroscopy, x-ray structure analysis, and molecular modeling. It was found that NMR resonances of the OH and aromatic protons in N-(o-hydroxybenzyl)cytisine were doubled because of the presence of two conformers in solution. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 165–168, March–April, 2008.     

Evaluation of the <Emphasis Type="Italic">Q</Emphasis><Subscript><Emphasis Type="Italic">y</Emphasis></Subscript> absorption band maximum in a light-harvesting complex of the bacterial photosynthetic center <Emphasis Type="Italic">Thermochromatium tepidum</Emphasis>

Excitation energies of the bacteriochlorophyll (BChl) chromophores embedded in the photosynthetic light-harvesting complex of the purple bacterium Thermochromatium tepidum are computed using the time-dependent density functional theory based upon the fragmental molecular orbital (FMO-TDDFT) method. The results are correlated with the empirically based estimates of the Q _y absorption maximum, as well as with the observed large red shift induced by the binding of calcium.     

Synthesis of 6-methyl-8<Emphasis Type="Italic">H</Emphasis>-dibenzo[<Emphasis Type="Italic">a</Emphasis>,<Emphasis Type="Italic">g</Emphasis>]quinolizin-8-imines <Emphasis Type="Italic">via Reissert</Emphasis> compounds

Alkylation of Reissert compounds derived from 3-methylisoquinolines with several 2-cyanobenzylbromides followed by hydrolytic cleavage provided the corresponding 1-benzyl-3-methylisoquinolines. Treatment of the latter with methylmagnesiumiodide caused cyclization to the title compounds rather than formation of 2-acetylbenzylisoquinolines.     

<Emphasis Type="Italic">Z</Emphasis>-and <Emphasis Type="Italic">E</Emphasis>-conformers of <Emphasis Type="Italic">N</Emphasis>-chloroacetylcytisine

N-Chloroacetylcytisine was synthesized by acylation of (–)-cytisine. Stable Z- and E-conformers with respect to rotational isomerism around the N-12–CO bond were found in PMR spectra at room temperature. The point at which PMR resonances of the Z- and E-conformers coalesced upon heating was measured. The transition barrier between the conformers was estimated.     

Stability of <Emphasis Type="Italic">s</Emphasis>-, <Emphasis Type="Italic">p</Emphasis>-, and <Emphasis Type="Italic">d</Emphasis>-element diphosphates in water

The mean atomic Gibbs energies of formation of (Δ _f ? _at ⁰ ) of s-, p-, and d-element diphosphates have been calculated using ion increments of the Gibbs energy (Δ _f G ⁰). The diphosphate hydrolysis kinetics is considered, and a correlation between the Δ _f ? _at ⁰ values and the hydrolysis rate constants is presented.