Avoiding gas-phase calculations in theoretical p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> predictions

CBS-QB3, two simplified and less computationally demanding versions of CBS-QB3, DFT-B3LYP, and HF quantum chemistry methods have been used in conjunction with the CPCM continuum solvent model to calculate the free energies of proton exchange reactions in water solution following an isodesmic reaction approach. According to our results, the precision of the predicted pK _a values when compared to experiment is equivalent to that of the thermodynamic cycles that combine gas-phase and solution-phase calculations. However, in the aqueous isodesmic reaction schema, the accuracy of the results is less sensitive to the presence of explicit water molecules and to the global charges of the involved species since the free energies of solvation are not required. In addition, this procedure makes easier the prediction of pK _a values for molecules that undergo large conformational changes in solvation process and makes possible the pK _a prediction of unstable species in gas-phase such as some zwitterionic tautomers. The successive pK _a values of few amino acids corresponding to the ionization of the α-carboxylic acid and α-amine groups, which is one of the problematic cases for thermodynamic cycles, were successfully calculated by employing the aqueous isodesmic reaction yielding mean absolute deviations of 0.22 and 0.19 pK _a units for the first and second ionization processes, respectively.     

Ionization of some derivatives of benzamide, oxamide and malonamide in DMF-water mixture

The ionization of six compounds of bis-phenolic amides was studied spectrophotochemically in DMF-water mixture. The compounds showed two pK_a values in the range of 5.97-7.32 for pK_a1 and 7.61-8.44 for pK_a2. The obtained values of K_a were normalized using the distribution diagrams of the different species and found to be in the range of 5.81-7.42 for pK_a1 and 7.48-8.27 for pK_a2.     

Chiral recognition and enantiomer assays of N-(3,5-dinitrobenzoyl)amino acid derivatives using electrospray ionization–mass spectrometry

A pair of pseudoenantiomers, anilide derivatives of N-pivaloylproline were prepared and used as chiral selectors for enantiomer discrimination of amides or esters of N-(3,5-dinitrobenzoyl)amino acids in single-stage electrospray ionization/mass spectrometric experiments. Addition of a chiral analyte to a solution of the two pseudoenantiomeric chiral selectors affords selector–analyte complexes in the electrospray ionization mass spectrum where the ratio of these complexes is dependent on the enantiomeric composition of the analyte. The relationship between the ratio of the selector–analyte complexes in the electrospray ionization mass spectrum and the enantiomeric composition of the analyte can be used to relate the extent of the measured enantioselectivity and for quantitative enantiomeric composition determinations. Effects of the added cationic ions (H⁺, Li⁺, Na⁺ and K⁺) and instrument conditions on the selector–analyte ion intensity and the enantioselectivity (α_MS) were investigated. The percent ratio of the sum of the selector–analyte ion counts and the total ion counts decreases accordingly with the increase of the desolvation temperature for H⁺, Na⁺ and K⁺. The ratio for Li⁺ kept almost constant. The best α_MS was observed at a desolvation temperature of 200 °C with the added H⁺. The cone voltage has little effects on the α_MS values though the intensities of selector–analyte complexes are decreased at higher cone voltages. The observed MS enantioselectivities are comparable to the HPLC enantioselectivities and the sense of chiral recognition by MS is consistent with what is observed chromatographically. Quantitative enantiomeric composition determinations for five different samples of N-(3,5-dinitrobenzoyl)leucinyl butylamide at four different concentrations were performed. The average % difference between the HPLC and MS enantiomer determinations is 6.8% and 3.7% for the calibration lines constructed at a concentration of the analyte of 125 μM and 12.5 μM, respectively.     

A Novel RP-LC Method for Determination of pK a Values of Some Anticancer Agents and Their Assay

A simple, reliable, and rapid RP-LC method has been developed for the determination of some anticancer drugs (daunorubicin, doxorubicin and vincristine sulfate) in their dosage forms and human urine. These compounds are well separated on a C18 column using the mobile phase consisting of a mixture of acetonitrile (50:50; v/v) at a flow rate of 1.5 mL min^?1. The analyte peaks were detected at 235 nm for doxorubicin and daunorubicin, and 220 nm for vincristine. Linearity was obtained in different concentration ranges between 0.10 and 12 μg mL^?1 for all compounds. Good sensitivity for all analytes was observed with DAD detection. LOD and LOQ of the method were found satisfying. The proposed method has been extensively validated in accordance with ICH guidelines and obtained results proved that the proposed method was precise, accurate, selective, and sensitive for simultaneous analysis of studied compounds. All analytical procedures including sample preparation, flow rate, and run time were at low levels. Also, pK _a values were determined using the dependence of the retention factor on the pH of the mobile phase. The effect of the mobile phase composition on the ionization constant was studied by measuring the pK _a at different methanol–water mixtures, ranging between 45 and 60 % (v/v).     

The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu^?-Ala-Lys⁺ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (pK _a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic pK _a of lysine amino acid.     

Hydration of gas-phase gramicidin S (M + 2H)2+ ions formed by electrospray: The transition from solution to gas-phase structure

The hydration of doubly protonated gas-phase ions of gramicidin S formed by electrospray ionization was investigated. Under “gentle” electrospray conditions, a near Gaussian distribution of (M + 2H + nH₂O)²⁺ ions with n up to 50 can be readily formed. These extensively hydrated gas-phase ions should have structures similar to those in solution. For intermediate extents of hydration, the “naked” or unsolvated ion is present in unusually high abundance. This is attributed to a competition between solvation of the charges by water vs intramolecular self-solvation via hydrogen bonding. In addition, “magic” numbers of attached water molecules are observed for n = 8, 11, and 14. These magic numbers are attributed to favorable arrangements of water molecules surrounding the charge and surface of the peptide in the gas phase. These results are indicative of a gentle stepwise transformation from the solution-phase structure of the ion to the preferred gas-phase structure as solvent evaporates from the hydrated ions.     

Determination of the ionization constants of natural cyclodextrins by high-resolution 1H-NMR and photon correlation spectroscopy

The purpose of this investigation has been to establish reference pK _a values in D₂O for the three natural CDs by high-resolution ¹H-NMR, according to the recent guidelines provided by the IUPAC for the determination of extreme pK _a values. The most alkaline conditions achieved in this study than in previous pH potentiometric assays have made possible to deduce the pK _a for the three acidic groups of each CD. In addition, we have studied the effects of the ionization of ??-CD on the aggregation properties of this macrocycle in H₂O by dynamic light scattering (DLS) as a function of pH. This procedure provides an indirect way of measuring the pK _a of ??-CD either by tracking the percentage of scattered light or the hydrodynamic radii of the species involved and reveals that the aggregates of ??-CD break and reduce their size progressively upon ionization of the OH^? groups in positions 2 and 3.     

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.     

A theoretical study of the limits of the acidity of carbon acids in phase transfer catalysis in water and in liquid ammonia

The acidities of a large number of carbon acids have been theoretically calculated for the gas-phase and for DMSO solution. The gas-phase values, both ΔH and ΔG, are very well correlated with the available experimental data. From the calculated ΔG values in DMSO and the pKas in the same solvent, a homogeneous set of pK _a (DMSO) values was devised that was used to generate pK _a (water). These last pK _as were used to establish the limits of the acidity of carbon acids for reactions under PTC conditions both alkylations and H/D exchange. A step further led to the pK _as in liquid ammonia and from them to the virtual use of PTC using liquid ammonia instead of water.      

Effect of Mobile Phase on Electrospray Ionization Efficiency

Electrospray (ESI) ionization efficiencies (IE) of a set of 10 compounds differing by chemical nature, extent of ionization in solution (basicity), and by hydrophobicity (tetrapropylammonium and tetraethylammonium ion, triethylamine, 1-naphthylamine, N,N-dimethylaniline, diphenylphthalate, dimethylphtahalate, piperidine, pyrrolidine, pyridine) have been measured in seven mobile phases (three acetonitrile percentages 20%, 50%, and 80%, and three different pH-adjusting additives, 0.1% formic acid, 1 mM ammonia, pH 5.0 buffer combination) using the relative measurement method. MS parameters were optimized separately for each ion. The resulting relative IE data were converted into comparable logIE values by anchoring them to the logIE of tetrapropylammonium ion taking into account the differences of ionization in different solvents and thereby making the logIE values of the compounds comparable across solvents. The following conclusions were made from analysis of the data. The compounds with pK _a values in the range of the solution pH values displayed higher IE at lower pH. The sensitivity of IE towards pH depends on hydrophobicity being very strong with pyridine, weaker with N,N-dimethylaniline, and weakest with 1-naphthylamine. IEs of tetraalkylammonium ions and triethylamine were expectedly insensitive towards solution pH. Surprisingly high IEs of phthalate esters were observed. The differences in solutions with different acetonitrile content and similar pH were smaller compared with the pH effects. These results highlight the importance of hydrophobicity in electrospray and demonstrate that high hydrophobicity can sometimes successfully compensate for low basicity. Graphical Abstract

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Mitigation of signal suppression caused by the use of trifluoroacetic acid in liquid chromatography mobile phases during liquid chromatography/mass spectrometry analysis via post‐column addition of ammonium hydroxide

A method has been developed to reduce the mass spectrometric ion signal suppression associated with the use of TFA as an additive in LC mobile phases. Through post‐column infusion of diluted NH₄OH solution to LC eluents, the ammonium ion introduced causes the neutral analyte‐TFA ion pair to dissociate which consequently releases the protonated analyte as free ions into the gas phase (through regular electrospray ionization mechanisms). An ion signal improvement from 1.2 to 20 times for a variety of compounds had been achieved through the application of this method. The molar ratios of NH₄OH:TFA which result in a reduction of signal suppression were determined to be between 0.5:1 and 50:1. In addition, it was shown that this NH₄OH infusion method could reduce the level of doubly‐charged species and the product ions formed via in‐source collision. The use of diluted NH₄OH solution is favorable since it is compatible with mass spectrometry analysis, and it is applicable in both positive and negative‐ion generation mode. Copyright © 2012 John Wiley & Sons, Ltd.     

Polynuclear Branched Tetrazole Systems. 2. New 2-(5-Tetrazolyl)ethylpodands and Their NH-Acidity

Nine new polynuclear 2-(5-tetrazolyl)ethyl podands have been obtained by the azidation of the corresponding nitriles. Using Bjerrum distribution functions, the values of pK _a ¹, pK _a ², pK _a ³, and pK _a ⁴ have been determined by a potentiometric method for 14 polynuclear tetrazoles in aqueous and aqueous methanolic solution. The found values lie in the range from 3.5 to 7.5 pH units. The overall rules and the sequence of the ionization of the spatially separated tetrazole fragments in these podand systems are discussed.     

Prediction of the separation of phenols by capillary zone electrophoresis

The effect of pH and ionic strength on the migration of neutral acids in capillary zone electrophoresis (CZE) has been studied for several phenols. The mobilities of the phenols and the efficiency of the capillary have been related to the studied factors. The mobility can be related to the pH of the running buffer through the mobility of the phenolate ion, and the conditional acidity pK value of the phenol at the working ionic strength. This allows prediction of the migration of the phenol, solely from its pK_a^′ value (literature pK_a corrected for the ionic strength of the solution) and mobility of the anion, which can be easily calculated from the mobility at a basic pH value and the pK_a^′ value. Combination of the predicted mobility with the efficiency allows estimation of the resolution of the consecutive peaks obtained for a mixture of phenols. This method has been tested for two groups of phenols of environmental interest.     

Injection of reagent ions into the selvedge region in fast-atom bombardment mass spectrometry

A divided probe that incorporates a potassium aluminosilicate glass target and an analyte/glycerol matrix target, spatially separated, was used to inject potassium ions (K⁺) into the high-pressure “selvedge” region formed above the analyte/glycerol matrix target during fast-atom bombardment (FAB); [M+K]⁺ adduct ions that represent the types of gas-phase neutral molecules present in the selvedge region are observed. Computer modeling assisted in designing the divided target and an additional ion optical element for the FAB ion source to optimize interactions between K⁺ ions and the desorbed neutral molecules. The capability of injecting K⁺ ions into the FAB experiment has utility in both mechanistic studies and analyses. Experimental results here are consistent with a model for the desorption/ionization processes in FAB in which some types of neutral analyte molecules are desorbed intact and are subsequently protonated by glycerol chemical ionization. Unstable protonated molecules undergo unimolecular decomposition to yield observed fragment ions. The use of K⁺ cationization of analytes for molecular weight confirmation is demonstrated, as well as its utility in FAB experiments in which mixtures are encountered.     

Capillary electrokinetic fractionation mass spectrometry (CEkF/MS): Technology setup and application to metabolite fractionation from complex samples coupled at‐line with ultrahigh‐resolution mass spectrometry

Capillary electrokinetic fractionation (CEkF) is investigated as a new, simple, and robust approach for semipreparative and analytical sample analysis based on pK_a‐dependant pH‐driven electrophoretic mobility. CEkF was optimized with contactless conductivity detection and conducted with 10 kV reverse voltage for 10 min, then coupled on/at‐line to ESI/MS. We propose a semi‐empirical model with 14 representative compounds based on the correlation between sample/medium pH regulating the partial charge, the electrokinetic loading of the capillary and intensity (I) of analytes. According to the model, an empirical function (I = f (pH)) could be derived to calculate the acid dissociation constant (pK_a) of various model compounds based on their pH‐dependant MS intensity profiles with the RSD < 4.05. Using the ultrahigh‐resolution of ion cyclotron resonance Fourier transform MS, the pK_a model was further illustrated in real samples into the structure prediction of important compounds in wine over two vintages. The established CEkF was successfully used to selectively fractionate sulfur compounds from the complex wine samples at pH 1.66. The proposed CEkF approach should allow in the future the simultaneous pK_a evaluation of multiple constituents without complicated separation out of a complex mixture in metabolomics or environmental chemistry.     

Tributylphosphine, excellent organocatalyst for conjugate additions of non-nucleophilic N-containing compounds

Conjugate additions of non-nucleophilic N-containing compounds such as amides, thioamides, sulfonamides, and electron-poor anilines with different Michael acceptors can be promoted through the use of tributylphosphine. The range of useful pK_a's of nucleophiles has been established (pK_a<25) and new insights into the mechanism proposed.     

Infrared spectrometric study of the interaction between 2-dimethylamino-3,3-dimethyl-1 azirine and some phenol derivatives

The H-bonded complexes between 2-dimethylamino-3,3-dimethyl-1-azirine (TMAAZ) and some phenol derivatives have been studied by IR spectrometry in carbon tetrachloride. The equilibrium constants at 300, 315 and 328 K and the ? ΔH°, ? Δν_OH and Δν_CN values have been determined. The comparison with previously studied OH … N complexes shows that TMAAZ forms stronger complexes than would be expected from the pK_a value. These facts are discussed in terms of steric, hybridization, solvation and charge transfer effects. From a pK_a of 8, the IR spectrum shows the appearance of ion pairs N⁺-H …^?O. A predominance of protonated species can be calculated for a pK_a of 6. This can explain why 1,2-ring cleavage whose first step is probably the formation of an azirinium cation, occurs for acids characterized by pK_a values lower than 5 but not for enolizable ketones having pK_a values higher than 9.     

Kinetics and mechanism of the defluorination of 8-fluoropurine nucleosides in basic and acidic media

For investigating the stability of C(8)-fluorine bond in 8-fluoropurine nucleosides some protected 8-fluoroguanosine, 8-fluoroinosine and 8-fluoroadenosine derivatives were prepared by direct fluorination of acetyl-protected purine nucleosides with elemental fluorine in solvents such as chloroform, acetonitrile and nitromethane. Fluorination reactions conducted in chloroform medium gave better yields of 8-fluoropurines. The fluorination yields were slightly lower when acetonitrile or nitromethane was used as solvent, but the product purification was found to be much easier. When the synthesized, protected fluoronucleosides were subjected to standard basic (NH₃ in methanol or 2-propanol) and acidic (HCl in methanol) deprotection conditions relevant to nucleoside chemistry, an efficient defluorination reaction took place. The kinetics of these defluorination reactions were conveniently followed, under pseudo-first-order reaction conditions, using ¹⁹F NMR spectroscopy. ¹H NMR, LC-MS and mass spectroscopy identified the products of the kinetic reaction mixtures. The defluorination reaction rate constants (k_obs) in basic media depended upon the electron density at C(8) while the k_obs data in acidic medium were determined by the pK_a of N⁷. An addition-elimination based mechanism (S_NAr) has been proposed for the defluorination reactions of these 8-fluoropurine nucleosides.     

The mechanism of the sonochemical degradation of benzoic acid in aqueous solutions

The sonolytic degradation of benzoic acid in aqueous solution was investigated at an ultrasonic frequency of 355 kHz. The degradation rate was found to be dependent upon the solution pH and the surface activity of the solute. The degradation rate was favoured at a solution pH lower than the pK _a of benzoic acid. At pH < pK _a, HPLC, GC and ESMS analysis showed that benzoic acid could be degraded both inside the bubble by pyrolysis and at the bubble/solution interface by the reaction with OH radicals. At higher pH (> pK _a) benzoic acid could only react with OH radicals in the bulk solution. During the sonolytic degradation of benzoic acid, mono-hydroxy substituted intermediates were observed as initial products. Further OH radical attack on the mono-hydroxy intermediates led to the formation of di-hydroxy derivatives. Continuous hydroxylation of the intermediates led to ring opening followed by complete mineralization. Mineralization of benzoic acid occurred at a rate of < 40μM/h.     

Enantiomer assays of amino acid derivatives using tertiary amine appended trans-4-hydroxyproline derivatives as chiral selectors in the gas phase

A pair of pseudo-enantiomers, tertiary amine appended trans-4-hydroxyproline derivatives were designed, synthesized, and evaluated as chiral selectors for enantiomer analysis of DNB-amino acid and their amides, in single-stage electrospray ionization/mass spectrometric experiments. The chiral selectors were designed to remove the interaction of the hydroxyl group of trans-4-hydroxyproline as well as separate the ionization site from the sites required for effective chiral recognition. Addition of a chiral analyte to a solution containing two pseudo-enantiomeric chiral selectors, affords selector-analyte complexes in the electrospray ionization mass spectrum where the ratio of these complexes is dependent on the enantiomeric composition of the analyte. The relationship between the ratio of the selector-analyte complexes in the electrospray ionization mass spectrum and the enantiomeric composition of the analyte can be used to relate the extent of the measured enantioselectivity and for quantitative enantiomeric composition determinations. Effects of acid modifiers (ammonium chloride, acetic acid, formic acid and hydrochloric acid) and instrument conditions on the selector-analyte ion intensity and the enantioselectivity (α_MS) were investigated. The largest α_MS was observed using ammonium chloride at a concentration around 0.5-1 mM at desolvation temperature of 150 °C. Capillary voltage has little effects on α_MS values. The sense of chiral recognition by MS is consistent with what is observed chromatographically. Quantitative enantiomeric composition determinations for N-(3,5-dinitrobenzoyl) leucinyl butylamide were performed. A comparison to the enantioselectivities towards a scope of analytes observed by chiral HPLC using a 3,5-dimethylanilide-proline-derived chiral stationary phase, is presented.