Investigation of ionization equilibria of L-aspartic and L-glutamic acids in water at a microscopic level by DFT method

The pK_a values of different dissociable groups of L-Aspartic and L-Glutamic acids in vacuo and in aqueous medium over a wide pH range have been estimated by DFT/B3LYP/6-31G(d) and 6-31G++(d,p) methods. For both the amino acids discrete water molecules (n?=?0, 3 and 6) have been used to get the first hydration sphere. Starting from a low pH, all possible tautomers resulting from each dissociation step are assumed to exist in a cyclic equilibrium. The structures of the species involved in the dissociation and tautomerization processes have been optimized in vacuo and also in aqueous medium considering H-bonded water molecules under the PCM formalism. For obtaining pK_a in aqueous medium the difference in Gibbs energy of the clusters H₃O⁺.mH₂O and (H₂O) _m+1 (m?=?an integer) is necessary and has been evaluated from computed literature data. Calculations reveal that in vacuo the neutral or less charged species predominate but in aqueous medium the zwitterionic or more chargeable forms contribute appreciably. The Gibbs energy changes for the microscopic cyclic equilibria have been estimated theoretically. These lead to overall (macroscopic) pK_a values for the ionization steps which are in good agreement with available experimental data for both the amino acids.     

The pKa theoretical estimation of C―H,N―H,O―H and S―H acids in dimethylsulfoxide solution

A scheme for the pK_a estimation of organic acids in dimethylsulfoxide (DMSO) solution based on quantum chemical calculations is proposed. The procedure of pK_a calculation requires several steps. The first is the calculation of the gas phase acidity of the compound. The G3MP2B3, G4MP2 as well as CBS‐QB3 composite methods made it possible to estimate values of gas phase acidities of an extensive set of structures with a high confidence level (standard deviations equal to 1.15, 1.13 and 1.29 kcal mol^?1, respectively; the test set included 91 compounds). The second step is the computation of the solvation correction with the integral equation formalism version of polarizable continuum model (IEF‐PCM)–B3LYP/6‐311+G(d,p) approximation. Within the bounds of our approach, the medium properties were covered only by the PCM model, i.e. the proposed procedure neglects specific interactions between DMSO and the solute. It was determined that the approach to pK_a estimation mentioned above is the most balanced in terms of accuracy, resource intensity and computation time cost. In the third step, the error of the pK_a calculation was decreased by correlation allowances. Correlation allowances were determined for each acid class (62 С―Н, 55 N―Н, 24 O―Н and 5 S―Н acids) in the range of 50 units in terms of logarithmic scale using the test set including 146 compounds. Seven O―H acids showing the ability to form cyclic dimers were separated into a discrete group. The proposed methodology was applied to the estimation of pK_a for trans‐ and cis‐dimethyl‐4,5‐dihydro‐3H‐pyrazol‐3,5‐dicarboxylates as well as for 5‐fluorouracil subject to competitive dissociation, the latter by N1―H or N3―H bonds. Copyright © 2014 John Wiley & Sons, Ltd.     

Higher reactivity of 3‐pyridinium boronic acid compared with 3‐pyridinium boronate ion toward 4‐isopropyltropolone in acidic aqueous solution: fundamental reaction analyses for an effective organoboron‐based chemosensor

The pK_as of 3‐pyridylboronic acid and its derivatives were determined spectrophotometrically. Most of them had two pK_as assignable to the boron center and pyridine moiety. The pK_a assignment performed by ¹¹B nuclear magnetic resonance spectroscopy revealed that both boron centers in 3‐pyridylboronic acid [3‐PyB(OH)₂] and the N‐methylated derivative [3‐(N‐Me)Py⁺B(OH)₂] have strong acidities (pK_a = 4.4 for both). It was found that introduction of a substituent to pyridine‐C atom in 3‐pyridylboronic acid drastically increased the acidity of the pyridinium moiety, but decreased the acidity of the boron center, whereas the introduction to pyridine‐N atom had no influence on the acidity of the boron center. Kinetic studies on the complexation reactions of 3‐pyridinium boronic acid [3‐HPy⁺B(OH)₂] with 4‐isopropyltropolone (Hipt) carried out in strongly acidic aqueous solution indicated that the positive charge on the boronic acid influenced little on its reactivity; 3‐HPy⁺B(OH)₂ reacts with Hipt and protonated H₂ipt⁺, and its reactivity was in line with those of a series of boronic acids. Kinetics in weakly acidic aqueous solution revealed that 3‐HPy⁺B(OH)₂ reacts with Hipt faster than its conjugate boronate [3‐HPy⁺B(OH)₃^–], which is consistent with our recent results. The reactivity of 3‐(N‐Me)Py⁺B(OH)₂ towards Hipt was also examined kinetically; the reactivities of 3‐(N‐Me)Py⁺B(OH)₂ and 3‐(N‐Me)Py⁺B(OH)₃^– are almost the same as those of their original 3‐HPy⁺B(OH)₂ and 3‐HPy⁺B(OH)₃^–, respectively. Copyright © 2012 John Wiley & Sons, Ltd.     

Kinetics and mechanism of the anilinolysis of aryl 4‐nitrophenyl thionocarbonates in aqueous ethanol

The reactions of bis(4‐nitrophenyl), 3‐chlorophenyl 4‐nitrophenyl, and 3‐methoxyphenyl 4‐nitrophenyl thionocarbonates ( 1 , 2 , and 3 , respectively) with a series of anilines are subjected to a kinetic investigation in 44 wt.% ethanol–water, at 25.0 °C and an ionic strength of 0.2 M. Under aniline excess, pseudo‐first‐order rate coefficients (k_obs) are found. Plots of k_obs versus aniline concentration are linear, with the slopes (k_N) pH independent, k_N being the rate coefficient for the anilinolysis of the thionocarbonates. The Brønsted plot (log k_N vs. pK_a of anilinium ions) for thionocarbonate 1 is linear, with slope (β) 0.62, which is consistent with a concerted mechanism. The Brønsted plots for thionocarbonates 2 and 3 are curved, with slopes 0.1 at high pK_a for both reaction series and slopes 0.84 and 0.79 at low pK_a for the reactions of 2 and 3 , respectively. The latter plots are in accordance to stepwise mechanisms, through a zwitterionic tetrahedral intermediate (T^±) and its anionic analogue (T^?), the latter being formed by deprotonation of T^± by the basic form of the buffer (HPO). The Brønsted curves are explained by a change in the rate‐limiting step, from deprotonation of T^± at low pK_a, to its formation at high pK_a. The influence of the amine nature and the non‐leaving and electrophilic groups of the substrate on the kinetics and mechanism is also discussed. Copyright © 2010 John Wiley & Sons, Ltd.     

Computational study of the proton affinity and basicity of structurally diverse α1‐adrenoceptor ligands

The α₁‐adrenoceptor is a target for the treatment of several conditions from hypertension to benign prostatic hyperplasia. In this paper, we describe a new analysis approach to explore the conformational space of several ligands of the α₁‐adrenoceptor and we also present the calculation of their proton affinity and basicity. For each compound a conformational search followed by a semi‐empirical optimisation was performed and a selection of conformations for each ligand was subjected to further optimisation using density functional theory methods. Different positions were explored to determine the favoured site of protonation, and then, the proton affinity (in the gas phase) and basicity (using the polarisable continuum model for the aqueous solution) were calculated for each of them. In addition, an alternative method using one explicit water molecule in combination with the polarisable continuum model for aqueous solvent was explored. Moreover, the acid dissociation constant (pK_a) in water of these 26 compounds was calculated because this is an important parameter for a ligand when binding to its receptor. The experimental pK_a values of six of these ligands and those of two compounds with a very low and a very large pK_a were used to validate the theoretical methodology. Copyright © 2011 John Wiley & Sons, Ltd.     

A novel computational strategy for the pKa estimation of drugs by non‐linear regression of multiwavelength spectrophotometric pH‐titration data exhibiting small spectral changes

A new computational procedure for the protonation model building of a multiwavelength and multivariate spectra treatment is proposed for the special case of small changes in spectra. The absorbance change Δ_i for the ith spectrum divided with the instrumental standard deviation s_inst(A) represents the signal‐to‐error ratio SER of the spectra studied. The determination of the number of chemical components in a mixture is the first important step for further quantitative analysis in all forms of spectral data treatment. Most index‐based methods of the factor analysis can always predict the correct number of components, and even the presence of a minor one, when the SER is higher than 10. The Wernimont–Kankare procedure in the program INDICES performs reliable determinations of the instrumental standard deviation of the spectrophotometer used s_inst(A), correctly predicts the number of light‐absorbing components present, and also solves ill‐defined problems with severe collinearity in spectra or very small changes in spectra. The mixed dissociation constants of three drugs, haemanthamine, lisuride, and losartan, including diprotic molecules at ionic strengths of I = 0.5 and 0.01 and at 25°C were determined using two different multiwavelength and multivariate treatments of the spectral data, SPECFIT32 and SQUAD(84) non‐linear regression analyses and INDICES factor analysis, even in the case of small absorbance changes in spectra. The dissociation constant pK_a was estimated by non‐linear regression of {pK_a, I} data at 25°C: for haemanthamine pK_a = 7.28(1) at I = 0.50, for lisuride pK_a = 7.86(1) and for losartan pK_a,1 = 3.60(1), pK_a,2 = 4.73(1) at I = 0.01. Goodness‐of‐fit tests for the various regression diagnostics enabled the reliability of the parameter estimates found to be proven. PALLAS and MARVIN predict pK_a being based on the structural formulae of the drug compounds in agreement with the experimental value. Copyright © 2007 John Wiley & Sons, Ltd.     

One‐scale basicities of diaminobenzenes and diaminonaphthalenes: from aniline to proton sponge

Basicity constants, pK_a, for a wide range of mono‐protonated diaminobenzenes and diaminonaphthalenes, including dimethylamino derivatives were for the first time uniformly measured in 20% aqueous ethanol (29 compounds) and 80% aqueous dioxane (39 compounds) spanning from aniline to 1,8‐bis(dimethylamino)naphthalene (‘proton sponge’). The dioxane system proved to be more versatile and because of better solubility of N‐alkylated polyaminoarenes allowed to add to the same scale some superbasic bis(dialkylamino)‐, tetrakis(dialkylamino)‐, and hexakis(dialkylamino)naphthalenes, thus extending the scale for almost 10 pK_a units, revealing possible limits of basicity changes in aromatic amines. The basicity of reference bases, pyridine and triethylamine, was also measured in these solvent systems. A group of N‐alkylated compounds was found to be less basic in aqueous dioxane when compared with their NH₂‐analogs. This anomaly was not observed in aqueous ethanol. Other basicity trends and correlations between different basicity scales were also discussed. Copyright © 2016 John Wiley & Sons, Ltd.     

Substituent effects on the pH‐dependent multiequilibria of flavylium salt analogs of anthocyanins

Substituent effects on the hydration, tautomerization, and isomerization equilibria of flavylium salts can be described by a series of linear free energy relationships (LSER) based on Hammett correlations. The positions on the flavylium rings were classified as either activated (para‐like) or nonactivated (meta‐like) to decide which σ value to employ (σ_R or σ_m, respectively), while the steric effects of substituents at C‐3 were included via the E_S parameter. Based on these relationships, we then show that it is possible to predict values of the “apparent pK_a” (pK_ap) of flavylium ions that were not included in the original data set, as well as those of several naturally occurring anthocyanins. The value of pK_ap provides a measure of the thermodynamic stability of the flavylium cation as a function of pH and is directly related to the pH range in which the color of the flavylium cation form of anthocyanins persists in aqueous solution. Copyright © 2011 John Wiley & Sons, Ltd.     

N‐Chlorination rate of five‐membered heterocyclic nitrogen compounds

The kinetics of N‐chlorination reaction of pyrrolidine, pyrrolidone, succinimide, 5,5,‐dimethyloxazolidine‐2,4‐dione, 5,5‐dimethylhydantoin and 1‐hydroximethyl‐5,5‐dimethylhydantoin with HOCl in aqueous solution were studied at 25 °C, constant ionic strength and under isolation conditions in a wide pH range. The set of compounds studied in this paper is characterized by having different functional groups and the same cyclic structure, consisting of a five‐member ring with a nitrogen atom in the ring, which is susceptible to be chlorinated. This series of compounds covers nine pK_a units, and the kinetic studies allow us to know, like, the presence of an amino, amide or imide group modify the reactivity of nitrogenous compound. Experimental data were fitted to the first‐order kinetic equation. All reactions were found to be of first order in both HOCl and nitrogenous compound concentration. Kinetics studies demonstrate that some of these compounds are hydrolyzed in alkaline medium. In each case, reaction mechanism in agreement with the experimental results is proposed. The results were compared with other compounds with similar cyclic structure (2‐oxazolidinone and proline). Copyright © 2016 John Wiley & Sons, Ltd.     

A thioester substrate binds to the enzyme Arthrobacter thioesterase in two ionization states: evidence from Raman difference spectroscopy

4‐Hydroxybenzoyl‐CoA (4‐HB‐CoA) thioesterase from Arthrobacter is the final enzyme catalyzing the hydrolysis of 4‐HB‐CoA to produce coenzyme A and 4‐hydroxybenzoic acid in the bacterial 4‐chlorobenzoate dehalogenation pathway. Using a mutation E73A that blocks catalysis, stable complexes of the enzyme and its substrate can be analyzed by Raman difference spectroscopy. Here we have used Raman difference spectroscopy, in the non‐resonance regime, to characterize 4‐HB‐CoA bound in the active site of the E73A thioesterase. In addition, we have characterized complexes of the wild‐type enzyme complexed with the unreactive substrate analog 4‐hydroxyphenacyl‐CoA (4‐HP‐CoA). Both sets of complexes show evidence for two forms of the ligand in the active site: one population has the 4‐hydroxy group protonated, 4‐OH; while the second has the group as the hydroxide, 4‐O⁻. For bound 4‐HP‐CoA, X‐ray data show that glutamate 78 is close to the 4‐OH in the complex and it is likely that this is the proton acceptor for the 4‐OH proton. Although the pK_a of the 4‐OH group on the free substrate in aqueous solution is 8.6, the relative populations of ionized and neutral 4‐HB‐CoA bound to E73A remain invariant between pH 7.3 and 9.8. The invariance with pH suggests that the 4‐OH and the ‐COO⁻ of E78 constitute a tightly coupled pair where their separate pK_a ‘s lose their individual qualities. Narrow band profiles are seen in the CO double bond and C‐S regions, suggesting that the hydrolyzable thioester group is rigidly bound in the active site in a syn gauche conformation. Copyright © 2011 John Wiley & Sons, Ltd.     

Functionalized surfactant mediated reactions of carboxylate,phosphate and sulphonate esters

Nucleophilic reactivity of some functionalized surfactants, i.e. quaternary pyridinium aldoximes towards the hydrolysis of p‐nitrophenyl acetate (PNPA), p‐nitrophenyl benzoate (PNPB), p‐nitrophenyldiphenyl phosphate (PNPDPP) and p‐nitrophenyl p‐toluene sulphonate (PNPTS) has been studied at pH 7.1 and 27 °C. Addition of functionalized surfactant to reaction medium causes progressive increase in the rate of hydrolysis and reaches a maximum and then decreases due to further addition of surfactant. An increase in the alkyl chain length of functionalized surfactants resulted in an increase in the first‐order rate constant. The apparent pK_a and CMC of functionalized surfactants have also been determined by spectrophotometric and conductometric methods, respectively. Copyright © 2009 John Wiley & Sons, Ltd.     

Fluorescence properties of the anti-tumour alkaloid luotonin A and new synthetic analogues: pH modulation as an approach to their fluorimetric quantitation in biological samples

Luotonin A is an alkaloid structurally related to the natural anti-tumour agent camptothecin. The fluorescence behaviour of luotonin A and a series of six analogues is described in the present work. The influence of solvent polarity and pH on the native fluorescence properties of these alkaloids was studied, finding that in organic solvents or in aqueous solutions (pH 5.5–7.2) the neutral form of the luotonin derivatives emit in the region of 410–450 nm but, in both media, acidification to pH values below 3.0 causes a new emission band to appear at about 500 nm. An ESPT reaction occurs due to the protonation of the basic nitrogen atoms of the pentacyclic ring. Acid-base titrations of luotonin A and its derivatives in aqueous and acetonitrile media were carried out in order to determine their pK_a^? values which were around 2, showing these compounds to be very weak bases. In aqueous media, the absence of an iso-emissive point in the emission spectra suggests the existence of more than two species in the proton transfer equilibria. The basicity of the luotonin A derivatives is increased in organic media, and a good correlation between the pK_a^? values and the chemical structure was found. The protonation of luotonin A was also studied by ¹H-NMR and ¹³C-NMR experiments, which proved the protonation of the nitrogen atoms at the positions 5 and 6 of the pentacyclic ring. The fluorescence quantum yields were determined in ethanol and in aqueous solutions under neutral and acidic conditions. The fluorescence quantum yields were higher in water for the case of the more polar compounds, and the opposite result was obtained for the more hydrophobic ones. The remarkable and interesting fluorescence properties of luotonin A prompted the development of its fluorimetric analytical quantitation, obtaining very good analytical features.     

Specific radiation damage to acidic residues and its relation to their chemical and structural environment

Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X‐ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side‐chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side‐chains. This suggests that residues with higher pK_a values are more vulnerable to damage than those with a lower pK_a. However, such a correlation was not found when calculated pK_a values were inspected. (ii) Acidic side‐chains located in the enzymatic active site are the most radiation‐sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.     

Kinetic study of the formation of N‐chloro compounds using N‐chlorosuccinimide

Second‐order rate constants were determined for the chlorination reaction of 2,2,2‐trifluoethylamine and benzylamine with N‐chlorosuccinimide at 25 °C and an ionic strength of 0.5 M. These reactions were found to be of first order in both reagents. According to the experimental results, a mechanism reaction was proposed in which a chlorine atom is transferred between both nitrogenous compounds. Kinetics studies demonstrate that the hydrolysis process of the chlorinating agent does not interfere in the chlorination process, under the experimental conditions used in the present work. Free‐energy relationships were established using the results obtained in the present work and others available in the literature for chlorination reactions with N‐chlorosuccinimide, being the pK_a range included between 5.7 and 11.22. Copyright © 2014 John Wiley & Sons, Ltd.     

Kinetics and mechanism of the reactions of aryl chlorodithioformates with pyridines and secondary alicyclic amines

The reactions of pyridines and secondary alicyclic (SA) amines with phenyl and 4‐nitrophenyl chlorodithioformates (PClDTF and NPClDTF, respectively) are subjected to a kinetic study in aqueous ethanol (44 wt% ethanol) solution, at 25.0 °C, and an ionic strength of 0.2 M (KCl). The reactions are studied spectrophotometrically. Under amine excess, pseudo‐first‐order rate coefficients (k_obs) are found. Plots of k_obs versus [amine] are linear and pH independent, with slope k_N. The Brønsted‐type plots (log k_N vs. pK_a of aminium ions) are linear for the reactions of PClDTF with SA amines (slope β of 0.3) and pyridines (β = 0.26) and those of NPClDTF with pyridines (β = 0.30). For the reaction of NPClDTF with SA amines the Brønsted‐type plot is biphasic, with slopes β₁ = 0.2 (at high pKa) and β₂ = 1.1 (at low pKa). The pK_a value at the center of curvature (pK) is 7.7. The magnitude of the slopes indicates that the mechanisms of these reactions are stepwise, with the formation of a zwitterionic tetrahedral intermediate as the rate‐determining step, except for the reaction of NPClDTF with SA amines where there is a change in the rate‐determining step, from formation to breakdown of the tetrahedral intermediate, as the amine basicity decreases. Copyright © 2009 John Wiley & Sons, Ltd.     

Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide‐promoted cleavages of phosphorothioate and phosphate triesters in water and methanol

The base‐promoted solvolysis of a series of O,O‐dimethyl O‐aryl and O,O‐dimethyl O‐alkyl phosphorothioates (1) as well as O,O‐dimethyl O‐aryl and O,O‐dimethyl O‐alkyl phosphates (2) was studied computationally by density functional theory methods in methanol and water continuum media to determine the transition between concerted and stepwise processes. In addition, an experimental study was undertaken on the solvolysis of these series in basic methanol and water. The computations indicate that the solvolytic mechanism for series 1 involves lyoxide attack anti to the leaving group in a concerted manner with good leaving groups having pK_a^Lg values < 12.3 in methanol and in a stepwise fashion with the formation of a 5‐coordinate thiophosphorane intermediate when the pK_a^Lg > 12.3. A similar transition from concerted to stepwise mechanism occurs with series 2 in methanol as well as with series 1 and 2 in water, although for the aqueous solvolyses with hydroxide nucleophile, the transitions between concerted and stepwise mechanisms occur with better leaving groups than in the case in methanol. The computational data allow the construction of Brønsted plots of log k₂^?OS versus pK_a^Lg in methanol and water, which are compared with the experimental Brønsted plots determined with these series previously and with new data determined in this work. Both the computational and experimental Brønsted data reveal discontinuities in the plots between substrates bearing O‐aryl and O‐alkyl leaving groups, with the gradients of the plots being far steeper than, and non‐collinear with, the O‐aryl leaving groups for solvolysis of the O‐alkyl‐containing substrates. These discontinuities signify that care should be exercised in interpreting breaks in Brønsted plots in terms of changes in rate‐limiting steps that signify the formation of an intermediate during a solvolytic process. Copyright © 2011 John Wiley & Sons, Ltd.     

K‐edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration

Sulfur K‐edge XANES (X‐ray absorption near‐edge structure) spectroscopy is an excellent tool for determining the speciation of sulfur compounds in complex matrices. This paper presents a method to quantitatively determine the kinds of sulfur species in natural samples using internally calibrated reference spectra of model compounds. Owing to significant self‐absorption of formed fluorescence radiation in the sample itself the fluorescence signal displays a non‐linear correlation with the sulfur content over a wide concentration range. Self‐absorption is also a problem at low total absorption of the sample when the sulfur compounds are present as particles. The post‐edge intensity patterns of the sulfur K‐edge XANES spectra vary with the type of sulfur compound, with reducing sulfur compounds often having a higher post‐edge intensity than the oxidized forms. In dilute solutions (less than 0.3–0.5%) it is possible to use sulfur K‐edge XANES reference data for quantitative analysis of the contribution from different species. The results show that it is essential to use an internal calibration system when performing quantitative XANES analysis. Preparation of unknown samples must take both the total absorption and possible presence of self‐absorbing particles into consideration.     

Kinetics and mechanism of the pyridinolysis of diaryl carbonates

The reactions of 4‐methylphenyl and 4‐chlorophenyl 4‐nitrophenyl carbonates ( 1 and 2 , respectively), phenyl, 4‐methylphenyl, 4‐chlorophenyl, and 4‐nitrophenyl 2,4‐dinitrophenyl carbonates ( 3 , 4 , 5 , and 6 , respectively), and bis(2,4‐dinitrophenyl) carbonate ( 7 ) with a series of pyridines are studied kinetically at 25.0 °C in 44 wt% ethanol–water and an ionic strength of 0.2 M (KCl). The reactions are followed spectrophotometrically and under excess amine pseudo‐first‐order rate coefficients (k_obs) are found. For all these reactions, plots of k_obs versus free amine concentration at constant pH are linear, the slope (k_N) being independent of pH. The Brønsted‐type plots (log k_N vs. pK_a of the conjugate acids of the pyridines) are all biphasic (linear portions at high and low pK_a and a curvature in between). These plots are in accordance with a stepwise mechanism, through a zwitterionic tetrahedral intermediate (T^±), and a change in the rate‐determining step from formation of T^± to its breakdown to products, as the pyridine basicity decreases. Also studied are the effects of the leaving, non‐leaving, and electrophilic groups of the substrate, and of the amine nature, on the value (value at the center of curvature of the Brønsted‐type plots). Copyright © 2008 John Wiley & Sons, Ltd.