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.     

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.     

Cooperativity effects of intramolecular OH…O interactions on pKa values of polyolalkyl sulfonic acids in the gas phase and solution: a density functional theory study

Density functional theory method and B3LYP/6‐311++G(d,p) level of theory were used to determine the acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution (H₂O, DMSO, and CH₃CN) phase. Polarized continuum model was applied to calculate pK_a values of alkyl sulfonic acids and polyolalkyl sulfonic acids. A comparison between acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution phase indicates that the acidity strength of polyolalkyl sulfonic acids enhances with the increase of the cooperativity effect of intramolecular hydrogen bonds in polyolalkyl sulfonic acids. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of cooperativity effect on the acidity of polyolalkyl sulfonic acids. Copyright © 2014 John Wiley & Sons, Ltd.     

Defined-sector explicit solvent in the continuum model approach for computational prediction of pK a

Accurate prediction of the acidity dissociation constant (K _a) is a challenge for the theory of proton-transfer reactions, making first-principles prediction of pK _a within 0.5?pK units of experimental values a benchmark of broad interest. In the present contribution, the defined-sector explicit solvent in continuum cluster model, which considers the structure-to-chemical affinity relationship of the carboxyl functional group, is presented. The model demonstrates predictable solvent networks based on established ‘preferred’ conformations found in a training set. Predictability within 1?kcal?mol^–1 accuracy is shown for a full set of carboxylic acid systems with varying functionality.     

Computational (MP2 and DFT) modeling of the substrate/inhibitor interaction with the LDH active pocket in the gas phase and aqueous solution: bimolecular charged (pyruvate/oxamate–guanidinium cation) and neutral adducts (pyruvic/oxamic acids–guanidine)

Two types of bimolecular adducts were studied for the substrate and inhibitor of lactate dehydrogenase (LDH), one type of adducts between ionic species, α‐keto‐carboxylates (pyruvate and oxamate) and the guanidinium cation, and the other type of adducts between neutral species, α‐ketocarboxylic (pyruvic and oxamic) acids and guanidine. Calculations were performed in the gas phase and aqueous solution using the MP2 and PCM methods and the 6‐31++G** basis set. Application of the DFT(B3LYP) and PCM methods led to similar results. A change of the adducts' preference was observed when proceeding from the gas phase to aqueous solution. This change is in good agreement with the acidity–basicity scales in both phases. Formation constant (K_HB) for adduct between neutral species is greater for pyruvic than for oxamic acid in the gas phase, whereas a reverse situation takes place in aqueous solution, where the K_HB value for adduct between ionic species is smaller for pyruvate than for oxamate. The water molecules favor interactions of more polar oxamate with the guanidinium cation. Stronger interaction with this cation, a model of the arginine fragment of the LDH pocket, suggests that oxamate (inhibitor of LDH) has stronger binding properties in aqueous solution than pyruvate (substrate of LDH). Copyright © 2008 John Wiley & Sons, Ltd.     

Stability of benzoporphyrin photosensitizers in water/ethanol mixtures: pKa determination and self‐aggregation processes

Benzoporphyrin monoacid derivatives, here named B3A and B3B, are promising new drugs for photodynamic therapy. Although both isomers show interesting characteristics as photosensitizing compounds, they have some distinct physicochemical properties such as the tendency to self‐aggregate in water‐rich media. Because pH drives the presence of each species, the pK_a of these compounds assumes strategic importance. However, traditional micro‐titration methods and UV–Vis absorption techniques fail to give reliable pK_a values due to the characteristics of this highly complex system, such as the precipitation of hydrophobic species, close pK_a values, and high absorption band superposition. In the present work, chemometric tools are employed to evaluate pK_a, and the kinetic tendency of monomers to undergo self‐aggregation is investigated. In solvent mixtures at low water percentage in ethanol, both B3A and B3B are stabilized in a monomeric state. However, in mixtures with a high water content, self‐aggregation takes place, mainly under a mild pH acid condition (3 < pH < 6), in which the prevalent protolytic species of both isomers is the neutral charged form, compounds with carboxylic and porphyrin free‐base groups. It is demonstrated that both isomers can undergo aggregation following a self‐catalytic mechanism, which is 2000 times slower to B3A than B3B. For B3A, the aggregation is manifested by a decrease in the monomer band with the aggregation band probably superposed to that of the monomer. For B3B, together with the decrease in the monomer band, a new band related to self‐aggregates is observed. Copyright © 2010 John Wiley & Sons, Ltd.     

Experimental and computational study on the aqueous acidity constants of some new aminobenzoic acid compounds

The acidity constants of three new aminobenzoic acid derivatives were determined using potentiometric and spectrophotometric methods in 0.10 M aqueous potassium nitrate solution as supporting electrolyte. The potentiometric data and UV–Vis absorption spectra of solutions were recorded in the course of their pH-metric titration with a standard base solution. The protolytic equilibrium constants, concentration distribution diagrams and number of components involved have been calculated. The relative pK_a values for three acids were also calculated using ab initio quantum mechanical method at the HF/6-31G** level of theory in combination with CPCM continuum solvation method. The influence of substituents on the ionization constants of the studied molecular structures was investigated. The satisfactory agreement between the experimentally derived and theoretically calculated pK_a values provides solid support for the acid–base reactions proposed in this work.     

The aqueous Raman optical activity spectra of 4(R)‐hydroxyproline: theory and experiment

Vibrational Raman optical activity (ROA) spectra have been measured for aqueous solutions of 4(R)‐hydroxyproline at three different pH values and are compared with theoretical results calculated for several conformations of anionic, cationic and zwitterionic 4(R)‐hydroxyproline using density functional theory (DFT) and the polarizable continuum model (PCM). The experimental ROA bands have been ascribed to the normal modes by comparison of the experimental and calculated vibrational frequencies and ROA intensities. Overall, using PCM for geometry optimization and force field calculations gives simulated Raman and ROA spectra that agree with the main features of the experimental spectra, whereas using PCM also in the calculations of optical tensors seems more problematic. Copyright © 2010 John Wiley & Sons, Ltd.     

Basicity of neutral organic superbases with vinamidine structure in gas phase and acetonitrile: a density functional theory study

The gas‐phase proton affinities (PAs) for a set of molecules with vinamidine structure are considered and their basicities in acetonitrile. It is shown that introducing double bonds to the imidazoline rings at the proton attachment site resulted in decrease in PA of the parent vinamidine. The increase in PA can be obtained by inducing modifications to the imidazoline ring at the junction of two diazepinylium rings. Placing methyl and dimethylamino substituents on the perimeter of the molecule further increased their gas‐phase PAs. Studied vinamidine molecules are superbases, which possess PA values in the range between 261.0 and 284.2 kcal mol^–1 in the gas phase and pK_a values of 24.6–31.9 units in acetonitrile. Dismembering proton attachment site by opening the two diazepinylium and imidazoline rings resulted in the largest drop in PA values, indicating its importance in constraining the positions of imino nitrogen atoms in the neutral form of the molecule. Vinamidine molecules studied here present important pieces of the ladder of highly basic organic compounds for they possess accessible vinamidine molecular framework. Copyright © 2012 John Wiley & Sons, Ltd.     

Structural studies on Na0.75CoO2 thermoelectric material at high pressures

The crystal structure of Na_0.75CoO₂ was studied at ambient and low temperatures down to 10 K at pressures up to 40 GPa using synchrotron x-rays and a diamond cell in angle dispersion geometry. A reduction in the c/a ratio was observed at both conditions with the application of pressure. An increase in Co–O bond lengths and a decrease in Na–O bond lengths were observed above 10 GPa. The results of the density functional calculations performed agree well with the pressure induced bond length changes. The anomalous change in the c/a ratio and bond lengths indicate a pressure induced isostructural phase transition above 10 GPa. Bulk modulus calculations show this compound is less compressible than its hydrated analogues.     

A high‐level theoretical study into the atmospheric phase hydration,bond dissociation enthalpies,and acidity of aldehydes

CBS‐Q//B3, G4(MP2), and G4 composite method calculations were used to estimate atmospheric phase standard state (298.15 K, 1 atm) free energies of hydration (Δ_hydrG°_(g)), hydration equilibrium constants (log K_hydr,(g)), bond dissociation enthalpies (BDEs), and enthalpies (Δ_dH°_(g)) and free energies (Δ_dG°_(g)) of aldehydic proton acid dissociation for various substituted aldehydes with electron withdrawing and electron releasing groups. Good quality log K_hydr,(g) correlations with the Swain–Lupton resonance effect parameters R and R⁺ were found, allowing extension of the model to predict log K_hydr,(g) values for 487 substituted aldehydes having available R‐values and 108 substituted aldehydes having available R⁺ values. Good correlations were also found between experimental aqueous phase hydration equilibrium constants (log K_hydr,(aq)) and summative R/R⁺ values for peripheral substituents on a range of carbonyl derivatives (aldehydes, ketones, esters, and amides), suggesting that the structure–reactivity modeling approach can be extended to include all possible combinations of R₁C(O)R₂ carbonyl substitution in both gas and aqueous systems. Computationally derived BDEs and Δ_dH°_(g)/Δ_dG°_(g) were in good agreement with the limited experimental and theoretical datasets. BDEs did not generally correlate with any of the Hammett substituent constants or Swain–Lupton parameters considered. Gas phase acidities exhibited high correlation coefficients with Hammett inductive substituent constants (σ_I) and field effect parameters (F), allowing these to be employed as surrogates for estimating the gas phase aldehydic proton acidities of a larger potential compound range. The resulting models will be of use in predicting the environmental behavior for a broad range of environmentally relevant compounds containing carbonyl functionalities. 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.     

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.     

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.     

Kinetics of base‐catalyzed cyclization of 2,6‐dinitrophenylsulfanyl ethanenitrile and 2,4,6‐trinitrophenylsulfanyl ethanenitrile

The kinetics of base catalyzed cyclization of 2,6‐dinitrophenylsulfanyl ethanenitrile and 2,4,6‐trinitrophenylsulfanyl ethanenitrile giving 2‐cyano‐7‐nitrobenzo[d]thiazole‐3‐oxide and 2‐cyano‐5,7‐dinitrobenzo[d]thiazole‐3‐oxide respectively was studied in methanolic methoxyacetate, acetate, trichlorophenoxide, N‐methylmorpholine, and N‐methylpiperidine buffers at 25 °C and I = 0.1 mol L^?1. It was found that reaction involves both general acid and general base catalyses whose manifestation depends on the pK_a of the acid‐buffer component and the ratio of both buffer components. In weakly basic buffers the rate‐limiting step is C? H bond breaking in the cyclic intermediate, while in strongly basic buffers the rate‐limiting step is the general acid‐catalyzed elimination of hydroxyl group from the intermediate. Copyright © 2008 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.     

Investigation of sorption phenomena by solid phase extraction and liquid chromatography for the determination of some ether derivatives of tetrabromobisphenol A

Observed sorption and chromatographic behaviour served as a starting point for the examination of four ether derivatives of the flame retardant tetrabromobisphenol A (TBBPA): dihydroxyethyl (DHEE), dimethyl (DMe), diallyl (DAE) and dibromopropyl (DBPE). To date, there is little or no information about these compounds in the scientific literature. The targets in the present study had calculated log K_ow values of 6.0–10. A broad range of different types of solvents were used in order to elucidate the mechanisms of sorption onto silica (glass) and two solid phase extraction cartridges based on polystyrene divinylbenzene polymers, hydroxylated (Isolute ENV+) and vinylpyrrolidone (Oasis HLB) containing units. Also, three chromatographic columns (C18, C8 and dual C18‐based, i.e. a polar ligand together with C18 on a silica surface) were evaluated. The following were observed: desorption of the targets from silica surface by 1‐propanol showed the best results and the yields were further improved by silylation of the surface. Regardless of the experimental test conditions applied, the lowest recovery was seen for the DMe derivative, followed by TBBPA itself, which had calculated log K_ow values in between the other targets. A washing solution containing up to 70% methanol could be used without elution of the targets from the solid phase extraction cartridge . The dihydroxethyl ether derivative of TBBPA is most probably not affected by environmental relevant pH due to a likely high pK_a (ca 15). Also, this study shows that the polar character of the dual‐phase column was not as pronounced as asserted by the manufacturer. Copyright © 2009 John Wiley & Sons, Ltd.     

Hartree–Fock and density functional theory study of remote substituent effects on heterolytic Fe―C bond energies of p‐G‐C6H4CH2Fe(CO)2(η5‐C5H5) and p‐G‐C6H4(H)(CN)CFe(CO)2(η5‐C5H5)

Knowledge of the strength of the metal–ligand bond breaking and formation is fundamental for an understanding of the thermodynamics underlying many important stoichiometric and catalytic organometallic reactions. Quantum chemical calculations at different levels of theory have been used to investigate heterolytic Fe―C bond energies of para‐substituted benzyldicarbonyl(η⁵‐cyclopentadienyl)iron, p‐G‐C₆H₄CH₂Fp [1, G = NO₂, CN, COMe, CO₂Me, CF₃, Br, Cl, F, H, Me, MeO, NMe₂; Fp = (η⁵‐C₅H₅)(CO)₂Fe], and para‐substituted α‐cyanobenzyldicarbonyl(η⁵‐cyclopentadienyl)iron, p‐G‐PANFp [2, PAN = C₆H₄CH(CN)]. The results show that BP86 and TPSSTPSS can provide the best price/performance ratio and more accurate predictions in the study of ΔH_het(Fe―C)'s. The good linear correlations [r = 0.98 (g, 1a), 0.99 (g, 2b)] between the substituent effects of heterolytic Fe―C bond energies [ΔΔH_het(Fe―C)'s] of series 1 and 2 and the differences of acidic dissociation constants (ΔpK_a) of C―H bonds of p‐G‐C₆H₄CH₃ and p‐G‐C₆H₄CH₂CN imply that the governing structural factors for these bond scissions are similar. And the excellent linear correlations [r = ?1.00 (g, 1c), ?0.99 (g, 2d)] between ΔΔH_het(Fe―C)'s and the substituent σ_p^? constants show that these correlations are in accordance with Hammett linear free energy relationships. The polar effects of these substituents and the basis set effects influence the accuracy of ΔH_het(Fe―C)'s. ΔΔH_het(Fe―C)'s(1, 2) follow the Capto‐dative Principle. The detailed knowledge of the factors that determine the Fp―C bond strengths would greatly aid in understanding reactivity patterns in many processes. Copyright © 2011 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.