Correlations and predictions of pKa values of fluorophenols and bromophenols using hydrogen-bonded complexes with ammonia

Density functional theory calculations have been preformed on a series of the hydrogen-bonded fluorophenol-ammonia and bromophenol-ammonia complexes. Intermolecular and intramolecular properties, particularly those related to hydrogen bonding, have been carefully analyzed. Several properties, such as the bond length and stretching frequency of the hydroxyl group, the hydrogen bond length and binding energy, are shown to be highly correlated with each other and are linearly correlated with known experimental pKa values of the halogenated phenols. The linear correlations have been used to predict the pKa values of all fluorophenols and bromophenols in the series. The predicted pKa values are shown to be consistent from different molecular properties and are in good agreement with available experimental values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow the effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations.     

Theoretical study of hydrogen-bonded complexes of chlorophenols with water or ammonia: Correlations and predictions of pKa values

A simple practical method for predicting the acidity constants (as pKa values) of chlorophenols is proposed based on density functional theory calculations of a series of hydrogen-bonded complexes of phenol and 19 different congeners of chlorophenol, with a single probe molecule, either water or ammonia. Relevant structural parameters and molecular properties of these complexes, primarily involving the acidic hydroxyl group, are examined and plotted against the known pKa values of 14 chlorophenols and phenol. Strong linear correlations are found for these compounds. Such correlations are used to determine the pKa values of five chlorophenols whose experimental acidities have large uncertainties. Similar predicted pKa values are obtained by using different structural parameters and molecular properties for the complexes with either probe molecule. The study may be extended to determine the acidity of other compounds with a single acidic functional group.     

Accurate pKa determination for a heterogeneous group of organic molecules.

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.     

Acidity distribution of carboxyl groups in Loy Yang brown coal: its analysis and the change by heat treatment

Brown coals have a considerable number of acidic functional groups of which the main component is carboxyl groups, and the acidity has a wide distribution. In this paper, changes of the acidity distribution were examined by aqueous titration when brown coal was heat-treated to control its acidity distribution. For Loy Yang brown coal from Australia dried at 50 degrees C under vacuum (LY50), the acid dissociation constant, Ka, was distributed over a wide pKa range between 2 and 9. Then, using Gaussian functions, the acidity distribution was divided into four groups, which were characterized by average pKa values: average pKa value of 3.8 (hereafter referred to as Group A), 5.2 (Group B), 6.8 (Group C), and 8.3 (Group D). Among them, Groups A, B, and C were assigned to carboxyl groups. From the changes of the number of carboxyl groups when brown coal was heat-treated up to 400 degrees C, it was found that the way of decrease was different among these acidic groups. The decrease of the amount of carboxyl groups in Group C was significant, and at 325 degrees C most of them disappeared. On the other hand, the carboxyl groups in Group A remained even at a high temperature of 400 degrees C. We estimated approximately the structures around carboxyl groups for LY50 and their structural changes by heat treatment using the known pKa values for simple carboxylic acids and the pKa values calculated by the MOPAC program for complicated carboxylic acids.     

Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins

In this report, we present a computational methodology for the pKa prediction of proteins, based on linear-scaling molecular orbital calculations for their solution-conformations obtained from NMR measurements. The method is used to predict the pKa values of five carboxylic acids (Asp7, Glu10, Glu19, Asp27, and Glu43) in turkey ovomucoid third domain (OMTKY3), and six aspartates residues (Asp 22, Asp 44, Asp 54, Asp 75, Asp 83, and Asp 93) in barnase. For OMTKY3, all the predicted pKa values are within 1 pH units from the available experimental ones, except for the case of Glu 43. For barnase, the root-mean-square deviation from experiment is 1.46 pH units. As a result, the proposed pKa calculation method correctly reproduces the relative order of the pKa values among the carboxylic acids located in different sites of the proteins. The calculated pKa values are decomposed into the contributions of short- and long-range structural difference effects. The results indicate that in both proteins the pKa value of the given carboxylic acid is partially influenced by long-range interactions with distant charged residues, which significantly contribute to determining the relative order of the pKa values. The current methodology based on LSMO provides us useful information about the titration behavior in a protein.     

On the limits of highest-occupied molecular orbital driven reactions: the frontier effective-for-reaction molecular orbital concept

We carried out Hartree-Fock (HF) and density functional theory calculations for 61 compounds, the conjugated bases of carboxylic acids, phenols, and alcohols, and analyzed their acid-base behavior using molecular orbital (MO) energies and their dependence on solvent effects. Despite the well-known correlation between highest-occupied MO (HOMO) energies and pKa, we observed that HOMO energies are inadequate to describe the acid-base behavior of these compounds. Therefore, we established a criterion to identify the best frontier MO for describing pKa values and also to understand why the HOMO approach fails. The MO that fits our criterion provided very good correlations with pKa values, much better than those obtained by HOMO energies. Since they are the frontier molecular orbitals that drive the acid-base reactions in each compound, they were called frontier effective-for-reaction MOs, or FERMOs. By use of the FERMO concept, the reactions that are HOMO driven, and those that are not, can be better explained, independently from the calculation method used, as both HF and Kohn-Sham methodologies lead to the same FERMO.     

Molecular structures and properties of the complete series of bromophenols: Density functional theory calculations

The complete series of 19 bromophenols have been studied by density functional theory (DFT) calculations at the B3LYP/6-311G++(d,p) level. The molecular structures and properties of bromophenols are strongly influenced by intramolecular hydrogen bonding of ortho-bromine, steric and inductive effects of substituted bromine, and other intramolecular electrostatic interactions. Systematic trends in several structural parameters and molecular properties of bromophenols have been found with the increasing number of bromine substitutions, including increase in O-H bond length, decrease in C-O bond length, red shift in O-H stretching frequency, and blue shift in O-H torsional frequency. Correlations among several key molecular parameters as well as those with available aqueous pKa values are examined. Comparisons with chlorophenols have indicated that the inductive effect of substituted bromine appears larger and bromophenols are slightly stronger acids than chlorophenols.     

In-Block Derivatization of Herbicidal Carboxylic Acids by Pentafluorobenzyl Bromide

Abstract

Herbicidal carboxylic acids were analyzed via ECD gas chromatography of their pentafluorobenzyl esters. The derivatives were formed by direct injection of a mixture of the acids and pentafluorobenzyl bromide in acetone; yields showed marked dependence on pKa of the acids. Carboxylic acids which have pKa values greater than 4.5 yielded the corresponding derivatives in poor yield unless triethylamine is included in the mixture. The procedure is fast and particularly convenient for low-level screening, identification and analysis of highly acidic chlorobenzoic, chlorophenoxyalkanoic, and arylacetic acids in the presence of less acidic carboxylic acids and phenols.     

Atomic layer deposition of organic-inorganic hybrid materials based on saturated linear carboxylic acids

Atomic layer deposition (ALD) has successfully provided thin films of organic-inorganic hybrid materials based on saturated linear carboxylic acids and trimethylaluminium (TMA). Films were grown for seven carboxylic acids: oxalic, malonic, succinic, glutaric, pimelic, suberic and sebacic acid, i.e. ranging from 2 to 10 carbon atoms in the molecular structure. These processes show exceptionally high growth rates; up to 4.3 nm/cycle for the pimelic acid-TMA system. Quartz crystal microbalance measurements of the growth dynamics indicate that all systems are of a self limiting ALD-type. Nevertheless, temperature dependent growth was observed in several systems. The width of the ALD windows shows correlations with the length of the carbon chains. Fourier transform infrared spectroscopy clearly proved that the deposited films are of a hybrid character, where the carboxylic acids primarily form bidentate complexes, though bridging complexes may also form. All films are X-ray amorphous as deposited. The films were further analyzed by atomic force microscopy for surface roughness and topography, UV-Vis spectroscopy and ellipsometry for optical properties, and the goniometer method for measuring sessile drops for surface wetting properties. Apart from the oxalic and malonic acid-TMA systems, the films are stable in contact with water. The films are generally smooth, transparent and have a refractive index close to 1.5. The complete coverage and accurate growth control offered by the ALD technique is here proven to provide surface-functionalized hybrid materials resembling metal-organic frameworks (MOF), probably as rather dense structures, yet with substantial potential for applications.     

Large pKa shifts of alpha-carbon acids induced by copper(II) complexes

A series of synthetic receptors (4-6) incorporating metal ions, specifically copper(II), were examined for their ability to enhance the acidity of active methylene compounds. The copper(II) complexes were observed to reduce the pKa of 1,3-diketone carbon acids in acetonitrile by as much as 12 pKa units. The relatively large pKa reduction achieved by the complex is attributed to the electrostatic interaction between the anionic pi system of the enolate and the copper(II) ions. The cage structure and hydrogen bonding sites in receptors 4 and 5 lead to a very modest further enhancement of the acidity relative to that with 6. This study provides insight into the way in which metalloenzymes stabilize an enolate intermediate.     

Self-assembled 1,2-bis[4-(4-(10-decyloxy)phenylazo)]benzoylhydrazine dimer and its hydrogen-bonded complexes

We report the synthesis and investigation of a new self-assembled benzoylhydrazine-based compound, namely 1,2-bis[4-(4-(10-decyloxy)phenylazo)]benzoylhydrazine and their hydrogen-bonded complexes with different carboxylic acid derivatives, of which some exhibit liquid crystalline properties and some are non-mesogens. The conversion of the non-liquid crystalline target compound that is free from carboxylic acid to liquid crystalline complexes containing various carboxylic acids can probably be rationalised through the breaking of intermolecular hydrogen bonding within the supramolecular assembly by carboxylic acid dopants. The enhancement of liquid crystalline properties of benzoylhydrazine compounds with respect to various carboxylic dopants is documented. Other salient features can be exemplified by the formation of discotic columnar phase as shown by the azo-linkage containing 4-(4′-(10-decyloxy)phenylazo)benzoic acid-doped complex.     

Polymer Supported Synthesis of 2,3,4,6-Tetra-O-Acetyl-β-D-Glucopyranosyl Esters of Aromatic Carboxylic Acids

Aromatic carboxylic acids bound to Amberlyst A-26 react with α-acetobromoglucose to form 2,3,4,6-tetra-O-acetyl-1-0-aroyl-β-D-glucopy ranose derivatives in good yield. Glucosylation occurs satisfactorily with carboxylic acids and nitrophenols (pKa 7–4), but not with phenols whose pKa values are higher (pka ～ 10). Selective glucosylation at the carboxylic group is easily achieved in the case of phenolic acids.     

Co-crystallization of glycine anhydride with the hydroxybenzoic acids: Controlled formation of dimers via synthons cooperation and structural characterization

The results of crystallographic analyses on 1:1 and 1:4 well-defined co-crystals formed between glycine anhydride and each of 4-hydroxybenzoic acid and 3,5-dihydroxybenzoic acid are described. Neutral molecules are connected via heteromeric O-H···O and N-H···O contacts leading to different packing arrangements of supramolecular chains. On the basis of the molecular structures of glycine anhydride and carboxylic acid guests, the hydrogen bonds are arranged to give centrosymmetric synthons V and VII which are noteworthy for their robustness. Hydrogen-bond interactions between glycine anhydride and aromatic acid provide sufficient driving force to direct molecular recognition and crystal packing. Utilization of the orientation of functional groups of the building blocks, the acidity, and weak interactions provides a route for the creation of novel supra- molecular architectures in the crystal lattice. Both two co-crystals contain the expected hydrogen-bonded motifs, and there has been no proton transfer from either of the two carboxylic acids to the aza compound moiety. This demonstrates that glycine anhydride is very capable of affecting the construction of binary co-crystals in a predictable and rationale manner. It is noted that synthons VⅢ and IX are fairly large, but the real challenge in crystal engineering is to find a big enough synthon that occurs often enough. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

Synthesis and acid-base properties of (1H-benzimidazol-2-yl-methyl)phosphonate (Bimp2-). Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N-1)H and the phosphonate group

The synthesis of (1H-benzimidazol-2-yl-methyl)phosphonic acid, H2(Bimp)+/-, is described: 2-chloromethylbenzimidazole was reacted with ethylchloroformate to give 1-carboethoxy-2-chloromethylbenzimidazole which was treated with trimethyl phosphite and after hydrolysis with aqueous HBr H2(Bimp)+/- was obtained. In H2(Bimp)+/- one proton is at the N-3 site and the other at the phosphonate group; both acidity constants were determined in aqueous solution by potentiometric pH titrations (25 degrees C; I = 0.1 M, NaNO3) and this furnished the pKa values of 5.37 +/- 0.02 and 7.41 +/- 0.02, respectively. The acidity constant for the release of the primary proton from the P(O)(OH)2 group of H3(Bimp)+ was estimated: pKa = 1.5 +/- 0.2. Moreover, Bimp2- can be further deprotonated at its neutral (N-1/N-3)H site to give the benzimidazolate residue, but this reaction occurs only in strongly alkaline solution (KOH); application of the H_ scale developed by G. Yagil (J. Phys. Chem., 1967, 71, 1034) together with UV spectrophotometric measurements gave pKa = 14.65 +/- 0.12. Comparisons with acidity constants taken from the literature show that this latter pKa value is far too large and this allows the conclusion that an intramolecular hydrogen bond is formed between the (N-1/N-3)H site and the phosphonate group of Bimp2-; the formation degree of this hydrogen-bonded isomer is estimated to be 98 +/- 2%. The general relevance of this and the other results are shortly discussed and the species distribution for the Bimp system in dependence on pH is provided.     

Quantitative evaluation of Lewis acidity of metal ions with different ligands and counterions in relation to the promoting effects of Lewis acids on electron transfer reduction of oxygen

The g(zz) values of ESR spectra of superoxide (O(2)(.-) complexes of metal ion salts acting as Lewis acids with different ligands and counterions were determined in acetonitrile at 143 K. The binding energies (DeltaE) of (O(2)(.-)/Lewis acid complexes have been evaluated from deviation of the g(zz) values from the free spin value. The DeltaE value is quite sensitive to the difference in the counterions and ligands of metal ion salts acting as Lewis acids. On the other hand, the fluorescence maxima of the singlet excited states of 10-methylacridone/Lewis acid complexes are red-shifted as compared with that of 10-methylacridone, and the relative emission energies (Deltahnu(f)) vary significantly depending on the Lewis acidity of metal ion salts with different counterions and ligands. The promoting effects of Lewis acids were also examined on electron transfer from cobalt(II) tetraphenylporphyrin to oxygen in acetonitrile at 298 K, which does not occur in the absence of Lewis acids under otherwise the same experimental conditions. Both DeltaE and Deltahnu(f) values are well correlated with the promoting effects of Lewis acids on the electron transfer reduction of oxygen. Such correlations indicate that DeltaE and Deltahnu(f) values can be used as quantitative measures of Lewis acidity of metal ion salts with different ligands and counterions. The Lewis acidity thus determined can also be applied to predict the promoting effects of Lewis acids on organic synthesis.     

Acidity of a Cu-bound histidine in the binuclear center of cytochrome C oxidase

Cytochrome c oxidase (CcO) is a crucial enzyme in the respiratory chain. Its function is to couple the reduction of molecular oxygen, which takes place in the Fea3-CuB binuclear center, to proton translocation across the mitochondrial membrane. Although several high-resolution structures of the enzyme are known, the molecular basis of proton pumping activation and its mechanism remain to be elucidated. We examine a recently proposed scheme (J. Am. Chem. Soc. 2004, 126, 1858; FEBS Lett. 2004, 566, 126) that involves the deprotonation of the CuB-bound imidazole ring of a histidine (H291 in mammalian CcO) as a key element in the proton pumping mechanism. The central feature of that proposed mechanism is that the pKa values of the imidazole vary significantly depending on the redox state of the metals in the binuclear center. We use density functional theory in combination with continuum electrostatics to calculate the pKa values, successively in bulk water and within the protein, of the Cu-bound imidazole in various Cu- and Cu-Fe complexes. From pKas in bulk water, we derived a value of -266.34 kcal.mol(-1) for the proton solvation free energy (Delta). This estimate is in close agreement with the experimental value of -264.61 kcal.mol(-1) (J. Am. Chem. Soc. 2001, 123, 7314), which reinforces the conclusion that Delta is more negative than previous values used for pKa calculations. Our approach, on the basis of the study of increasingly more detailed models of the CcO binuclear center at different stages of the catalysis, allows us to examine successively the effect of each of the two metals' redox states and of solvation on the acidity of imidazole, whose pKa is approximately 14 in bulk water. This analysis leads to the following conclusions: first, the effect of Cu ligation on the imidazole acidity is negligible regardless of the redox state of the metal. Second, results obtained for Cu-Fe complexes in bulk water indicate that Cu-bound imidazole pKa values lie within the range of 14.8-16.6 throughout binuclear redox states corresponding to the catalytic cycle, demonstrating that the effect of the Fe oxidation states is also negligible. Finally, the low-dielectric CcO proteic environment shifts the acid-base equilibrium toward a neutral imidazole, further increasing the corresponding pKa values. These results are inconsistent with the proposed role of the Cu-bound histidine as a key element in the pumping mechanism. Limitations of continuum solvation models in pKa calculations are discussed.     

High-throughput evaluation of lipophilicity and acidity by new gradient HPLC methods

There is a need for fast testing of drug candidates for properties of pharmacokinetics and pharmacodynamics importance, in particular lipophilicity and acidity. These two parameters can conveniently be estimated by gradient reversed-phase HPLC. Appropriate conventional organic solvent gradient and the new pH gradient HPLC procedures are presented. The chromatographic parameter of lipophilicity, log kw, can be determined from two organic solvent gradient runs instead of 6-8 runs necessary in the standard isocratic (polycratic) approach. The newly introduced pH gradient reversed-phase HPLC consists in a programmed increase during the chromatographic run of the eluting power of the mobile phase with regards to ionizable analytes. The eluting strength of the mobile phase increases due to its increasing (in case of acidic analytes) or decreasing (basic analytes) pH, whereas the content of organic modifier remains constant. It has been theoretically and experimentally demonstrated that the pKa and log kw values can be evaluated based on retention data from a pH gradient run, combined with appropriate data from two organic solvent gradient runs. The gradient HPLC-derived log kw parameters correlate well with analogous parameters determined isocratically as well as with reference lipophilicity parameter log P (logarithm of n-octanol/water partition coefficient). Also, the HPLC-derived pKa parameters correlate to the literature pKa values (w(w)pKa), conventionally determined by titrations in water. The approach described allows rapid and high-throughput assessment of log kw and pKa for large series of drugs candidates, also when the analytes are available in a form of mixture, e.g. produced by combinatorial synthesis.     

Determination of dissociation constants of weak acids by deconvolution of proton binding isotherms derived from potentiometric data

Potentiometric titration of six carboxylic acid analytes were measured in aqueous and semiaqueous solvents to determine the effect of the solvent composition on the dissociation constants of the acids. The analytes studied were monoprotic (formic acid, acetic acid), diprotic (maleic and succinic acid) and triprotic (1, 2, ranging in composition from 0 to 80% by volume dioxane. The methodology used to assess the acidity constants was deconvolution of the proton binding isotherm of each analyte in each of the solvents. The dissociation constants agreed with those reported in the literature for titration in water. In the presence of the organic component, correlations relating the acidity constants with properties of the media were also found. In particular, affinity distributions derived from potentiometric titration data were used to assess the solvent media for resolving dissociation constants of weak acids and bases.