Accurate pKa determinations for some organic acids using an extended cluster method

An Accurate Approach for Computational pKa Determination of Phenolic Compounds

Computational chemistry is a valuable tool, as it allows for in silico prediction of key parameters of novel compounds, such as pKa. In the framework of computational pKa determination, the literature offers several approaches based on different level of theories, functionals and continuum solvation models. However, correction factors are often used to provide reliable models that adequately predict pKa. In this work, an accurate protocol based on a direct approach is proposed for computing phenols pKa. Importantly, this methodology does not require the use of correction factors or mathematical fitting, making it highly practical, easy to use and fast. Above all, DFT calculations performed in the presence two explicit water molecules using CAM-B3LYP functional with 6-311G+dp basis set and a solvation model based on density (SMD) led to accurate pKa values. In particular, calculations performed on a series of 13 differently substituted phenols provided reliable results, with a mean absolute error of 0.3. Furthermore, the model achieves accurate results with -CN and -NO₂ substituents, which are usually excluded from computational pKa studies, enabling easy and reliable pKa determination in a wide range of phenols.

On the Accuracy of the Direct Method to Calculate pKa from Electronic Structure Calculations

The direct method (HA_(soln) ⇌ A_(soln)^– + H_(soln)⁺) for calculating pK_a of monoprotic acids is as efficient as thermodynamic cycles. A selective adjustment of proton free energy in solution was used with experimental pK_a data. The procedure was analyzed at different levels of theory. The solvent was described by the solvation model density (SMD) model, including or not explicit water molecules, and three training sets were tested. The best performance under any condition was obtained by the G4CEP method with a mean absolute error close to 0.5 units of pK_a and an uncertainty around ±1 unit of pK_a for any training set including or excluding explicit solvent molecules. PM6 and AM1 performed very well with average absolute errors below 0.75 units of pK_a but with uncertainties up to ±2 units of pK_a, using only the SMD solvent model. Density functional theory (DFT) results were highly dependent on the basis functions and explicit water molecules. The best performance was observed for the local spin density approximation (LSDA) functional in almost all calculations and under certain conditions, as high as those obtained by G4CEP. Basis set complexity and explicit solvent molecules were important factors to control DFT calculations. The training set molecules should consider the diversity of compounds.

Origin of Acid-Base Catalytic Effects on Formaldehyde Hydration

The mechanisms of hydronium- and hydroxide-catalyzed formaldehyde hydrations were investigated by quantum mechanical/molecular mechanical molecular dynamics in combination with flexible coordinates. A stepwise bimolecular and a concerted termolecular mechanism were found with a hydronium catalyst. The latter is more favorable and better consistent with experiment. Structurally, a dipole-bound species initially arranges the nucleophile in a favorable configuration for both routes, significantly enhancing the reactive collisions. On the one hand, the hydronium catalyst also plays a role of a reactant in the bimolecular path. On the other hand, only a stepwise mechanism was found with a hydroxide catalyst. Overall, hydroxide is a stronger catalyst than a hydronium when it is in contact distance with formaldehyde.

Absolute pKa Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation

Absolute pKa values of the amino acid side chains of arginine, aspartate, cysteine, histidine, and tyrosine; the C- and N-terminal group of tyrosine; and the tryptophan radical cation are calculated using a revised density functional based molecular dynamics simulation technique introduced previously [ Cheng , J. ; Sulpizi , M. ; Sprik , M. J. Chem. Phys. 2009 , 131 , 154504 ]. In the revised scheme, acid deprotonation is considered as a dissociation rather than a proton transfer reaction, and a correction term for treating the proton as a hydronium ion is suggested. The acidity constants of the amino acids are obtained from the vertical energy gaps for removal or insertion of the acidic proton and the computed solvation free energy of the proton. The unsigned mean error relative to experimental results is 2.1 pKa units with a maximum error of 4.0 pKa units. The estimated mean statistical uncertainty due to the finite length of the trajectories is ±1.1 pKa units. The solvation structures of the protonated and deprotonated amino acids are analyzed in terms of radial distribution functions, which can serve as reference data for future force field developments.

Secondary deuterium isotope effects on the acidity of glycine

Secondary deuterium isotope effects (IE) on the acidity (pK(a)) of glycine were measured by ¹³C NMR titration. It was found that deuteration decreases the pK(a) by 0.034 ± 0.002. The experimental data are supported by theoretical calculations, which, in turn, allowed to relate the acidity decrease to the lowering of glycine vibrational frequencies upon deuteration.

Acidity constants from DFT-based molecular dynamics simulations

In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Brønsted pK(a) when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK(a) values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.

Determination by ultraviolet absorption spectrometry and theoretical calculation of dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one

The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one was determined by ultraviolet absorption spectrometry method based on the absorption spectra of 1,2,3,9-tetrahydro-4H-carbazol-4-one at different pH in ethanol-water mixed solvents. The results show that the pK(b) was a good linear function of the volume fraction of ethanol in the concentration range studied. The dissociation constant of 1, 2, 3,9-tetrahydro-4H-carbazol-4-one in water were determined by extrapolation to be 14.04 under the condition of this experiment. The accurate pK(b) calculations of 1,2,3,9-tetrahydro-4H-carbazol-4-one have been investigated using the combination of the extended clusters-continuum model with the polarizable continuum solvation model (PCM). The calculations are performed at the B3LYP/6-31G levels. The formation of molecular clusters by means of the 1,2,3,9-tetrahydro-4H-carbazol-4-one wrapped up with water molecules leads to the weakness of the interaction between the polar solvents and the 1,2,3,9-tetrahydro-4H-carbazol-4-one, hence, the accuracy of pK(b) has been enhanced. The dissociation constant of 1,2,3,9-tetrahydro-4H-carbazol-4-one in water were calculated to be 14.10 and agreed well with experimental data.