Thermodynamic cycle for the calculation of ab initio pKa values for hydroxamic acids

A Combined Experimental and Computational Study of Chrysanthemin as a Pigment for Dye-Sensitized Solar Cells

The theoretical study of chrysanthemin (cyanidin 3-glucoside) as a pigment for TiO₂-based dye-sensitized solar cells (DSSCs) was performed with the GAUSSSIAN 09 simulation. The electronic spectra of neutral and anionic chrysanthemin molecules were calculated by density functional theory with B3LYP functional and DGDZVP basis set. A better energy level alignment was found for partially deprotonated molecules of chrysanthemin, with the excited photoelectron having enough energy in order to be transferred to the conduction band of TiO₂ semiconductor in DSSCs. In addition, we used the raw aqueous extracts of roselle (Hibiscus sabdariffa) calyces as the source of chrysanthemin and the extracts with various pH values were tested in DSSCs. The extracts and photosensitized semiconductor layers were characterized by UV-Vis spectroscopy, and DSSCs based on raw extracts were characterized by current density-voltage measurements.

Ab Initio Simulation of pH-Sensitive Biomarkers in Magnetic Resonance Imaging

An ab initio simulation scheme is introduced as a theoretical prescreening approach to facilitate and enhance the research for pH-sensitive biomarkers. The proton ¹H and carbon ¹³C nuclear magnetic resonance (NMR) chemical shifts of the recently published marker for extracellular pH, [1,5-¹³C₂]zymonic acid (ZA), and the as yet unpublished ( Z)-4-methyl-2-oxopent-3-enedioic acid (OMPD) were calculated with ab initio methods as a function of the pH. The influence of the aqueous solvent was taken into account either by an implicit solvent model or by explicit water molecules, where the latter improved the accuracy of the calculated chemical shifts considerably. The theoretically predicted chemical shifts allowed for a reliable NMR peak assignment. The p K_a value of the first deprotonation of ZA and OMPD was simulated successfully whereas the parametrization of the implicit solvent model does not allow for an accurate description of the second p K_a. The theoretical models reproduce the pH-induced chemical shift changes and the first p K_a with sufficient accuracy to establish the ab initio prescreening approach as a valuable support to guide the experimental search for pH-sensitive biomarkers.

High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge

Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.

Polyhydroxamicalkanoate as a bioinspired acetylcholinesterase-based catalyst for acetylthiocholine hydrolysis and organophosphorus dephosphorylation: experimental studies and theoretical insights

A biomimetic polymer revealed a acetylcholinesterase-based performance.

Empirically Fitted Parameters for Calculating pKa Values with Small Deviations from Experiments Using a Simple Computational Strategy

Two empirically fitted parameters have been derived for 74 levels of theory. They allow fast and reliable pKa calculations using only the Gibbs energy difference between an acid and its conjugated base in aqueous solution (ΔGs(BA)). The parameters were obtained by least-squares fits of ΔGs(BA) vs experimental pKa values for phenols, carboxylic acids, and amines using training sets of 20 molecules for each chemical family. Test sets of 10 molecules per family-completely independent from the training set-were used to verify the reliability of the fitting parameters method. It was found that, except for MP2, deviations from experiments are lower than 0.5 pKa units. Moreover, mean unsigned errors lower than 0.35 pKa units were found for the 98.6%, 98.6%, and 94.6% of the tested levels of theory for phenols, carboxylic acids and amines, respectively. The parameters estimated here are expected to facilitate computationally based estimations of pKa values of species for which this magnitude is still unknown, with uncertainties similar to the experimental ones. However, the present study deals only with molecules of modest complexity, thus the reliability of the FP method for more complex systems remains to be tested.

The AIBLHiCoS Method: Predicting Aqueous pKa Values from Gas-Phase Equilibrium Bond Lengths

The proposed AIBLHiCoS method predicts a given compound's pKa in aqueous solution from a single ab initio bond length only, after geometry optimization in the gas phase. Here we provide simple and predictive equations for naphthols and chemically similar biomolecules. Each linear equation corresponds to a High-Correlation Subset (HiCoS) that expresses the novel type of linear free energy relationship discovered here. The naphthol family exhibits a clear and strong relationship with the phenol family, with the "active" C-O bond always producing the highest correlations. The proposed method can isolate erroneous experiments and operate in non-aqueous solution and at different temperatures. Moreover, the existence of "active fragments" is demonstrated in a variety of sizable biomolecules for which the pKa is successfully predicted.

Quantum mechanical based approaches for predicting pKa values of carboxylic acids: evaluating the performance of different strategies

The FP method is recommended for estimating pK_a values of carboxylic acids for which this information is still unknown, especially in combination with the PBE0 functional (MUE = 0.26) and the SMD solvent model.

THEORETICAL CALCULATION OF pKb VALUES FOR ANILINES AND SULFONAMIDE DRUGS IN AQUEOUS SOLUTION

In this work, calculations of p K b values have been performed for aniline and its substituted derivatives and sulfonamide drugs by using Gaussian 98 software package. Gas-phase energies were calculated with HF /6-31 G ** and B3LYP /6-31 G ** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor-like polarizable continuum model (CPCM) and the integral equation formalism-polarizable continuum model (IEFPCM) at the same levels which have been used for geometry determination in the gas-phase. The results show that the calculated p K b values using the B3LYP /6-31 G ** are better than those using the corresponding HF /6-31 G **. At first, the correlation equation was found to determine the p K b values of the investigated anilines. Then, this correlation equation was used to calculate the p K b values of the sulfonamide drugs. The results obtained indicate that the PCM model is a suitable solvation model for calculating p K b values in comparison to the other solvation models. For the investigated compounds a good agreement between the experimental and the calculated p K b values was also observed.

Studies of the H-D exchange mechanism of malonganenone B

Malonganenone B (1) exhibits an unusual H-D exchange of a formyl proton when in deuteric-NMR solvents. Synthetic and kinetic investigations were made to probe the mechanism of this exchange, which appears to occur via an uncommon and transient amine-amide NHC intermediate.