pK-Yay: A Black-Box Method Using Density Functional Theory and Implicit Solvation Models to Compute Aqueous pKa Values of Weak and Strong Acids

Determination of the Hammett Acidity of HF/Base Reagents

Harnessing the acidity of HF/base reagents is of paramount importance to improve the efficiency and selectivity of fluorination reactions. Yet, no general method has been reported to evaluate their acidic properties, and experimental designs are still relying on a trial-and-error approach. We report a new method based on 19F NMR spectroscopy which allows highly sensitive measures and short-time analyses. Advantageously, the basic properties of the indicators can be determined upstream by DFT calculations, affording a simple yet robust semiempirical approach. In particular, the indicators used in this study were rationally designed to fit on the conceptually appealing and commonly used Hammett scale. This method has been applied to commercially available and recently developed HF/base reagents.

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

Molecular docking assisted exploration on solubilization of poorly soluble drug remdesivir in sulfobutyl ether-tycyclodextrin

Objective

To study structure-specific solubilization effect of Sulfobutyl ether-β-cyclodextrin (SBE-β-CD) on Remdesivir (RDV) and to understand the experimental clathration with the aid of quantum mechanics (QM), molecular docking and molecular dynamics (MD) calculations.

Methods

The experiment was carried out by phase solubility method at various pH and temperatures, while the concentration of Remdesivir in the solution was determined by HPLC. The complexation mechanism and the pH dependence of drug loading were investigated following a novel procedure combining QM, MD and molecular docking, based on accurate pKa predictions.

Results

The phase solubility and solubilization effect of RDV in SBE-β-CD were explored kinetically and thermodynamically for each assessed condition. An optimal drug / SBE-β-CD feeding molar ratio was determined stoichiometrically for RDV solubility in pH1.7 solution. The supersaturated solubility was examined over time after pH of the solution was adjusted from 1.7 to 3.5. A possible hypothesis was raised to elucidate the experimentally observed stabilization of supersaturation based on the proposed RDV Cation A /SBE-β-CD pocket conformations.

Conclusion

The computational explorations conformed to the experimentally determined phase solubilization and well elucidated the mechanism of macroscopic clathration between RDV and SBE-β-CD from the perspective of microscopic molecular calculations.

Graphical Abstract

The Ionic Product of Water in the Eye of the Quantum Cluster Equilibrium

The theoretical description of water properties continues to be a challenge. Using quantum cluster equilibrium (QCE) theory, we combine state-of-the-art quantum chemistry and statistical thermodynamic methods with the almost historical Clausius-Clapeyron relation to study water self-dissociation and the thermodynamics of vaporization. We pay particular attention to the treatment of internal rotations and their impact on the investigated properties by employing the modified rigid-rotor-harmonic-oscillator (mRRHO) approach. We also study a novel QCE parameter-optimization procedure. Both the ionic product and the vaporization enthalpy yield an astonishing agreement with experimental reference data. A significant influence of the mRRHO approach is observed for cluster populations and, consequently, for the ionic product. Thermodynamic properties are less affected by the treatment of these low-frequency modes.

Multiobjective Evaluation of Amine-Based Absorbents for SO2 Capture Process Using the pK a Mathematical Model

The screening of high-efficiency and low-energy consumption absorbents is critical for capturing SO₂. In this study, absorbents with better performance are screened based on mechanism, model, calculation, verification, and analysis methods. The acidity coefficient (pK _a) values of ethylenediamine (EDA), piperazine (PZ), 1-(2-hydroxyethyl)piperazine (HEP), 1,4-bis(2-hydroxyethyl)piperazine (DIHEP), and 1-(2-hydroxyethyl)-4-(2-hydroxypropyl)piperazine (HEHPP) are calculated by quantum chemical methods. A mathematical model of the SO₂ cyclic absorption capacity per amine (α_c) in the amine-based SO₂ capture process is built based on the electroneutrality of the solution. Another model of desorption reaction heat (Q _des) is also built based on the van't Hoff equation. Correspondingly, α_c and Q _des of the above five diamines are calculated and verified with the experimental data. The results show that α_c of the diamine changes with the increase in the pK _a value, and the increase in the pK _a value directly leads to changes in Q _des. The order of α_c of the above five diamines is EDA > PZ > HEHPP > HEP > DIHEP, and the order of Q _des is EDA > PZ > HEHPP > DIHEP > HEP. The multiobjective analysis between α_c and Q _des suggests that it is not advisable to simply pursue a higher α_c while ignoring Q _des. The compound quaternary system absorbent has a wider range of α_c than the single ternary absorbent, which is the direction of absorbent development. This study is expected to strengthen absorbent screening for the amine-based SO₂ capture process from flue gas.

Computational Estimation of the Acidities of Pyrimidines and Related Compounds

Pyrimidines are key components in the genetic code of living organisms and the pyrimidine scaffold is also found in many bioactive and medicinal compounds. The acidities of these compounds, as represented by their pKas, are of special interest since they determine the species that will prevail under different pH conditions. Here, a quantum chemical quantitative structure-activity relationship (QSAR) approach was employed to estimate these acidities. Density-functional theory calculations at the B3LYP/6-31+G(d,p) level and the SM8 aqueous solvent model were employed, and the energy difference ∆EH2O between the parent compound and its dissociation product was used as a variation parameter. Excellent estimates for both the cation → neutral (pKa1, R2 = 0.965) and neutral → anion (pKa2, R2 = 0.962) dissociations were obtained. A commercial package from Advanced Chemical Design also yielded excellent results for these acidities.

Predicting pKa Values of Quinols and Related Aromatic Compounds with Multiple OH Groups

Quinonoid compounds play central roles as redox-active agents in photosynthesis and respiration and are also promising replacements for inorganic materials currently used in batteries. To design new quinonoid compounds and predict their state of protonation and redox behavior under various conditions, their pK_a values must be known. Methods that can predict the pK_a values of simple phenols cannot reliably handle complex analogues in which multiple OH groups are present and may form intramolecular hydrogen bonds. We have therefore developed a straightforward method based on a linear relationship between experimental pK_a values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pK_a values when intramolecular hydrogen bonds are present. Our approach has been validated by showing that predicted and experimental values for over 100 quinols and related compounds differ by an average of only 0.3 units. This accuracy makes it possible to select proper pK_a values when experimental data vary, predict the acidity of quinols and related compounds before they are made, and determine the sites and orders of deprotonation in complex structures with multiple OH groups.

Anti-bacterial and super-hydrophilic bamboo charcoal with amidoxime modified for efficient and selective uranium extraction from seawater

With the growing demand for nuclear energy, uranium extraction from seawater (UES) is becoming increasingly important due to the ocean reserves 4.5 billion tons for uranium(VI) [U(VI)]. Herein, two kinds of amidoxime modified bamboo charcoal (AOOBCS and AOOBCH) with porous structure, anti-bacterial, and super-hydrophilic properties were successfully synthetized by two etching methods (soaking and hydrothermal). The super-hydrophilic property of AOOBCH accelerated the contact between the amidoxime group and uranyl ions (UO₂²⁺), and promoted the action of anti-bacterial substances (bamboo-quinone) on bacteria to restrain the form of bacterial membrane. In addition, the amidoxime groups not only didn't destroy the super-hydrophilic surface, but also adjusted the adsorbents' pK_a by changing the amidoxime grafting rate. Under PH = 7, the adsorption capacity of AOOBCH was about 1.97 times that of AOOBCS and 2.95 times that of BC. Importantly, the AOOBCH exhibited ultra-high uptake capacity (6.37 mg g^-1) and exceptional selectivity for U(VI) in 100-fold interfering ions simulated seawater system due to the chelation between C(NH₂)NOH and UO₂²⁺ to form a more stable coordination structure (E_ads = -36.56 eV). Benefiting from the superior performance and selectivity, the AOOBCH is a potential candidate for UES.