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Longuet M, Vitse K, Martin-Mingot A, Michelet B, Guégan F, Thibaudeau S. Determination of the Hammett Acidity of HF/Base Reagents. J Am Chem Soc 2024; 146:12167-12173. [PMID: 38626381 DOI: 10.1021/jacs.4c02344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
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.
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Affiliation(s)
- Mélissa Longuet
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
| | - Kassandra Vitse
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
| | - Agnès Martin-Mingot
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
| | - Bastien Michelet
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
| | - Frédéric Guégan
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
| | - Sébastien Thibaudeau
- UMR-CNRS 7285, IC2MP, Université de Poitiers, 4 rue Michel Brunet, TSA 51106, Poitiers Cedex 9 86073, France
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Pereira RW, Ramabhadran RO. Accurate Computation of Aqueous p Kas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box p K-Yay Method. J Phys Chem A 2023; 127:9121-9138. [PMID: 37862610 DOI: 10.1021/acs.jpca.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
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.
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Affiliation(s)
- Roshni W Pereira
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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Zhang Y, Zhao Z, Wang K, Lyu K, Yao C, Li L, Shen X, Liu T, Guo X, Li H, Wang W, Lai TT. Molecular docking assisted exploration on solubilization of poorly soluble drug remdesivir in sulfobutyl ether-tycyclodextrin. AAPS OPEN 2022; 8:9. [PMID: 35498163 PMCID: PMC9035334 DOI: 10.1186/s41120-022-00054-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
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 ![]()
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Kirchner B, Ingenmey J, von Domaros M, Perlt E. The Ionic Product of Water in the Eye of the Quantum Cluster Equilibrium. Molecules 2022; 27:molecules27041286. [PMID: 35209075 PMCID: PMC8877775 DOI: 10.3390/molecules27041286] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, Beringstr. 4, 53115 Bonn, Germany
- Correspondence:
| | - Johannes Ingenmey
- CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université, F-75005 Paris, France;
| | - Michael von Domaros
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany;
| | - Eva Perlt
- Otto Schott Institute of Materials Research, Faculty of Physics and Astronomy, Friedrich-Schiller-Universität Jena, Löbdergraben 32, 07743 Jena, Germany;
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Wang D, Xie J, Li G, Meng W, Li J, Li D, Zhou H. Multiobjective Evaluation of Amine-Based Absorbents for SO 2 Capture Process Using the p K a Mathematical Model. ACS OMEGA 2022; 7:2897-2907. [PMID: 35097284 PMCID: PMC8792931 DOI: 10.1021/acsomega.1c05766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/21/2021] [Indexed: 05/04/2023]
Abstract
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 (αc) 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, αc and Q des of the above five diamines are calculated and verified with the experimental data. The results show that αc 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 αc 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 αc and Q des suggests that it is not advisable to simply pursue a higher αc while ignoring Q des. The compound quaternary system absorbent has a wider range of αc 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.
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Affiliation(s)
- Dongliang Wang
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
| | - Jiangpeng Xie
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
| | - Guixian Li
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
| | - Wenliang Meng
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
| | - Jingwei Li
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
| | - Delei Li
- Baiyin
Nonferrous Group Co. LTD, Baiyin, Gansu 730900, China
| | - Huairong Zhou
- School
of Petrochemical Engineering, Lanzhou University
of Technology, Lanzhou, Gansu 730050, China
- Key
Laboratory of Low Carbon Energy and Chemical Engineering of Gansu
Province, Lanzhou, Gansu 730050, China
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Holt RA, Seybold PG. Computational Estimation of the Acidities of Pyrimidines and Related Compounds. Molecules 2022; 27:385. [PMID: 35056699 PMCID: PMC8782049 DOI: 10.3390/molecules27020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 01/01/2022] [Indexed: 12/02/2022] Open
Abstract
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.
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Affiliation(s)
| | - Paul G. Seybold
- Department of Chemistry, Wright State University, Dayton, OH 45435, USA;
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Morency M, Néron S, Iftimie R, Wuest JD. Predicting p Ka Values of Quinols and Related Aromatic Compounds with Multiple OH Groups. J Org Chem 2021; 86:14444-14460. [PMID: 34613729 DOI: 10.1021/acs.joc.1c01279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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 pKa values must be known. Methods that can predict the pKa 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 pKa values and calculated differences in energy between quinols and their deprotonated forms. Simple adjustments allow reliable predictions of pKa 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 pKa 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.
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Affiliation(s)
- Mathieu Morency
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Sébastien Néron
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - Radu Iftimie
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
| | - James D Wuest
- Département de Chimie, Université de Montréal, Montréal, Québec H2V 0B3, Canada
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Wang Y, Lin Z, Zhang H, Liu Q, Yu J, Liu J, Chen R, Zhu J, Wang J. Anti-bacterial and super-hydrophilic bamboo charcoal with amidoxime modified for efficient and selective uranium extraction from seawater. J Colloid Interface Sci 2021; 598:455-463. [PMID: 33930749 DOI: 10.1016/j.jcis.2021.03.154] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022]
Abstract
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' pKa 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 (Eads = -36.56 eV). Benefiting from the superior performance and selectivity, the AOOBCH is a potential candidate for UES.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Zaiwen Lin
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Hongsen Zhang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China.
| | - Qi Liu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; HIT (Hainan) Military-Civilian Integration Innovation Research Institute Co. Ltd, Hainan 572427, China; Harbin Engineering University Capital Management Co. Ltd, Harbin 150001, China
| | - Jing Yu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Jingyuan Liu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Rongrong Chen
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; Institute of Advanced Marine Materials, Harbin Engineering University, 150001, China
| | - Jiahui Zhu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China
| | - Jun Wang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, China; Institute of Advanced Marine Materials, Harbin Engineering University, 150001, China; Harbin Engineering University Capital Management Co. Ltd, Harbin 150001, China.
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