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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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Fu B, Nazemi A, Levin BJ, Yang Z, Kulik HJ, Balskus EP. Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer. J Am Chem Soc 2022; 144:11110-11119. [PMID: 35704859 PMCID: PMC9248008 DOI: 10.1021/jacs.1c13580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Gut microbial decarboxylation
of amino acid-derived arylacetates
is a chemically challenging enzymatic transformation which generates
small molecules that impact host physiology. The glycyl radical enzyme
(GRE) indoleacetate decarboxylase from Olsenella uli (Ou IAD) performs the non-oxidative radical decarboxylation
of indole-3-acetate (I3A) to yield skatole, a disease-associated metabolite
produced in the guts of swine and ruminants. Despite the importance
of IAD, our understanding of its mechanism is limited. Here, we characterize
the mechanism of Ou IAD, evaluating previously proposed
hypotheses of: (1) a Kolbe-type decarboxylation reaction involving
an initial 1-e– oxidation of the carboxylate of
I3A or (2) a hydrogen atom abstraction from the α-carbon of
I3A to generate an initial carbon-centered radical. Site-directed
mutagenesis, kinetic isotope effect experiments, analysis of reactions
performed in D2O, and computational modeling are consistent
with a mechanism involving initial hydrogen atom transfer. This finding
expands the types of radical mechanisms employed by GRE decarboxylases
and non-oxidative decarboxylases, more broadly. Elucidating the mechanism
of IAD decarboxylation enhances our understanding of radical enzymes
and may inform downstream efforts to modulate this disease-associated
metabolism.
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Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Levin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
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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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Baldasare CA, Seybold PG. Computational Estimation of the Aqueous Acidities of Alcohols, Hydrates, and Enols. J Phys Chem A 2021; 125:3600-3605. [PMID: 33891821 DOI: 10.1021/acs.jpca.1c01330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alcohols are ubiquitous chemical species, and their acid dissociation constants are critical properties in many applications. It is useful to have a reliable and convenient computational procedure for estimating these acidities. Here we describe a quantitative structure-activity relationship (QSAR) for the pKas of alcohols in aqueous solution employing density functional theory computations at the B3LYP/6-31+G(d,p) level with the CPCM implicit solvent model for the aqueous solutions. For the pKas, the energy difference in solution between the parent compound and the anion, ΔE(H2O), was used as a single descriptor. High quality QSAR equations are obtained both for the gas-phase Gibbs energy changes (ΔGr0s, R2 = 0.9764) and the aqueous pKas (R2 = 0.9594). It is shown that the aqueous equation can also be used to estimate the pKas of fluorinated alcohols, hydrates formed by carbonyl compounds in aqueous solution, and enols that appear as minor components in keto-enol equilibria.
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Affiliation(s)
- Corey A Baldasare
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
| | - Paul G Seybold
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
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Anastasiadi RM, Berti F, Colomban S, Tavagnacco C, Navarini L, Resmini M. Simultaneous Quantification of Antioxidants Paraxanthine and Caffeine in Human Saliva by Electrochemical Sensing for CYP1A2 Phenotyping. Antioxidants (Basel) 2020; 10:antiox10010010. [PMID: 33374269 PMCID: PMC7823619 DOI: 10.3390/antiox10010010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
The enzyme CYP1A2 is responsible for the metabolism of numerous antioxidants in the body, including caffeine, which is transformed into paraxanthine, its main primary metabolite. Both molecules are known for their antioxidant and pro-oxidant characteristics, and the paraxanthine-to-caffeine molar ratio is a widely accepted metric for CYP1A2 phenotyping, to optimize dose–response effects in individual patients. We developed a simple, cheap and fast electrochemical based method for the simultaneous quantification of paraxanthine and caffeine in human saliva, by differential pulse voltammetry, using an anodically pretreated glassy carbon electrode. Cyclic voltammetry experiments revealed for the first time that the oxidation of paraxanthine is diffusion controlled with an irreversible peak at ca. +1.24 V (vs. Ag/AgCl) in a 0.1 M H2SO4 solution, and that the mechanism occurs via the transfer of two electrons and two protons. The simultaneous quantification of paraxanthine and caffeine was demonstrated in 0.1 M H2SO4 and spiked human saliva samples. In the latter case, limits of detection of 2.89 μM for paraxanthine and 5.80 μM for caffeine were obtained, respectively. The sensor is reliable, providing a relative standard deviation within 7% (n = 6). Potential applicability of the sensing platform was demonstrated by running a small scale trial on five healthy volunteers, with simultaneous quantification by differential pulse voltammetry (DPV) of paraxanthine and caffeine in saliva samples collected at 1, 3 and 6 h postdose administration. The results were validated by ultra-high pressure liquid chromatography and shown to have a high correlation factor (r = 0.994).
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Affiliation(s)
- Rozalia-Maria Anastasiadi
- Department of Chemistry, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Correspondence: (R.-M.A.); (M.R.)
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (F.B.); (C.T.)
| | - Silvia Colomban
- Aromalab, illycaffè S.p.A., Area Science Park, Localita’ Padriciano 99, 34149 Trieste, Italy; (S.C.); (L.N.)
| | - Claudio Tavagnacco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (F.B.); (C.T.)
| | - Luciano Navarini
- Aromalab, illycaffè S.p.A., Area Science Park, Localita’ Padriciano 99, 34149 Trieste, Italy; (S.C.); (L.N.)
| | - Marina Resmini
- Department of Chemistry, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Correspondence: (R.-M.A.); (M.R.)
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Raczyńska ED, Kurpiewski J, Igielska M, Kamińska B. Quantitative description of bond lengths alternation for caffeine−effects of ionization, proton-transfer, and noncovalent interaction. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Raczyńska ED, Gal JF, Maria PC, Kamińska B, Igielska M, Kurpiewski J, Juras W. Purine tautomeric preferences and bond-length alternation in relation with protonation-deprotonation and alkali metal cationization. J Mol Model 2020; 26:93. [PMID: 32248379 PMCID: PMC7256107 DOI: 10.1007/s00894-020-4343-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/05/2020] [Indexed: 11/03/2022]
Abstract
Quantum chemical calculations were carried out for deprotonated (P-) and protonated purine (PH+) and for adducts with one alkali metal cation (P-M+ and PM+, where M+ is Li+ or Na+) in the gas phase {B3LYP/6-311+G(d,p)}, a model of perfectly apolar environment, and for selected structures in aqueous solution {PCM(water)//B3LYP/6-311+G(d,p)}, a reference polar medium for biological studies. All potential isomers of purine derivatives were considered, the favored structures indicated, and the preferred sites for protonation/deprotonation and cationization reactions determined. Proton and metal cation basicities of purine in the gas phase were discussed and compared with those of imidazole and pyrimidine. Bond-length alternations in the P, PH+, P-M+, and PM+ forms were quantitatively measured using the harmonic oscillator model of electron delocalization (HOMED) indices and compared with those for P. Variations of the HOMED values when proceeding from the purine structural building blocks, pyrimidine and imidazole, to the bicyclic purine system were also examined. Generally, the isolated NH isomers exhibit a strongly delocalized π-system (HOMED > 0.8). Deprotonation slightly increases the HOMED values, whereas protonation and cationization change the HOMED indices in different way. For bidentate M+-adducts, the HOMED values are larger than 0.9 like for the largely delocalized P-. The HOMED values correlate well in a comprehensive relationship with the relative Gibbs energies (ΔG) calculated for individual isomers whatever the purine form is, neutral, protonated, or cationized. When PCM-DFT model was utilized for P-, PH+, PM+, and P-M+ (M+ = Li+) both electron delocalization and relative stability are different from those for the molecules in vacuo. The solvation effects cause a slight increase in HOMEDs, whereas the ΔEs decrease, but in different ways. Hence, contribution of particular isomers in the isomeric mixtures of PH+, PM+, and P-M+ also varies. HOMED variations for the favored neutral, deprotonated, protonated, and lithiated forms of purine in the gas phase and aqueous solution.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland.
| | - Jean-François Gal
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Pierre-Charles Maria
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Beata Kamińska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Małgorzata Igielska
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Julian Kurpiewski
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Weronika Juras
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
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Baldasare CA, Seybold PG. Computational Estimation of the Gas-Phase and Aqueous Acidities of Carbon Acids. J Phys Chem A 2020; 124:2152-2159. [PMID: 32058710 DOI: 10.1021/acs.jpca.9b11964] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon acids are compounds which ionize by dissociating along carbon-hydrogen bonds. Although commonly noted for the extremely low acidities of some members of this class, these compounds in fact display a wide range of pKas and upon proper substitution can even form strong acids. This study employs density functional theory to estimate the gas-phase acidities (ΔG°s) of these compounds and applies a quantitative structure-activity relationship (QSAR) method at the B3LYP/6-31+G** level with the CPCM aqueous solvent model to estimate their aqueous pKas. For the latter study, the energy difference ΔE(H2O) in water between the parent compounds and their dissociation products was used as a single parameter. Good quality QSAR regression equations were obtained for both the gas-phase (R2 = 0.9905) and aqueous (R2 = 0.9647) dissociations. These equations should be useful for the estimation of missing pKas for compounds in this class. A general discussion of the features affecting the pKas of these compounds is also given.
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Affiliation(s)
- Corey A Baldasare
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
| | - Paul G Seybold
- Department of Chemistry, Wright State University, Dayton, Ohio 45435, United States
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