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Csizi KS, Reiher M. Automated preparation of nanoscopic structures: Graph-based sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates. J Comput Chem 2024; 45:761-776. [PMID: 38124290 DOI: 10.1002/jcc.27276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for pK a prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in Brunken and Reiher (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost.
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Affiliation(s)
- Katja-Sophia Csizi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Markus Reiher
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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2
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Li X, Liu Y. Multiscale Study on the Intramolecular C-S Bond Formation Catalyzed by P450 Monooxygenase CxnD Involved in the Biosynthesis of Chuangxinmycin: The Critical Roles of Noncrystal Water Molecule and Conformational Change. Inorg Chem 2024; 63:4086-4098. [PMID: 38376137 DOI: 10.1021/acs.inorgchem.3c03748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Cytochrome P450 monooxygenase CxnD catalyzes intramolecular C-S bond formation in the biosynthesis of chuangxinmycin, which is representative of the synthesis of sulfur-containing natural heterocyclic compounds. The intramolecular cyclization usually requires the activation of two reaction sites and a large conformational change; thus, illuminating its detailed reaction mechanism remains challengeable. Here, the reaction pathway of CxnD-catalyzed C-S bond formation was clarified by a series of calculations, including Gaussian accelerated molecular dynamics simulations and quantum mechanical-molecular mechanical calculations. Our results revealed that the C-S formation follows a diradical coupling mechanism. CxnD first employs Cpd I to abstract the hydrogen atom from the imino group of the indole ring, and then, the resulted Cpd II further extracts another hydrogen atom from the thiol group of the side chain to afford a diradical intermediate, in which a noncrystal water molecule entering into the active site after the formation of Cpd I was proved to play an indispensable role. Moreover, the diradical intermediate cannot directly perform the coupling reaction. It should first undergo a series of conformational changes leading to the proximity of two reaction sites. It is the flexibility of the active site of the enzyme and the side chain of the substrate that makes the diradical coupling to be successful.
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Affiliation(s)
- Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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3
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Wolf S, Domes R, Domes C, Frosch T. Spectrally Resolved and Highly Parallelized Raman Difference Spectroscopy for the Analysis of Drug-Target Interactions between the Antimalarial Drug Chloroquine and Hematin. Anal Chem 2024; 96:3345-3353. [PMID: 38301154 PMCID: PMC10902819 DOI: 10.1021/acs.analchem.3c04231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Malaria is a severe disease caused by cytozoic parasites of the genus Plasmodium, which infiltrate and infect red blood cells. Several drugs have been developed to combat the devastating effects of malaria. Antimalarials based on quinolines inhibit the crystallization of hematin into hemozoin within the parasite, ultimately leading to its demise. Despite the frequent use of these agents, there are unanswered questions about their mechanisms of action. In the present study, the quinoline chloroquine and its interaction with the target structure hematin was investigated using an advanced, highly parallelized Raman difference spectroscopy (RDS) setup. Simultaneous recording of the spectra of hematin and chloroquine mixtures with varying compositions enabled the observation of changes in peak heights and positions based on the altered molecular structure resulting from their interaction. A shift of (-1.12 ± 0.05) cm-1 was observed in the core-size marker band ν(CαCm)asym peak position of the 1:1 chloroquine-hematin mixture compared to pure hematin. The oxidation-state marker band ν(pyrrole half-ring)sym exhibited a shift by (+0.93 ± 0.13) cm-1. These results were supported by density functional theory (DFT) calculations, indicating a hydrogen bond between the quinolinyl moiety of chloroquine and the oxygen atom of ferric protoporphyrin IX hydroxide (Fe(III)PPIX-OH). The consequence is a reduced electron density within the porphyrin moiety and an increase in its core size. This hypothesis provided further insights into the mechanism of hemozoin inhibition, suggesting chloroquine binding to the monomeric form of hematin, thereby preventing its further crystallization to hemozoin.
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Affiliation(s)
- Sebastian Wolf
- Leibniz Institute of Photonic Technology, 07745 Jena, Germany
| | - Robert Domes
- Leibniz Institute of Photonic Technology, 07745 Jena, Germany
| | - Christian Domes
- Leibniz Institute of Photonic Technology, 07745 Jena, Germany
| | - Torsten Frosch
- Biophotonics and Biomedical Engineering Group, Technical University Darmstadt, Merckstr. 25, 64283 Darmstadt, Germany
- Leibniz Institute of Photonic Technology, 07745 Jena, Germany
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4
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Pezzola S, Venanzi M, Galloni P, Conte V, Sabuzi F. Easy to Use DFT Approach for Computational pKa Determination of Carboxylic Acids. Chemistry 2024; 30:e202303167. [PMID: 37902415 DOI: 10.1002/chem.202303167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 10/31/2023]
Abstract
In pKa computational determination, the challenge in exploring and fostering new methodologies and approaches goes in parallel with the amelioration of computational performances. In this paper a "ready to use methodology" has been compared to other strategies, such as the re-shaping in solvation cavity (Bondi radius re-shaping), wanting to assess its reliability in predicting the pKa of a broad list of carboxylic acids. Thus, the functionals B3LYP and CAM-B3LYP have been selected, using SMD as continuum solvation model. Exploiting our previous results, two water molecules were made explicit on the reaction centre. Data show that our model (CAM-B3LYP/2H2 O) is capable to accurately predict pKa, leading to mean absolute error (MAE) values lower than 0.5. Noteworthy, good results were achieved in computing the pKa of substituents bearing nitro and cyano groups. Focusing on B3LYP, eventually remarkable outputs were obtained only when Bondi correction was applied to the complex with two water molecules. Hence, massive outcomes were obtained in foreseeing the trichloro and trifluoro acetic acid pKa. These findings demonstrated that no complex level of theory nor external factor is required to accurately predict carboxylic acids pKa, with MAE well below 0.5 units.
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Affiliation(s)
- Silvia Pezzola
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133, Roma, Italy
| | - Mariano Venanzi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133, Roma, Italy
| | - Pierluca Galloni
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133, Roma, Italy
| | - Valeria Conte
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133, Roma, Italy
| | - Federica Sabuzi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133, Roma, Italy
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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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Torralba-Sanchez TL, Di Toro DM, Dmitrenko O, Murillo-Gelvez J, Tratnyek PG. Modeling the Partitioning of Anionic Carboxylic and Perfluoroalkyl Carboxylic and Sulfonic Acids to Octanol and Membrane Lipid. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:2317-2328. [PMID: 37439660 DOI: 10.1002/etc.5716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Perfluoroalkyl carboxylic and sulfonic acids (PFCAs and PFSAs, respectively) have low acid dissociation constant values and are, therefore, deprotonated under most experimental and environmental conditions. Hence, the anionic species dominate their partitioning between water and organic phases, including octanol and phospholipid bilayers which are often used as model systems for environmental and biological matrices. However, data for solvent-water (SW) and membrane-water partition coefficients of the anion species are only available for a few per- and polyfluoroalkyl substances (PFAS). In the present study, an equation is derived using a Born-Haber cycle that relates the partition coefficients of the anions to those of the corresponding neutral species. It is shown via a thermodynamic analysis that for carboxylic acids (CAs), PFCAs, and PFSAs, the log of the solvent-water partition coefficient of the anion, log KSW (A- ), is linearly related to the log of the solvent-water partition coefficient of the neutral acid, log KSW (HA), with a unity slope and a solvent-dependent but solute-independent intercept within a PFAS (or CA) family. This finding provides a method for estimating the partition coefficients of PFCAs and PFSAs anions using the partition coefficients of the neutral species, which can be reliably predicted using quantum chemical methods. In addition, we have found that the neutral octanol-water partition coefficient, log KOW , is linearly correlated to the neutral membrane-water partition coefficient, log KMW ; therefore, log KOW , being a much easier property to estimate and/or measure, can be used to predict the neutral log KMW . Application of this approach to KOW and KMW for PFCAs and PFSAs demonstrates the utility of this methodology for evaluating reported experimental data and extending anion property data for chain lengths that are unavailable. Environ Toxicol Chem 2023;42:2317-2328. © 2023 SETAC.
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Affiliation(s)
| | - Dominic M Di Toro
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Olga Dmitrenko
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Jimmy Murillo-Gelvez
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Paul G Tratnyek
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, Oregon, USA
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7
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Medved' M, Di Donato M, Buma WJ, Laurent AD, Lameijer L, Hrivnák T, Romanov I, Tran S, Feringa BL, Szymanski W, Woolley GA. Mechanistic Basis for Red Light Switching of Azonium Ions. J Am Chem Soc 2023; 145:19894-19902. [PMID: 37656631 DOI: 10.1021/jacs.3c06157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Azonium ions formed by the protonation of tetra-ortho-methoxy-substituted aminoazobenzenes photoisomerize with red light under physiological conditions. This property makes them attractive as molecular tools for the photocontrol of physiological processes, for example, in photopharmacology. However, a mechanistic understanding of the photoisomerization process and subsequent thermal relaxation is necessary for the rational application of these compounds as well as for guiding the design of derivatives with improved properties. Using a combination of sub-ps/ns transient absorption measurements and quantum chemical calculations, we show that the absorption of a photon by the protonated E-H+ form of the photoswitch causes rapid (ps) isomerization to the protonated Z-H+ form, which can also absorb red light. Proton transfer to solvent then occurs on a microsecond time scale, leading to an equilibrium between Z and Z-H+ species, the position of which depends on the solution pH. Whereas thermal isomerization of the neutral Z form to the neutral E form is slow (∼0.001 s-1), thermal isomerization of Z-H+ to E-H+ is rapid (∼100 s-1), so the solution pH also governs the rate at which E/E-H+ concentrations are restored after a light pulse. This analysis provides the first complete mechanistic picture that explains the observed intricate photoswitching behavior of azonium ions at a range of pH values. It further suggests features of azonium ions that could be targeted for improvement to enhance the applicability of these compounds for the photocontrol of biomolecules.
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Affiliation(s)
- Miroslav Medved'
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University, Šlechtitelů 241/27, Olomouc, 783 71 Czech Republic
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 974 01 Banská Bystrica, Slovak Republic
| | - Mariangela Di Donato
- LENS, European Laboratory for Non-Linear Spectroscopy, via N. Carrara 1, 50019 Sesto Fiorentino, FI, Italy
- CNR-ICCOM, via Madonna del Piano 10, 50019 Sesto Fiorentino, FI, Italy
| | - Wybren Jan Buma
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Adèle D Laurent
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Lucien Lameijer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AF Groningen, The Netherlands
- Medical Imaging Center, University Medical Center Groningen, University of Groningen Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - Tomáš Hrivnák
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, 974 01 Banská Bystrica, Slovak Republic
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovak Republic
| | - Ivan Romanov
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Susannah Tran
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto M5S 3H6, Canada
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AF Groningen, The Netherlands
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AF Groningen, The Netherlands
- Medical Imaging Center, University Medical Center Groningen, University of Groningen Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto M5S 3H6, Canada
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Reyna-Luna J, Soriano-Agueda L, Vera CJ, Franco-Pérez M. Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn 2+, Cu 2+, and VO 2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models. J Comput Aided Mol Des 2023:10.1007/s10822-023-00506-4. [PMID: 37245168 DOI: 10.1007/s10822-023-00506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
We present a computational strategy based on thermodynamic cycles to predict and describe the chemical equilibrium between the 3d-transition metal ions Zn2+, Cu2+, and VO2+ and the widely used antineoplastic drug doxorubicin. Our method involves benchmarking a theoretical protocol to compute gas-phase quantities using DLPNO Coupled-Cluster calculations as reference, followed by estimating solvation contributions to the reaction Gibbs free energies using both explicit partial (micro)solvation steps for charged solutes and neutral coordination complexes, as well as a continuum solvation procedure for all solutes involved in the complexation process. We rationalized the stability of these doxorubicin-metal complexes by inspecting quantities obtained from the topology of their electron densities, particularly the bond critical points and non-covalent interaction index. Our approach allowed us to identify representative species in solution phase, infer the most likely complexation process for each case, and identify key intramolecular interactions involved in the stability of these compounds. To the best of our knowledge, this is the first study reporting thermodynamic constants for the complexation of doxorubicin with transition metal ions. Unlike other methods, our procedure is computationally affordable for medium-sized systems and provides valuable insights even with limited experimental data. Furthermore, it can be extended to describe the complexation process between 3d-transition metal ions and other bioactive ligands.
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Affiliation(s)
- Julieta Reyna-Luna
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México
| | - Luis Soriano-Agueda
- Donostia International Physics Center (DIPC), 20018, Donostia, Euskadi, Spain
| | - Christiaan Jardinez Vera
- Laboratorio de Modelado y Simulación Computacional en Nanomedicina, Escuela Superior de Apan, Universidad Autónoma del Estado de Hidalgo, Carretera Apan-Calpulalpan S/N, Colonia, 43920, Chimalpa Tlalayote, Hgo, México
| | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México.
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Domes R, Frosch T. Investigations on the Novel Antimalarial Ferroquine in Biomimetic Solutions Using Deep UV Resonance Raman Spectroscopy and Density Functional Theory. Anal Chem 2023; 95:7630-7639. [PMID: 37141178 DOI: 10.1021/acs.analchem.3c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Deep ultraviolet (DUV) resonance Raman experiments are performed, investigating the novel, promising antimalarial ferroquine (FQ). Two buffered aqueous solutions with pH values of 5.13 and 7.00 are used, simulating the acidic and neutral conditions inside a parasite's digestive vacuole and cytosol, respectively. To imitate the different polarities of the membranes and interior, the buffer's 1,4-dioxane content was increased. These experimental conditions should mimic the transport of the drug inside malaria-infected erythrocytes through parasitophorous membranes. Supporting density functional theory (DFT) calculations on the drug's micro-speciation were performed, which could be nicely assigned to shifts in the peak positions of resonantly enhanced high-wavenumber Raman signals at λexc = 257 nm. FQ is fully protonated in polar mixtures like the host interior and the parasite's cytoplasm or digestive vacuole (DV) and is only present as a free base in nonpolar ones, such as the host's and parasitophorous membranes. Additionally, the limit of detection (LoD) of FQ at vacuolic pH values was determined using DUV excitation wavelengths at 244 and 257 nm. By applying the resonant laser line at λexc = 257 nm, a minimal FQ concentration of 3.1 μM was detected, whereas the pre-resonant excitation wavelength 244 nm provides an LoD of 6.9 μM. These values were all up to one order of magnitude lower than the concentration found for the food vacuole of a parasitized erythrocyte.
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Affiliation(s)
- Robert Domes
- Leibniz Institute of Photonic Technology, Albert-Einstein Strasse 9, 07751 Jena, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, Albert-Einstein Strasse 9, 07751 Jena, Germany
- Biophotonics and Biomedical Engineering Group, Technical University Darmstadt, Merckstrasse 25, 64283 Darmstadt, Germany
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An Accurate Approach for Computational pKa Determination of Phenolic Compounds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238590. [PMID: 36500683 PMCID: PMC9736058 DOI: 10.3390/molecules27238590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
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.
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11
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Tretyakov E, Fedyushin P, Bakuleva N, Korlyukov A, Dorovatovskii P, Gritsan N, Dmitriev A, Akyeva A, Syroeshkin M, Stass D, Zykin M, Efimov N, Luneau D. Series of Fluorinated Benzimidazole-Substituted Nitronyl Nitroxides: Synthesis, Structure, Acidity, Redox Properties, and Magnetostructural Correlations. J Org Chem 2022. [PMID: 36198196 DOI: 10.1021/acs.joc.2c01793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A special series of nitronyl nitroxides was synthesized: 2-(benzimidazol-2'-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyls mono-, di-, tri-, or tetrafluorinated on the benzene ring. The structure of all paramagnets was unambiguously confirmed by single-crystal X-ray diffraction. It was found that in crystals, the radicals are assembled into chains due to intermolecular H-bonds between the benzimidazole moiety (H-bond donor) and the nitronyl nitroxide group or benzimidazole ring (H-bond acceptor). The magnetic properties of nitronyl nitroxides depend on the type of binding of radicals by H-bonds. The magnetic motif of 4-fluoro-, 5-fluoro-, 4,6-difluoro-, 4,5,6-trifluoro-, 4,5,7-trifluoro-, and 4,5,6,7-tetrafluoro-derivatives, as well as the nonfluorinated compound, consists of ferromagnetic chains (J/kB ≈ 20-40 K) formed by the McConnell type I mechanism. In the 5,6-difluoro- and 4,5-difluoro-derivatives, the distances between the paramagnetic centers are large, as a result of which the exchange interactions are weak. According to cyclic voltammetry, paramagnets are oxidized reversibly, while their reduction is a quasi-reversible electron transfer (EC mechanism); experimental redox potentials of radicals correlate well with the calculated values. Quantum chemical assessment of the acidity of benzimidazolyl-substituted nitronyl nitroxides revealed that the introduction of fluorine atoms into the benzene ring enhances the acidity of the paramagnets by more than 5 orders of magnitude.
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Affiliation(s)
- Evgeny Tretyakov
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky Prospect 47, Moscow119991, Russia
| | - Pavel Fedyushin
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky Prospect 47, Moscow119991, Russia
| | - Nadejda Bakuleva
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky Prospect 47, Moscow119991, Russia
| | - Alexander Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds, 28 Vavilov Street, Moscow119991, Russia
| | | | - Nina Gritsan
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya Str., Novosibirsk630090, Russia
| | - Alexey Dmitriev
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya Str., Novosibirsk630090, Russia
| | - Anna Akyeva
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky Prospect 47, Moscow119991, Russia
| | - Mikhail Syroeshkin
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky Prospect 47, Moscow119991, Russia
| | - Dmitri Stass
- V. V. Voevodsky Institute of Chemical Kinetics and Combustion, 3 Institutskaya Str., Novosibirsk630090, Russia
| | - Mikhail Zykin
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Leninsky Prospect 31, Moscow119991, Russia
| | - Nikolay Efimov
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Leninsky Prospect 31, Moscow119991, Russia
| | - Dominique Luneau
- Laboratoire des Multimatériaux et Interfaces (UMR 5615), Université Claude Bernard Lyon-1, Campus de La Doua, Villeurbanne Cedex69622, France
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12
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Rodriguez SA, Tran JV, Sabatino SJ, Paluch AS. Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models. J Comput Aided Mol Des 2022; 36:687-705. [PMID: 36117236 DOI: 10.1007/s10822-022-00474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022]
Abstract
Blind predictions of octanol/water partition coefficients and pKa at 298.15 K for 22 drug-like compounds were made for the SAMPL7 challenge. Octanol/water partition coefficients were predicted from solvation free energies computed using electronic structure calculations with the SM12, SM8 and SMD solvation models. Within these calculations we compared the use of gas- and solution-phase optimized geometries of the solute. Based on these calculations we found that in general the use of solution phase-optimized geometries increases the affinity of the solutes for water as compared to octanol, with the use of gas-phase optimized geometries resulting in the better agreement with experiment. The pKa is computed using the direct approach, scaled solvent-accessible surface model, and the inclusion of an explicit water molecule, where the latter two methods have previously been shown to offer improved predictions as compared to the direct approach. We find that the use of an explicit water molecule provides superior predictions, and that the predicted macroscopic pKa is sensitive to the employed microstates.
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Affiliation(s)
- Sergio A Rodriguez
- Instituto de Ciencias Químicas, Facultad de Agronomía y Agroindustrias, Universidad Nacional de Santiago del Estero, CONICET, Santiago del Estero, Argentina
| | - Jasmine Vy Tran
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Spencer J Sabatino
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA.
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13
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Mai BK, Neris NM, Yang Y, Liu P. C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp 3)-H Amination: A Combined Computational and Experimental Investigation. J Am Chem Soc 2022; 144:11215-11225. [PMID: 35583461 DOI: 10.1021/jacs.2c02283] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.
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Affiliation(s)
- Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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14
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Patel C, Roy D. Octanol-Water Partition Coefficients of Fluorinated Drug Molecules with Continuum Solvation Models. J Phys Chem A 2022; 126:4185-4190. [PMID: 35748869 DOI: 10.1021/acs.jpca.2c02172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we have examined the efficiency of continuum solvation models, used with density functional theory methods, in calculating octanol-water partition coefficients (logP) of 56 fluorine containing drug molecules. The solvation model based on density model computed logP values that are in good agreement with the benchmark values. The conductor-like polarizable continuum models computed results have issues in predicting correct trend, often with reversal of sign from benchmark. The choice of basis set does not show significant effect, and the selection of atomic radii affects geometry convergence during calculations.
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Affiliation(s)
- Chandan Patel
- Department of Applied Sciences, College of Engineering, Wellesley Road, Shivajinagar, Pune 411005, India
| | - Dipankar Roy
- Department of Biological Sciences, University of Alberta, CW 405, Biological Sciences Bldg., Edmonton, Alberta T6G 2E9, Canada
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15
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Costa AM, Cascales V, Castro-Alvarez A, Vilarrasa J. Computational Study of the Stability of Pyrrolidine-Derived Iminium Ions: Exchange Equilibria between Iminium Ions and Carbonyl Compounds. ACS OMEGA 2022; 7:18247-18258. [PMID: 35694469 PMCID: PMC9178767 DOI: 10.1021/acsomega.1c07020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The tendency of carbonyl compounds to form iminium ions by reaction with pyrrolidine or chiral pyrrolidine derivatives (in other words, the relative stability to hydrolysis of these iminium ions) has been computationally examined, mainly using the M06-2X/6-311+G(d,p) method. We have thus obtained the equilibrium positions for R-CH=O + CH2=CH-CH=N+R2* → R-CH=N+R2* + CH2=CH-CH=O reactions and for related exchanges. In these exchanges, there is a transfer of a secondary amine between two carbonyl compounds. Their relative energies may be used to predict which iminium species can be predominantly formed when two or more carbonyl groups are present in a reaction medium. In the catalytic Michael additions of nucleophiles to iminium ions arising from conjugated enals, dienals, and trienals, if the formation of the new Nu-C bond is favorable, the chances of amino-catalyzed reactions to efficiently proceed, with high conversions, depend on the calculated energy values for these exchange equilibria, where the iminium tetrafluoroborates of the adducts (final iminium intermediates) must be more prone to hydrolysis than the initial iminium tetrafluoroborates. The density functional theory (DFT) calculations indicate that the MacMillan catalysts and related oxazolidinones are especially suitable in this regard.
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16
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Durán R, Herrera B. Theoretical study of the substituent effect on the O–H insertion reaction of copper carbenoids. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02876-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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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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18
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Angizi S, Yu EYC, Dalmieda J, Saha D, Selvaganapathy PR, Kruse P. Defect Engineering of Graphene to Modulate pH Response of Graphene Devices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12163-12178. [PMID: 34624190 DOI: 10.1021/acs.langmuir.1c02088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Graphene-based pH sensors are a robust, durable, sensitive, and scalable approach for the sensitive detection of pH in various environments. However, the mechanisms through which graphene responds to pH variations are not well-understood yet. This study provides a new look into the surface science of graphene-based pH sensors to address the existing gaps and inconsistencies among the literature concerning sensing response, the role of defects, and surface/solution interactions. Herein, we demonstrate the dependence of the sensing response on the defect density level of graphene, measured by Raman spectroscopy. At the crossover point (ID/IG = 0.35), two countervailing mechanisms balance each other out, separating two regions where either a surface defect induced (negative slope) or a double layer induced (positive slope) response dominates. For ratios above 0.35, the pH-dependent induction of charges at surface functional groups (both pH-sensitive and nonsensitive groups) dominates the device response. Below a ratio of 0.35, the response is dominated by the modulation of charge carriers in the graphene due to the electric double layer formed from the interaction between the graphene surface and the electrolyte solution. Selective functionalization of the surface was utilized to uncover the dominant acid-base interactions of carboxyl and amine groups at low pH while hydroxyl groups control the high pH range sensitivity. The overall pH-sensing characteristics of the graphene will be determined by the balance of these two mechanisms.
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Affiliation(s)
- Shayan Angizi
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 Canada
| | - Eugene Yat Chun Yu
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 Canada
| | - Johnson Dalmieda
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 Canada
| | - Dipankar Saha
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 Canada
| | - P Ravi Selvaganapathy
- Department of Mechanical Engineering, McMaster University, Hamilton, L8S 4M1, Canada
| | - Peter Kruse
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1 Canada
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19
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Vassetti D, Oǧuz IC, Labat F. Generalizing Continuum Solvation in Crystal to Nonaqueous Solvents: Implementation, Parametrization, and Application to Molecules and Surfaces. J Chem Theory Comput 2021; 17:6432-6448. [PMID: 34488338 DOI: 10.1021/acs.jctc.1c00611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of a generalized finite-difference Poisson-Boltzmann (FDPB) continuum solvation model based on a self-consistent reaction field treatment to nonaqueous solvents. Implementation and reparametrization of the cavitation, dispersion, and structural (CDS) effects nonelectrostatic model are presented in CRYSTAL, with applications to both finite and infinite periodic systems. For neutral finite systems, computed errors with respect to available experimental data on free energies of solvation of 2523 solutes in 91 solvents, as well as 144 transfer energies from water to 14 organic solvents are on par with the reference SM12 solvation model for which the CDS parameters have been developed. Calculations performed on a TiO2 anatase surface and compared to VASPsol data revealed an overall very good agreement of computed solvation energies, surface energies, as well as band structure changes upon solvation in three different solvents, validating the general applicability of the reparametrized FDPB approach to neutral nonperiodic and periodic solutes in aqueous and nonaqueous solvents. For ionic species, while the reparametrized CDS model led to large errors on free energies of solvation of anions, addition of a corrective term based on Abraham's acidity of the solvent significantly improved the accuracy of the proposed continuum solvation model, leading to errors on aqueous pKa of a test set of 83 solutes divided by a factor of 4 compared to the reference solvation model based on density (SMD). Overall, therefore, these encouraging results demonstrate that the generalized FDPB continuum solvation model can be applied to a broad range of solutes in various solvents, ranging from finite neutral or charged solutes to extended periodic surfaces.
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Affiliation(s)
- Dario Vassetti
- Chemical Theory and Modelling Group, Institute of Chemistry for Life and Health Sciences, Chimie ParisTech, PSL University, CNRS, F-75005 Paris, France
| | - Ismail Can Oǧuz
- Chemical Theory and Modelling Group, Institute of Chemistry for Life and Health Sciences, Chimie ParisTech, PSL University, CNRS, F-75005 Paris, France
| | - Frédéric Labat
- Chemical Theory and Modelling Group, Institute of Chemistry for Life and Health Sciences, Chimie ParisTech, PSL University, CNRS, F-75005 Paris, France
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20
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Lawler R, Liu YH, Majaya N, Allam O, Ju H, Kim JY, Jang SS. DFT-Machine Learning Approach for Accurate Prediction of p Ka. J Phys Chem A 2021; 125:8712-8722. [PMID: 34554744 DOI: 10.1021/acs.jpca.1c05031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we propose a novel method of pKa prediction in a diverse set of acids, which combines density functional theory (DFT) method with machine learning (ML) methods. First, the DFT method with B3LYP/6-31++G**/SM8 is used to predict pKa, yielding a mean absolute error of 1.85 pKa units. Subsequently, such pKa values predicted from the DFT method are employed as one of 10 molecular descriptors for developing ML models trained on experimental data. Kernel Ridge Regression (KRR), Gaussian Process Regression, and Artificial Neural Network are optimized using three Pipelines: Pipeline 1 involving only hyperparameter optimization (HPO), Pipeline 2 involving HPO followed by a relative contribution analysis (RCA) and recursive feature elimination (RFE), and Pipeline 3 involving HPO followed by RCA and RFE on an expanded set of composite features. Finally, it is demonstrated that KRR with Pipeline 3 yields optimal pKa prediction at an MAE of 0.60 log units. This algorithm was then utilized to predict the pKa of 37 novel acids. The two most important features were determined to be the number of hydrogen atoms in the molecule and the degree of oxidation of the acid. The predicted pKa values were documented for future reference.
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Affiliation(s)
- Robin Lawler
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States.,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yao-Hao Liu
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Nessa Majaya
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Omar Allam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States.,G. W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hyunchul Ju
- Department of Mechanical Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Jin Young Kim
- Center for Hydrogen Fuel Cell Research, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Seung Soon Jang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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21
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Eckert P, Johs A, Semrau JD, DiSpirito AA, Richardson J, Sarangi R, Herndon E, Gu B, Pierce EM. Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2. J Inorg Biochem 2021; 223:111496. [PMID: 34271330 PMCID: PMC10569158 DOI: 10.1016/j.jinorgbio.2021.111496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as "methanobactins," which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for HgS coordination, and TD-DFT suggests a tetrahedral model for Zn2+ and Cd2+. We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.
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Affiliation(s)
- Peter Eckert
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeremy D Semrau
- Civil & Environmental Engineering, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jocelyn Richardson
- Structural Molecular Biology Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94306, USA
| | - Ritimukta Sarangi
- Structural Molecular Biology Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94306, USA
| | - Elizabeth Herndon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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22
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Chen G, Huang S, Shen Y, Kou X, Ma X, Huang S, Tong Q, Ma K, Chen W, Wang P, Shen J, Zhu F, Ouyang G. Protein-directed, hydrogen-bonded biohybrid framework. Chem 2021. [DOI: 10.1016/j.chempr.2021.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Rhodes Z, Simoska O, Dantanarayana A, Stevenson KJ, Minteer SD. Using structure-function relationships to understand the mechanism of phenazine-mediated extracellular electron transfer in Escherichia coli. iScience 2021; 24:103033. [PMID: 34522869 PMCID: PMC8426270 DOI: 10.1016/j.isci.2021.103033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/19/2021] [Accepted: 08/20/2021] [Indexed: 10/26/2022] Open
Abstract
Phenazines are redox-active nitrogen-containing heterocyclic compounds that can be produced by either bacteria or synthetic approaches. As an electron shuttles (mediators), phenazines are involved in several biological processes facilitating extracellular electron transfer (EET). Therefore, it is of great importance to understand the structural and electronic properties of phenazines that promote EET in microbial electrochemical systems. Our previous study experimentally investigated a phenazine-based library as an exogenous mediator system to facilitate EET in Escherichia coli. Herein, we combine our experimental data with density functional theory (DFT) calculations and multivariate linear regression modeling to understand the structure-function relationships in phenazine-based mediated EET. These calculations demonstrate that the computed redox properties of phenazines in lipophilic environments (e.g., cell membrane) correlate to experimental mediated current densities. Additional DFT-derived molecular properties were considered to develop a predictive model, which could be used in metabolic engineering approaches to introduce phenazines as endogenous mediators into bacteria.
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Affiliation(s)
- Zayn Rhodes
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Olja Simoska
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Keith J Stevenson
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Bolshoi Boulevard 30 Bld. 1, Moscow 121205, Russia
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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24
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Wan S, Xia S, Medford J, Durocher E, Steenwinkel TE, Rule L, Zhang Y, Luck RL, Werner T, Liu H. A ratiometric near-infrared fluorescent probe based on a novel reactive cyanine platform for mitochondrial pH detection. J Mater Chem B 2021; 9:5150-5161. [PMID: 34132313 PMCID: PMC8265329 DOI: 10.1039/d1tb00643f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A near-infrared reactive cyanine platform (probe A) was prepared by condensation of 9-chloro-1,2,3,4-tetrahydro-10-methyl-acridinium iodide with Fisher's aldehyde. A near-infrared fluorescent probe (probe B) was prepared by modifying a reactive chlorine atom of probe A with tert-butyl(2-aminoethyl)carbamate through a substitution reaction. The deprotection of the Boc group of probe B was achieved under an acidic condition, affording an amine-functionalized cyanine dye (probe C). A near-infrared ratiometric fluorescent probe (probe D) for mitochondrial pH detection was synthesized by conjugating a FRET coumarin donor to a FRET cyanine acceptor (probe C) through an amide bond connection. Probe A shows low fluorescence of 2% due to an electron-withdrawing chlorine atom, while probes B-D display high fluorescence quantum yields of 60%, 32%, and 35% in aqueous solutions containing 10% ethanol, respectively. Probes B-D show strong fluorescence with push-pull molecular structures in neutral and basic pH conditions. However, protonation of the probe's second amine at the 9-position under acidic condition disrupts the push-pull feature of the probes, resulting in fluorescence quenching of the new cyanine fluorophores. The probes can selectively stain mitochondria, while probe D was employed to detect pH changes in HeLa cells and Drosophila melanogaster first-instar larvae.
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Affiliation(s)
- Shulin Wan
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA.
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25
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Costa AM, Bosch L, Petit E, Vilarrasa J. Computational Study of the Addition of Methanethiol to 40+ Michael Acceptors as a Model for the Bioconjugation of Cysteines. J Org Chem 2021; 86:7107-7118. [PMID: 33914532 PMCID: PMC8631706 DOI: 10.1021/acs.joc.1c00349] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 12/17/2022]
Abstract
A long series of Michael acceptors are studied computationally as potential alternatives to the maleimides that are used in most antibody-drug conjugates to link Cys of mAbs with cytotoxic drugs. The products of the reaction of methanethiol (CH3SH/MeSH, as a simple model of Cys) with N-methylated ethynesulfonamide, 2-ethynylpyridinium ion, propynamide, and methyl ethynephosphonamidate (that is, with HC≡C-EWG) are predicted by the M06-2X/6-311+G(d,p) method to be thermodynamically more stable, in relation to their precursors, than that of MeSH with N-methylmaleimide and, in general, with H2C═CH-EWG; calculations with AcCysOMe and tBuSH are also included. However, for the addition of the anion (MeS-), which is the reactive species, the order changes and N-methylated 2-vinylpyridinium ion, 2,3-butadienamide, and maleimide may give more easily the anionic adducts than several activated triple bonds; moreover, the calculated ΔG⧧ values increase following the order HC≡C-SO2NHMe, N-methylmaleimide, HC≡C-PO(OMe)NHMe, and HC≡C-CONHMe. In other words, MeS- is predicted to react more rapidly with maleimides than with ethynephosphonamidates and with propynamides, in agreement with the experimental results. New mechanistic details are disclosed regarding the advantageous use of some amides, especially of ethynesulfonamides, which, however, are more prone to double additions and exchange reactions.
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Affiliation(s)
- Anna M. Costa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Lluís Bosch
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Elena Petit
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Jaume Vilarrasa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
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26
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Yan Y, Zhang Y, Xia S, Wan S, Vohs T, Tanasova M, Luck RL, Liu H. Ratiometric Near-Infrared Fluorescent Probes Based on Hemicyanine Dyes Bearing Dithioacetal and Formal Residues for pH Detection in Mitochondria. Molecules 2021; 26:molecules26072088. [PMID: 33917350 PMCID: PMC8038704 DOI: 10.3390/molecules26072088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/02/2022] Open
Abstract
Ratiometric near-infrared fluorescent probes (AH+ and BH+) have been prepared for pH determination in mitochondria by attaching dithioacetal and formal residues onto a hemicyanine dye. The reactive formyl group on probe BH+ allows for retention inside mitochondria as it can react with a protein primary amine residue to form an imine under slightly basic pH 8.0. Probes AH+ and BH+ display ratiometric fluorescent responses to pH changes through the protonation and deprotonaton of a hydroxy group in hemicyanine dyes with experimentally determined pKa values of 6.85 and 6.49, respectively. Calculated pKa values from a variety of theoretical methods indicated that the SMDBONDI method of accounting for solvent and van der Waals radii plus including a water molecule located near the site of protonation produced the closest overall agreement with the experimental values at 7.33 and 6.14 for AH+ and BH+ respectively.
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Affiliation(s)
- Yunnan Yan
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Yibin Zhang
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
| | - Shuai Xia
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Shulin Wan
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Tara Vohs
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Marina Tanasova
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
| | - Rudy L. Luck
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
| | - Haiying Liu
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA; (Y.Y.); (S.X.); (S.W.); (T.V.); (M.T.)
- Correspondence: (Y.Z.); (R.L.L.); (H.L.)
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27
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Rachuru S, Vandanapu J, Skelton AA. Theoretical Determination of pKas of P(1)-H Phospholes and their Comparison with N(1)-H Azoles. Aust J Chem 2021. [DOI: 10.1071/ch21122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
pKas of P(1)-H deprotonation of all phosphole group compounds, phosphole (C4H4PH), 1,2 and 1,3-diphospholes (C3H3PPH), 1,2,3, and 1,2,4-triphospholes (C2H2P2PH), tetraphosphole (CHP3PH), and pentaphosphole (P4PH) are determined by DFT calculations. We have compared these to the pKas of the analogue azole group compounds and the factors that cause the differences of these values are discussed in terms of the stabilities of both the phosphole anions and azole anions.
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28
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Abstract
Pentazole having the molecular formula HN5 is an archetypical five-membered homocyclic inorganic aromatic molecule consisting of five nitrogen atoms. A hydrogen atom is bonded to one of the nitrogens. Even though the molecule does not contain a carbon it appears last in the series of the heterocyclic azole family; the family containing one to five nitrogen atoms. This series of heterocyclic azoles is pyrrole, imidazole, pyrazole, triazole, tetrazole, and the last one is the pentazole. Barring pentazole, the rest of the members of the azole family are heterocyclic organic molecules. The pKa of N(1)H-acidity values of all the azole members are known, except for that of pentazole. In the present work we endeavoured to determine the pKa of pentazole by a graphical method and by performing theoretical DFT calculations.
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29
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Dutra FR, Silva CDS, Custodio R. On the Accuracy of the Direct Method to Calculate p Ka from Electronic Structure Calculations. J Phys Chem A 2020; 125:65-73. [PMID: 33356255 PMCID: PMC7872415 DOI: 10.1021/acs.jpca.0c08283] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
direct method (HA(soln) ⇌ A(soln)– + H(soln)+) for calculating
pKa of monoprotic acids is as efficient
as thermodynamic cycles. A selective adjustment of proton free energy
in solution was used with experimental pKa 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 pKa and an uncertainty around ±1
unit of pKa 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 pKa but with uncertainties up to ±2 units of pKa, 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.
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Affiliation(s)
- Felipe Ribeiro Dutra
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
| | - Cleuton de Souza Silva
- Instituto de Ciências Exatas e Tecnologia, Universidade Federal do Amazonas, Campus de Itacoatiara, 69100-021 Itacoatiara, Amazonas, Brazil
| | - Rogério Custodio
- Instituto de Química, Universidade Estadual de Campinas, P.O. Box 6154, Barão Geraldo, 13083-970 Campinas, São Paulo, Brazil
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30
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Kim Y, Mittal A, Robichaud DJ, Pilath HM, Etz BD, St. John PC, Johnson DK, Kim S. Prediction of Hydroxymethylfurfural Yield in Glucose Conversion through Investigation of Lewis Acid and Organic Solvent Effects. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04245] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yeonjoon Kim
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - Ashutosh Mittal
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - David J. Robichaud
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - Heidi M. Pilath
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - Brian D. Etz
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - Peter C. St. John
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - David K. Johnson
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
| | - Seonah Kim
- National Renewable Energy Laboratory, 15523 Denver West Parkway, Golden, Colorado 80401-3393, United States
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31
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Pinto AV, Magalhães AL. Intramolecular Hydrogen Bonds in Tip-Functionalized Single-Walled Carbon Nanotubes as pH-Sensitive Gates. J Phys Chem A 2020; 124:9542-9551. [PMID: 33169998 DOI: 10.1021/acs.jpca.0c03710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their discovery, carbon nanotubes and other related nanomaterials are in the spotlight due to their unique molecular structures and properties, having a wide range of applications. The cage-like structure of carbon nanotubes is especially appealing as a route to confine molecules, isolating them from the solvent medium. This study aims to explore and characterize, through density functional theory (DFT) calculations, covalent tip-functionalization of single-walled carbon nanotubes (SWCNTS) with carboxymethyl moieties that establish pH sensitive molecular gates. The response of the molecular gate to pH fluctuations arises from variations in the noncovalent interactions between functionalized groups, which depend on the extent of protonation, leading to conformational changes. Overall, the hydrogen bonds present in the molecular models under study, as evaluated through topological analysis and pKa calculations, suggest that functionalized SWCNTs may be suitable for the design of drug delivery systems to enhance the efficiency of some pharmacological treatments, or even in the area of catalysis and separation processes, through their incorporation in nanocomposites.
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Affiliation(s)
- A V Pinto
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - A L Magalhães
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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32
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Pereira RW, Ramabhadran RO. pK-Yay: A Black-Box Method Using Density Functional Theory and Implicit Solvation Models to Compute Aqueous p Ka Values of Weak and Strong Acids. J Phys Chem A 2020; 124:9061-9074. [PMID: 32970437 DOI: 10.1021/acs.jpca.0c06298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The concept of pKa is very important in chemistry and biology. Over the past two decades, electronic structure calculations have made huge strides toward becoming reliable counterparts to experiments in determining solution-phase pKa values. However, invariably, the computation of pKa values involves the use of methods whose error bars are intrinsically larger (definitely >2 kcal/mol with density functionals) than the accuracy desired for the estimation of pKa values (<1 or 1.5 pKa units). This scenario presents an ample scope for innovation in developing systematic error cancellation methods even today. In this work, we have developed the pK-Yay method. It is a user-friendly black-box method used to compute aqueous pKa values of strong and weak acids employing routinely used and computationally inexpensive density functionals and implicit solvation models. It does not require the use of any explicit solvent molecule or modifying any other parameter in an electronic structure program. As part of evaluating the method, a comprehensive test set of 26 weak and strong organic and mineral acids covering 35 pKa units (20 to -15) was assembled. The detailed description of the method, its performance with different functionals (ωB97X-D performed best for organic acids with a mean absolute error (MAE) of 0.8 pKa units, and B2-PLYP performed best for strong acids with an MAE of 1.6 pKa units), the strengths and limitations in the present version, and a future scope to improve the accuracy and reduce its empirical nature are presented herein.
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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, and 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, and Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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33
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Patel DH, East ALL. Semicontinuum (Cluster-Continuum) Modeling of Acid-Catalyzed Aqueous Reactions: Alkene Hydration. J Phys Chem A 2020; 124:9088-9104. [PMID: 33074670 DOI: 10.1021/acs.jpca.0c07011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
An effort is made to reduce the errors of continuum solvation models (CSMs) with semicontinuum modeling to achieve 3 kcal mol-1 agreement with experiment for acid-catalysis activation Gibbs energies. First, two underappreciated CSM issues are reviewed: errors in the CSM solvation Gibbs energies grow beyond 5 kcal mol-1 (i) as ions are made smaller and (ii) as water clusters grow larger. Second, the computational reproduction of the known Gibbs energies (ΔrG and Δ‡G) of the paradigmatic reaction ethene + H2O + H3O+ → TS+ → ethanol + H3O+ is attempted. It is argued that, despite the >5 kcal mol-1 solvation errors for ions, it is possible to employ error cancellation strategies to reduce the errors in the reaction and activation Gibbs energies to 3 kcal mol-1 accuracy. A new 3 kcal mol-1 effect due to solvent-molecule "placement" (confinement from 1 M bulk concentration) was isolated and proved useful. Third, computational reproduction of the known entropies (ΔrS and Δ‡S) of the paradigmatic reaction is attempted using Trouton's constant and neglect of solvent structure reorganization effects (which must cancel well for this reaction); this worked well for ΔrS but needs empirical correction of ∼11 cal mol-1 K-1 for Δ‡S due to solvent disorientation when H3O+ is consumed. These entropy estimates allow for enthalpy (ΔrH and Δ‡H) estimation from the Gibbs energy values. Fourth, two recommended options, including A + H3O+·2W → [AHOH2+·2W]‡, are shown to also work well for the activations of propene and isobutene.
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Affiliation(s)
- Darpan H Patel
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Allan L L East
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
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34
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Jennings JJ, Milic M, Targos K, Franz AK. NMR quantification of H-bond donating ability for bioactive functional groups and isosteres. Eur J Med Chem 2020; 207:112693. [PMID: 32862126 DOI: 10.1016/j.ejmech.2020.112693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/15/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022]
Abstract
The H-bond donating ability for 127 compounds including drug fragments and isosteres have been quantified using a simple and rapid method with 31P NMR spectroscopy. Functional groups important to medicinal chemistry were evaluated including carboxylic acids, alcohols, phenols, thioic acids and nitrogen group H-bond donors. 31P NMR shifts for binding to a phosphine oxide probe have a higher correlation with equilibrium constants for H-bonding (log KHA) than acidity (pKa), indicating that these binding experiments are representative of H-bonding ability and not proton transfer. Additionally, 31P NMR binding data for carboxylic acid isosteres correlates with physicochemical properties such as lipophilicity, membrane permeability and plasma protein binding. This method has been used to evaluate the H-bond donating ability of small molecule drug compounds such as NSAIDs and antimicrobials.
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Affiliation(s)
- Julia J Jennings
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Mira Milic
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Karina Targos
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States
| | - Annaliese K Franz
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, United States.
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35
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Rodriguez SA, Baumgartner MT. Betanidin p K a Prediction Using DFT Methods. ACS OMEGA 2020; 5:13751-13759. [PMID: 32566840 PMCID: PMC7301574 DOI: 10.1021/acsomega.0c00904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
Betalains can be used in food, drugs, and cosmetic industries and have shown their bioactive potential. These properties are strongly influenced by pH and other physicochemical conditions. The pK a values for the polyprotic Betanidin (Bd) molecule are unknown, and they are crucial to elucidate the oxidation mechanism in which its pigment is involved. In the present study, the values of pK a for all protic groups of Bd were analyzed using five hybrid density functionals (B3LYP, B3PW91, ωB97XD, PBE0, and M06-2X), five basis sets (6-31+G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d,p), and 6-311++G(d,p)) and the solvation model based on density (SMD) implicit solvation model. Moreover, one and three explicit water molecules were added to improve the solvation free energy values. Furthermore, the values of pK a of betanin, betalamic acid, and cyclo-dihydroxyphenylalanine (DOPA) were studied. Based on these analyses, we propose the acid-base behavior of Bd in water and develop new tools to understand their chemical reactivity.
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Affiliation(s)
- Sergio A. Rodriguez
- CONICET,
Instituto de Ciencias Químicas, FAyA, UNSE, Av. Belgrano Sur 1912, Santiago del Estero 4200, Argentina
| | - Maria T. Baumgartner
- INFIQC-Dpto.
Química Orgánica, Fac. Ciencias Químicas, UNC, Ciudad Universitaria, Córdoba 5000, Argentina
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36
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Zhu D, Zheng W, Chang H, Xie H. A theoretical study on the p Ka values of selenium compounds in aqueous solution. NEW J CHEM 2020. [DOI: 10.1039/d0nj01124j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The pKa values of different kinds of selenium compounds (R-SeH) were investigated by using the ωB97XD method with a SMD model.
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Affiliation(s)
- Danfeng Zhu
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Wenrui Zheng
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Huifang Chang
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Hongyun Xie
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
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37
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Maier S, Thapa B, Raghavachari K. G4 accuracy at DFT cost: unlocking accurate redox potentials for organic molecules using systematic error cancellation. Phys Chem Chem Phys 2020; 22:4439-4452. [DOI: 10.1039/c9cp06622e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study presents a cost-effective error cancellation protocol to predict the redox potentials of 46 organic molecules with near-G4 accuracy.
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Affiliation(s)
- Sarah Maier
- Department of Chemistry
- Indiana University
- Bloomington
- USA
| | - Bishnu Thapa
- Department of Chemistry
- Indiana University
- Bloomington
- USA
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38
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Liu D, Thomas T, Gong H, Li F, Li Q, Song L, Azhagan T, Jiang H, Yang M. A mechanism of alkali metal carbonates catalysing the synthesis of β-hydroxyethyl sulfide with mercaptan and ethylene carbonate. Org Biomol Chem 2019; 17:9367-9374. [PMID: 31621741 DOI: 10.1039/c9ob01816f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reaction of β-hydroxyethylation is essential to the current practice of organic chemistry. Here, we proposed a new and green route to synthesize 2-hydroxyethyl n-alkyl sulfide with n-alkyl mercaptan and ethylene carbonate (EC) in the presence of alkali carbonates as catalysts and revealed the mechanism by experiments and theoretical calculations. The reaction reported proceeds rapidly with high yields when it is performed at 120 °C and the catalytic loading is ∼1 mol%. This protocol is applicable to other mercaptans to synthesize the corresponding β-hydroxyethyl sulfide. Density functional theory-based calculations show the energy profile for the reaction pathway. The rate-determining step is the ring-opening of EC. A negatively charged O atom of alkali carbonates approaches the S atom of -SH under the influence of hydrogen bonds. An activated S atom that carries more negative charge serves as a nucleophilic reagent and assists in the ring-opening of EC by reducing the Mayer bond orders of the C1-O1 bond in EC. Alkali cations also contribute to the C1-O1 bond cleavage. The energy barrier for the ring-opening of EC decreases with the decrease of electronegativity of alkali cations. Subsequent transference of a H atom leads to the formation of β-hydroxyethyl sulfide, the dissociation of CO2 and the reduction of K2CO3.
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Affiliation(s)
- Dongliang Liu
- College of Chemistry, Chemical Engineering and Environment Engineering, Liaoning Shihua University, Fushun 113001, China.
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39
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Lian P, Guo L, Devarajan D, Parks JM, Painter SL, Brooks SC, Smith JC. The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. J Comput Chem 2019; 41:147-155. [PMID: 31603259 DOI: 10.1002/jcc.26081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023]
Abstract
To assess the chemical reactivity, toxicity, and mobility of pollutants in the environment, knowledge of their species distributions is critical. Because their direct measurement is often infeasible, speciation modeling is widely adopted. Mercury (Hg) is a representative pollutant for which study of its speciation benefits from modeling. However, Hg speciation modeling is often hindered by a lack of reliable thermodynamic constants. Although computational chemistry (e.g., density functional theory [DFT]) can generate these constants, methods for directly coupling DFT and speciation modeling are not available. Here, we combine computational chemistry and continuum-scale modeling with curated online databases to ameliorate the problem of unreliable inputs to Hg speciation modeling. Our AQUA-MER databases and web server (https://aquamer.ornl.gov) provides direct speciation results by combining web-based interfaces to a speciation calculator, databases of thermodynamic constants, and a computational chemistry toolkit to estimate missing constants. Although Hg is presented as a concrete use case, AQUA-MER can also be readily applied to other elements. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Peng Lian
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Luanjing Guo
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Deepa Devarajan
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831
| | - Scott L Painter
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
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40
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Thapa B, Raghavachari K. Accurate p Ka Evaluations for Complex Bio-Organic Molecules in Aqueous Media. J Chem Theory Comput 2019; 15:6025-6035. [PMID: 31596078 DOI: 10.1021/acs.jctc.9b00606] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite the numerous computational efforts on estimating acid dissociation constant (pKa's), an accurate estimation of pKa's of bio-organic molecules in the aqueous medium is still a challenge. The major difficulty lies in the accurate description of the aqueous environment and the cost and accuracy of quantum mechanical (QM) methods. Herein, we report a well-defined quantum chemical protocol for accurately calculating pKa's of a wide range of bio-organic molecules in aqueous media. The performance of our method has been assessed using test sets containing molecules with a range of sizes and a variety of functional groups, including alcohols, phenols, amines, and carboxylic acids, and obtained an impressive mean absolute accuracy of 0.5 pKa units. For the smaller molecules, we use a high-level QM method (CBS-QB3) and a calibrated explicit-implicit solvation model that yields accurate pKa values for a range of functional groups. For the larger molecules, we combine this approach with an efficient error-cancellation scheme that eliminates the systematic errors in different density functional methods to yield accurate pKa values for simple to complex molecular systems. Our protocol is efficient, applicable to large molecules, covers all the common functional groups present in bio-organic molecules, and should find widespread applications in diverse research areas including drug-protein binding, catalysis, and chemical synthesis.
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Affiliation(s)
- Bishnu Thapa
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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41
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Baetzold RC. Density Functional Calculations for Aqueous Silver Clusters Containing Water and Nitrate Ligands. J Phys Chem B 2019; 123:8300-8312. [PMID: 31478667 DOI: 10.1021/acs.jpcb.9b06634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The incorporation of a nitrate ion into silver-water aqueous clusters has been examined using PBE0 density functional theory with the solvent model density (SMD) solvation model. The Gibbs free energy of solvation and other thermodynamic variables are calculated using the harmonic/rigid rotor/ideal gas model at 298.15 K for aqueous solutes including the effects of solute relaxation in water and with London dispersive forces at the D3 level. Free energies of solvation for Ag+ and NO3- were found to agree well with experimental values of -118.2 and -60.1 kcal/mol, respectively, calculated using cluster-continuum models with six to eight water molecules and including solute relaxation and London D3 dispersive interactions. An analysis of data of varying cluster size upon calculated free energy is presented. A direct procedure is applied to aqueous clusters such as Agnz(NO3-)(H2O)5, Agnz(H2O)5, and (NO3-)(H2O)6 n = 1-4; z = 0, +1 in the SMD solvent representation to calculate equilibrium constants for nitrate association with silver clusters in solution that includes fully relaxed solutes. The equilibrium structures of the nitrate-containing clusters involve one or more bonds from nitrate oxygen to positive silver clusters. Water molecules interact with nitrate through H atoms, and overall, the structure represents a silver nitrate cluster with water ligands having similarity to a close ion pair in many aspects. The neutral silver atom is attached to nitrate through H-bonded water molecules. The ratio of nitrate-containing silver clusters to nitrate-free clusters using a calculated equilibrium constant of 0.51 L/mol for Ag+ is small in the range of many experiments. Similar values are found for positive silver clusters up to four atoms in size. The resulting procedures were applied to aqueous clusters of Agn(NO3)m+(n-m) that have been previously experimentally studied for silver reduction in aqueous solution. A chain-like structure with collinear and bidentate oxygen bonds to silver was found, and the equilibrium constants for clustering were determined. A simplified model calculation for the reduction of Ag(H2O)6+ clusters in the presence of silver clusters in aqueous media was studied to understand catalytic effects observed in these systems. The reduction potentials vary with silver cluster size indicating a more favorable reduction caused by the presence of larger silver clusters.
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Martínez RJ, Farrell J. Water splitting activity of oxygen-containing groups in graphene oxide catalyst in bipolar membranes. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112556] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Xu L, Coote ML. Methods To Improve the Calculations of Solvation Model Density Solvation Free Energies and Associated Aqueous pKa Values: Comparison between Choosing an Optimal Theoretical Level, Solute Cavity Scaling, and Using Explicit Solvent Molecules. J Phys Chem A 2019; 123:7430-7438. [DOI: 10.1021/acs.jpca.9b04920] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Longkun Xu
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Mirzaei S, Ivanov MV, Timerghazin QK. Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and pKa Values of Thiols. J Phys Chem A 2019; 123:9498-9504. [DOI: 10.1021/acs.jpca.9b02340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Saber Mirzaei
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
| | - Maxim V. Ivanov
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
| | - Qadir K. Timerghazin
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1414, United States
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Asaduzzaman A, Riccardi D, Afaneh AT, Cooper CJ, Smith JC, Wang F, Parks JM, Schreckenbach G. Environmental Mercury Chemistry - In Silico. Acc Chem Res 2019; 52:379-388. [PMID: 30689347 DOI: 10.1021/acs.accounts.8b00454] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mercury (Hg) is a global environmental contaminant. Major anthropogenic sources of Hg emission include gold mining and the burning of fossil fuels. Once deposited in aquatic environments, Hg can undergo redox reactions, form complexes with ligands, and adsorb onto particles. It can also be methylated by microorganisms. Mercury, especially its methylated form methylmercury, can be taken up by organisms, where it bioaccumulates and biomagnifies in the food chain, leading to detrimental effects on ecosystem and human health. In support of the recently enforced Minamata Convention on Mercury, a legally binding international convention aimed at reducing the anthropogenic emission of-and human exposure to-Hg, its global biogeochemical cycle must be understood. Thus, a detailed understanding of the molecular-level interactions of Hg is crucial. The ongoing rapid development of hardware and methods has brought computational chemistry to a point that it can usefully inform environmental science. This is particularly true for Hg, which is difficult to handle experimentally due to its ultratrace concentrations in the environment and its toxicity. The current account provides a synopsis of the application of computational chemistry to filling several major knowledge gaps in environmental Hg chemistry that have not been adequately addressed experimentally. Environmental Hg chemistry requires defining the factors that determine the relative affinities of different ligands for Hg species, as they are critical for understanding its speciation, transformation and bioaccumulation in the environment. Formation constants and the nature of bonding have been determined computationally for environmentally relevant Hg(II) complexes such as chlorides, hydroxides, sulfides and selenides, in various physical phases. Quantum chemistry has been used to determine the driving forces behind the speciation of Hg with hydrochalcogenide and halide ligands. Of particular importance is the detailed characterization of solvation effects. Indeed, the aqueous phase reverses trends in affinities found computationally in the gas phase. Computation has also been used to investigate complexes of methylmercury with (seleno)amino acids, providing a molecular-level understanding of the toxicological antagonism between Hg and selenium (Se). Furthermore, evidence is emerging that ice surfaces play an important role in Hg transport and transformation in polar and alpine regions. Therefore, the diffusion of Hg and its ions through an idealized ice surface has been characterized. Microorganisms are major players in environmental mercury cycling. Some methylate inorganic Hg species, whereas others demethylate methylmercury. Quantum chemistry has been used to investigate catalytic mechanisms of enzymatic Hg methylation and demethylation. The complex interplay between the myriad chemical reactions and transport properties both in and outside microbial cells determines net biogeochemical cycling. Prospects for scaling up molecular work to obtain a mechanistic understanding of Hg cycling with comprehensive multiscale biogeochemical modeling are also discussed.
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Affiliation(s)
- Abu Asaduzzaman
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- School of Science, Engineering and Technology, Penn State Harrisburg, 777 West Harrisburg Pike, Middletown, Pennsylvania 17057, United States
| | - Demian Riccardi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Akef T. Afaneh
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, P.O. Box 19117,
postal code 19117, Al-Salt, Jordan
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Feiyue Wang
- Centre for Earth Observation Science and Department of Environment and Geography, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
| | - Jerry M. Parks
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
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Correlation between molecular acidity (pKa) and vibrational spectroscopy. J Mol Model 2019; 25:48. [DOI: 10.1007/s00894-019-3928-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
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Zheng Y, Zheng W, Zhu D, Chang H. Theoretical modeling of pKa's of thiol compounds in aqueous solution. NEW J CHEM 2019. [DOI: 10.1039/c8nj06259e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The pKa's of different kinds of thiols (R-SH) were investigated by using the M06-2X method with a SMDsSAS model.
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Affiliation(s)
- Yuanyuan Zheng
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Wenrui Zheng
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Danfeng Zhu
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Huifang Chang
- College of Chemistry and Chemical Engineering
- Shanghai University of Engineering Science
- Shanghai 201620
- China
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Ristić MM, Petković M, Milovanović B, Belić J, Etinski M. New hybrid cluster-continuum model for pKa values calculations: Case study of neurotransmitters’ amino group acidity. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Smajlagic I, Durán R, Pilkington M, Dudding T. Cyclopropenium Enhanced Thiourea Catalysis. J Org Chem 2018; 83:13973-13980. [PMID: 30352160 DOI: 10.1021/acs.joc.8b02321] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An integral part of modern organocatalysis is the development and application of thiourea catalysts. Here, as part of our program aimed at developing cyclopropenium catalysts, the synthesis of a thiourea-cyclopropenium organocatalyst with both cationic hydrogen-bond donor and electrostatic character is reported. The utility of the this thiourea organocatalyst is showcased in pyranylation reactions employing phenols, primary, secondary, and tertiary alcohols under operationally simple and mild reaction conditions for a broad substrate scope. The addition of benzoic acid as a co-catalyst facilitating cooperative Brønsted acid catalysis was found to be valuable for reactions involving phenols and higher substituted alcohols. Mechanistic investigations, including kinetic and 1H NMR binding studies in conjunction with density function theory calculations, are described that collectively support a Brønsted acid mode of catalysis.
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Affiliation(s)
- Ivor Smajlagic
- Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Rocio Durán
- Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Melanie Pilkington
- Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
| | - Travis Dudding
- Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada
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Prasad S, Huang J, Zeng Q, Brooks BR. An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. J Comput Aided Mol Des 2018; 32:1191-1201. [PMID: 30276503 PMCID: PMC6342563 DOI: 10.1007/s10822-018-0167-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/25/2018] [Indexed: 12/30/2022]
Abstract
In this work we have developed a hybrid QM and MM approach to predict pKa of small drug-like molecules in explicit solvent. The gas phase free energy of deprotonation is calculated using the M06-2X density functional theory level with Pople basis sets. The solvation free energy difference of the acid and its conjugate base is calculated at MD level using thermodynamic integration. We applied this method to the 24 drug-like molecules in the SAMPL6 blind pKa prediction challenge. We achieved an overall RMSE of 2.4 pKa units in our prediction. Our results show that further optimization of the protocol needs to be done before this method can be used as an alternative approach to the well established approaches of a full quantum level or empirical pKa prediction methods.
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Affiliation(s)
- Samarjeet Prasad
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA.
- Biophysics and Biophysical Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA.
| | - Jing Huang
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Xihu District, Hangzhou, Zhejiang, China
| | - Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA
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