1
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Todorov P, Georgieva S, Peneva P, Nikolov S, Rangelov M, Todorova N, Pechlivanova D, Tchekalarova J. Synthesis, molecular docking, electrochemical and fluorimetric analysis of new caffeic and cinnamic acid-conjugated hemorphin derivatives designed as potential anticonvulsant and antinociceptive agents. Bioorg Chem 2024; 143:107063. [PMID: 38150935 DOI: 10.1016/j.bioorg.2023.107063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/17/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
Based on the pharmacophore model of opioid receptors, our team recently synthesized a series of short-chain hemorphin peptide analogs containing non-natural amino acids. They demonstrated anticonvulsant and antinociceptive activity with low neurotoxicity. In the present study, a series of novel bioconjugates of N-modified hemorphin analogs containing second pharmacophore cinnamic acids (CA) or caffeic (KA) were synthesized by a traditional solid-phase Fmoc chemistry method for peptide synthesis. Electrochemical and fluorimetric analysis, in vivo anticonvulsant and antinociceptive activity in mice were conducted on the compounds. The three CA acid- (H4-CA, H5-CA, and H7-CA) and three KA acid- (H4-KA, H5-KA, and H7-KA) conjugated hemorphin derivatives exhibited potency at the highest doses of 2 µg/5 µl, administered by intracerebroventricular (icv) mode, against seizure spread in the maximal electroshock test (MES) in mice. The KA-conjugated H5-KA derivate, at the lowest dose, was the only compound that suppressed clonic seizures in the subcutaneous pentylenetetrazol (scPTZ) test. Except for the H5-CA, all tested CA acid- and KA acid-conjugated peptide derivates had the potency to increase the latency for clonic seizures in a dose-dependent mode. The activity against the psychomotor seizures in the 6-Hz test was detected only for the H4-CA (0.5 µg) and H4-KA (0.5 µg and 1 µg), respectively. All investigated peptides showed a more pronounced antinociceptive effect in the "intraplantar formalin" test compared to the "hot plate" test. Shorter chain analogs showed a better antinociceptive profile against tonic pain. The data suggest a DOR and KOR-mediated mechanism of action. According to the docking analysis, H7-CA showed a different antinociceptive profile than other investigated peptides. The novel peptide derivates did not exhibit neurotoxicity in the rotarod test. Our findings suggest that conjugated CA and KA morphine peptides can be used to develop novel morphine-related analogs with anticonvulsant and antinociceptive activity.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria.
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
| | - Petia Peneva
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
| | - Spas Nikolov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria; Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
| | - Miroslav Rangelov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Daniela Pechlivanova
- Faculty of Medicine, Sofia University "St. Kliment Ohridski", 1407 Sofia, Bulgaria; Institute of Neurobiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Jana Tchekalarova
- Institute of Neurobiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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2
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Todorov P, Georgieva S, Tchekalarova J, Peneva P, Mateeva P, Assenov B, Dzhambazova E, Pechlivanova D. Synthesis, characterization and evaluation of anti-hyperalgesia, anticonvulsant and antioxidant activity of novel VV-hemorphin-5 analogs. Arch Pharm (Weinheim) 2023; 356:e2300267. [PMID: 37532631 DOI: 10.1002/ardp.202300267] [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: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Two series of new VV-hemorphin-5 analogs with structures Val-Val-Tyr-Xxx-Trp-Thr-Gln-NH2 and Adam-Val-Val-Tyr-Xxx-Trp-Thr-Gln-NH2 , where Xxx is Ac5c (1-aminocyclopentane-1-carboxylic acid), Ac6c (1-aminocyclohexane-1-carboxylic acid), Ac7c (1-aminocycloheptane-1-carboxylic acid), and Adam is the low-molecular-weight lipophilic adamantyl building block, were synthesized, characterized electrochemically and evaluated for antioxidant, anti-hyperalgesia, and anticonvulsant activity. The design of the compounds followed the strategy to improve the propensity for aqueous solubility and/or to increase their affinity for the target receptor or enzyme. The partition coefficient value shows that the peptide scaffold goes from hydrophilic to lipophilic with the increasing size of the cycloalkane ring and even more with the introduction of the adamantane. The peptides C5-V and C7-V were the only analogs that provoked an immediate antinociceptive effect changing the mechanical pain threshold. The six new peptide analogs produced a significant and long-lasting carrageenan model of inflammatory pain in rats. While the adamantane hemorphin analog Ad7-V was the only compound with the potency to suppress psychomotor seizures in the 6-Hz test, the C6-V and Ad6-V exhibited protective activity against the seizure spread in the maximal electroshock seizure test in mice. The active analogs did not show neurotoxicity or sedative effects. Our results revealed a structure-related specific activity of a newly designed hemorphin analog that could be used as a template for future modification and preparation of compounds with potential analgesic and anticonvulsant activity.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Jana Tchekalarova
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Petia Peneva
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Polina Mateeva
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Borislav Assenov
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Faculty of Medicine, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Elena Dzhambazova
- Faculty of Medicine, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Daniela Pechlivanova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Faculty of Medicine, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
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3
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Lan X, Dai Y, Jing W, Meng X, Liu F, Wang S, He A, Li N. DFT investigation on the carbonate radical formation in the system containing carbon dioxide and hydroxyl free radical. J Mol Graph Model 2022; 114:108182. [DOI: 10.1016/j.jmgm.2022.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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4
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Multiple-H-bonded-zwitterionic tetramer structure for L-(+)-2-chlorophenylglycine, as investigated by UV, IR and Raman spectroscopy and electronic structure calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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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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6
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Ryazantsev MN, Strashkov DM, Nikolaev DM, Shtyrov AA, Panov MS. Photopharmacological compounds based on azobenzenes and azoheteroarenes: principles of molecular design, molecular modelling, and synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Snigur D, Fizer M, Chebotarev A, Lukianova O, Bevziuk K. Protonation of quinoline yellow WS in aqueous solutions: Spectroscopic and DFT theoretical studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Bannan CC, Mobley DL, Skillman AG. SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model. J Comput Aided Mol Des 2018; 32:1165-1177. [PMID: 30324305 PMCID: PMC6438616 DOI: 10.1007/s10822-018-0169-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022]
Abstract
A variety of fields would benefit from accurate [Formula: see text] predictions, especially drug design due to the effect a change in ionization state can have on a molecule's physiochemical properties. Participants in the recent SAMPL6 blind challenge were asked to submit predictions for microscopic and macroscopic [Formula: see text]s of 24 drug like small molecules. We recently built a general model for predicting [Formula: see text]s using a Gaussian process regression trained using physical and chemical features of each ionizable group. Our pipeline takes a molecular graph and uses the OpenEye Toolkits to calculate features describing the removal of a proton. These features are fed into a Scikit-learn Gaussian process to predict microscopic [Formula: see text]s which are then used to analytically determine macroscopic [Formula: see text]s. Our Gaussian process is trained on a set of 2700 macroscopic [Formula: see text]s from monoprotic and select diprotic molecules. Here, we share our results for microscopic and macroscopic predictions in the SAMPL6 challenge. Overall, we ranked in the middle of the pack compared to other participants, but our fairly good agreement with experiment is still promising considering the challenge molecules are chemically diverse and often polyprotic while our training set is predominately monoprotic. Of particular importance to us when building this model was to include an uncertainty estimate based on the chemistry of the molecule that would reflect the likely accuracy of our prediction. Our model reports large uncertainties for the molecules that appear to have chemistry outside our domain of applicability, along with good agreement in quantile-quantile plots, indicating it can predict its own accuracy. The challenge highlighted a variety of means to improve our model, including adding more polyprotic molecules to our training set and more carefully considering what functional groups we do or do not identify as ionizable.
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Affiliation(s)
- Caitlin C Bannan
- Department of Chemistry, University of California, Irvine
- 2017 Summer Intern, OpenEye Scientific Software, Inc., Santa Fe, NM
| | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, 147 Bison Modular, Irvine, CA 92697, Tel.: +949-824-6383, Fax: +949-824-2949,
| | - A Geoffrey Skillman
- OpenEye Scientific Software, Inc. 9 Bisbee Court, Suite D, Santa Fe, NM 87508, Tel.: +505-473-7385,
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9
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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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10
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Zeng Q, Jones MR, Brooks BR. Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. J Comput Aided Mol Des 2018; 32:1179-1189. [PMID: 30128926 DOI: 10.1007/s10822-018-0150-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022]
Abstract
In this work, quantum mechanical methods were used to predict the microscopic and macroscopic pKa values for a set of 24 molecules as a part of the SAMPL6 blind challenge. The SMD solvation model was employed with M06-2X and different basis sets to evaluate three pKa calculation schemes (direct, vertical, and adiabatic). The adiabatic scheme is the most accurate approach (RMSE = 1.40 pKa units) and has high correlation (R2 = 0.93), with respect to experiment. This approach can be improved by applying a linear correction to yield an RMSE of 0.73 pKa units. Additionally, we consider including explicit solvent representation and multiple lower-energy conformations to improve the predictions for outliers. Adding three water molecules explicitly can reduce the error by 2-4 pKa units, with respect to experiment, whereas including multiple local minima conformations does not necessarily improve the pKa prediction.
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Affiliation(s)
- Qiao Zeng
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA.
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 12 South Drive, Building 12A Room 3053, Bethesda, MD, 20814, USA
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11
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Bevziuk K, Chebotarev A, Fizer M, Klochkova A, Pliuta K, Snigur D. Protonation of Patented Blue V in aqueous solutions: theoretical and experimental studies. J CHEM SCI 2018. [DOI: 10.1007/s12039-017-1411-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Walton JC. Enhanced Proton Loss from Neutral Free Radicals: Toward Carbon-Centered Superacids. J Phys Chem A 2018; 122:1422-1431. [DOI: 10.1021/acs.jpca.7b11796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16
9ST, United Kingdom
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13
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Walton JC. Radical-Enhanced Acidity: Why Bicarbonate, Carboxyl, Hydroperoxyl, and Related Radicals Are So Acidic. J Phys Chem A 2017; 121:7761-7767. [DOI: 10.1021/acs.jpca.7b08081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife, KY16 9ST, United Kingdom
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14
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Omelchuk K, Szczepański P, Shrotre A, Haddad M, Chagnes A. Effects of structural changes of new organophosphorus cationic exchangers on a solvent extraction of cobalt, nickel and manganese from acidic chloride media. RSC Adv 2017. [DOI: 10.1039/c6ra21695a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The effects of structural changes of organophosphorus cationic exchangers on metal-distribution curves (extraction efficiency vs. pH) have been investigated for the recovery of cobalt(ii), nickel(ii) and manganese(ii) from acidic chloride solutions.
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Affiliation(s)
- Kateryna Omelchuk
- PSL Research University
- Chimie ParisTech – CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
- France
| | - Piotr Szczepański
- Nicolaus Copernicus University in Toruń
- Faculty of Chemistry
- 87-100 Toruń
- Poland
| | - Akhilesh Shrotre
- PSL Research University
- Chimie ParisTech – CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
- France
| | - Mansour Haddad
- PSL Research University
- Chimie ParisTech – CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
- France
| | - Alexandre Chagnes
- PSL Research University
- Chimie ParisTech – CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
- France
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15
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Tshepelevitsh S, Trummal A, Haav K, Martin K, Leito I. Hydrogen-Bond Donicity in DMSO and Gas Phase and Its Dependence on Brønsted Acidity. J Phys Chem A 2016; 121:357-369. [DOI: 10.1021/acs.jpca.6b11115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sofja Tshepelevitsh
- Institute
of Chemistry, University of Tartu, 14a Ravila Street, Tartu 50411, Estonia
| | - Aleksander Trummal
- National Institute of Chemical Physics and Biophysics, 23 Akadeemia tee, Tallinn 12618, Estonia
| | - Kristjan Haav
- Institute
of Chemistry, University of Tartu, 14a Ravila Street, Tartu 50411, Estonia
| | - Kerli Martin
- Institute
of Chemistry, University of Tartu, 14a Ravila Street, Tartu 50411, Estonia
| | - Ivo Leito
- Institute
of Chemistry, University of Tartu, 14a Ravila Street, Tartu 50411, Estonia
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16
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Erkin AV, Klaptyuk IV, Gurzhii VV, Yuzikhin OS, Krutikov VI. Aryl ethers of 4-[(2-hydroxyethyl)sulfanyl]pyrimidine derivatives: Pathways of synthesis and fungicidal activity of their salt forms. RUSS J GEN CHEM+ 2016. [DOI: 10.1134/s1070363216060098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Seybold PG. Computational estimation of the acidities of some inorganic nitrogen acids. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1076582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Seybold PG, Shields GC. Computational estimation of pKa
values. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1218] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Paul G. Seybold
- Departments of Chemistry and Biochemistry; Wright State University; Dayton OH USA
| | - George C. Shields
- Department of Chemistry and College of Arts & Sciences; Bucknell University; Lewisburg PA USA
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19
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Kögel JF, Linder T, Schröder FG, Sundermeyer J, Goll SK, Himmel D, Krossing I, Kütt K, Saame J, Leito I. Fluoro- and Perfluoralkylsulfonylpentafluoroanilides: Synthesis and Characterization of NH Acids for Weakly Coordinating Anions and Their Gas-Phase and Solution Acidities. Chemistry 2015; 21:5769-82. [DOI: 10.1002/chem.201405391] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 11/07/2022]
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20
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Alkorta I, Popelier PLA. Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution. Chemphyschem 2014; 16:465-9. [PMID: 25382620 DOI: 10.1002/cphc.201402711] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Indexed: 11/11/2022]
Abstract
Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid (Spain).
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21
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Afaneh AT, Schreckenbach G. Conformation/Tautomerization effect on the pKa
values of lumazine and 6-thienyllumazine. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Akef T. Afaneh
- Department of Chemistry; University of Manitoba; Winnipeg MB Canada R3T 2N2
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22
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Alkorta I, Griffiths MZ, Popelier PLA. Relationship between experimental pK
a
values in aqueous solution and a gas phase bond length in bicyclo[2.2.2]octane and cubane carboxylic acids. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC; Juan de la Cierva, 3 E-28006 Madrid Spain
| | - Mark Z. Griffiths
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN Great Britain
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL Great Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB); 131 Princess Street Manchester M1 7DN Great Britain
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL Great Britain
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23
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Sutton CCR, Franks GV, da Silva G. First principles pKa calculations on carboxylic acids using the SMD solvation model: effect of thermodynamic cycle, model chemistry, and explicit solvent molecules. J Phys Chem B 2012; 116:11999-2006. [PMID: 22920269 DOI: 10.1021/jp305876r] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aqueous pK(a) values are calculated from first principles for a set of carboxylic acids using the SMD solvation model with various model chemistries, thermodynamic cycles, and treatments of explicit solvation. In all, 108 unique theoretical protocols are examined. The direct (D) and water proton exchange (PX) cycles are trialled along with a new approach, termed the semidirect (SD) cycle. The SD thermodynamic cycle offers some improvements over the D and PX schemes, as it bypasses the gas-phase heterolytic bond dissociation calculation required in the conventional D approach while also avoiding an aqueous OH(-) calculation required by the PX method when using water as the reference acid. With all three cycles, the recommended model chemistry employs M05-2X/cc-pVTZ Gibbs energies of solvation with a single discrete water molecule and a high-level composite method for the gas-phase reaction energies. With the SD cycle, these calculations result in a mean unsigned error of less than 1 pK(a) units, with respective mean signed error and maximum unsigned error of less than 0.5 and 2 pK(a) units. Similar results are obtained with the D and PX cycles, and further improvement is required in both the gas and aqueous phase ab initio energy calculations before we can truly discriminate between the thermodynamic cycles investigated here.
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Affiliation(s)
- Catherine C R Sutton
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010, Australia
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Seybold PG. Quantum Chemical‐QSPR Estimation of the Acidities and Basicities of Organic Compounds. ADVANCES IN QUANTUM CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396498-4.00015-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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