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Li L, Mayer RJ, Ofial AR, Mayr H. One-Bond-Nucleophilicity and -Electrophilicity Parameters: An Efficient Ordering System for 1,3-Dipolar Cycloadditions. J Am Chem Soc 2023; 145:7416-7434. [PMID: 36952671 DOI: 10.1021/jacs.2c13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Diazoalkanes are ambiphilic 1,3-dipoles that undergo fast Huisgen cycloadditions with both electron-rich and electron-poor dipolarophiles but react slowly with alkenes of low polarity. Frontier molecular orbital (FMO) theory considering the 3-center-4-electron π-system of the propargyl fragment of diazoalkanes is commonly applied to rationalize these reactivity trends. However, we recently found that a change in the mechanism from cycloadditions to azo couplings takes place due to the existence of a previously overlooked lower-lying unoccupied molecular orbital. We now propose an alternative approach to analyze 1,3-dipolar cycloaddition reactions, which relies on the linear free energy relationship lg k2(20 °C) = sN(N + E) (eq 1) with two solvent-dependent parameters (N, sN) to characterize nucleophiles and one parameter (E) for electrophiles. Rate constants for the cycloadditions of diazoalkanes with dipolarophiles were measured and compared with those calculated for the formation of zwitterions by eq 1. The difference between experimental and predicted Gibbs energies of activation is interpreted as the energy of concert, i.e., the stabilization of the transition states by the concerted formation of two new bonds. By linking the plot of lg k2 vs N for nucleophilic dipolarophiles with that of lg k2 vs E for electrophilic dipolarophiles, one obtains V-shaped plots which provide absolute rate constants for the stepwise reactions on the borderlines. These plots furthermore predict relative reactivities of dipolarophiles in concerted, highly asynchronous cycloadditions more precisely than the classical correlations of rate constants with FMO energies or ionization potentials. DFT calculations using the SMD solvent model confirm these interpretations.
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Affiliation(s)
- Le Li
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Robert J Mayer
- CNRS, ISIS, Université de Strasbourg, 8 Allee Gaspard Monge, 67000 Strasbourg, France
| | - Armin R Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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2
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Solvent effect, quantification and correlation analysis of the nucleophilicities of cyclic secondary amines. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Saini V, Sharma A, Nivatia D. A machine learning approach for predicting the nucleophilicity of organic molecules. Phys Chem Chem Phys 2022; 24:1821-1829. [PMID: 34986215 DOI: 10.1039/d1cp05072a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleophilicity provides important information about the chemical reactivity of organic molecules. Experimental determination of the nucleophilicity parameter is a tedious and resource-intensive approach. Herein, we present a novel machine learning protocol that uses key structural descriptors to predict the nucleophilicities of organic molecules, which agree well with the experimental values. A data driven approach was used where quantum mechanical molecular and thermodynamic descriptors from a wide range of structurally diverse nucleophiles and relevant solvents were extracted and modelled using advanced algorithms against the experimentally available nucleophilicity values. Despite the structural diversity of nucleophiles, we are able to achieve statistically robust models with a high predictive power using tree-based and neural network algorithms trained on an in-house developed unique dataset consisting of 752 nucleophilicity values and 27 molecular descriptors.
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Affiliation(s)
- Vaneet Saini
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Aditya Sharma
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
| | - Dhruv Nivatia
- IT Department, University Institute of Engineering & Technology, Panjab University, Chandigarh 160014, India
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Orlandi M, Escudero-Casao M, Licini G. Nucleophilicity Prediction via Multivariate Linear Regression Analysis. J Org Chem 2021; 86:3555-3564. [PMID: 33534569 PMCID: PMC7901016 DOI: 10.1021/acs.joc.0c02952] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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The concept of nucleophilicity is
at the basis of most transformations
in chemistry. Understanding and predicting the relative reactivity
of different nucleophiles is therefore of paramount importance. Mayr’s
nucleophilicity scale likely represents the most complete collection
of reactivity data, which currently includes over 1200 nucleophiles.
Several attempts have been made to theoretically predict Mayr’s
nucleophilicity parameters N based on calculation
of molecular properties, but a general model accounting for different
classes of nucleophiles could not be obtained so far. We herein show
that multivariate linear regression analysis is a suitable tool for
obtaining a simple model predicting N for virtually
any class of nucleophiles in different solvents for a set of 341 data
points. The key descriptors of the model were found to account for
the proton affinity, solvation energies, and sterics.
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Affiliation(s)
- Manuel Orlandi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.,CIRCC-Consorzio Interuniversitario per le Reattività Chimiche e la Catalisi, Padova Unit, via Marzolo 1, 35131 Padova, Italy
| | - Margarita Escudero-Casao
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.,CIRCC-Consorzio Interuniversitario per le Reattività Chimiche e la Catalisi, Padova Unit, via Marzolo 1, 35131 Padova, Italy
| | - Giulia Licini
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.,CIRCC-Consorzio Interuniversitario per le Reattività Chimiche e la Catalisi, Padova Unit, via Marzolo 1, 35131 Padova, Italy
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Pereira F, Xiao K, Latino DARS, Wu C, Zhang Q, Aires-de-Sousa J. Machine Learning Methods to Predict Density Functional Theory B3LYP Energies of HOMO and LUMO Orbitals. J Chem Inf Model 2016; 57:11-21. [PMID: 28033004 DOI: 10.1021/acs.jcim.6b00340] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Machine learning algorithms were explored for the fast estimation of HOMO and LUMO orbital energies calculated by DFT B3LYP, on the basis of molecular descriptors exclusively based on connectivity. The whole project involved the retrieval and generation of molecular structures, quantum chemical calculations for a database with >111 000 structures, development of new molecular descriptors, and training/validation of machine learning models. Several machine learning algorithms were screened, and an applicability domain was defined based on Euclidean distances to the training set. Random forest models predicted an external test set of 9989 compounds achieving mean absolute error (MAE) up to 0.15 and 0.16 eV for the HOMO and LUMO orbitals, respectively. The impact of the quantum chemical calculation protocol was assessed with a subset of compounds. Inclusion of the orbital energy calculated by PM7 as an additional descriptor significantly improved the quality of estimations (reducing the MAE in >30%).
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Affiliation(s)
- Florbela Pereira
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Kaixia Xiao
- Henan Engineering Research Center of Industrial Circulating Water Treatment, College of Chemistry and Chemical Engineering, Henan University , Kaifeng, 475004, PR China
| | - Diogo A R S Latino
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Chengcheng Wu
- Henan Engineering Research Center of Industrial Circulating Water Treatment, College of Chemistry and Chemical Engineering, Henan University , Kaifeng, 475004, PR China
| | - Qingyou Zhang
- Henan Engineering Research Center of Industrial Circulating Water Treatment, College of Chemistry and Chemical Engineering, Henan University , Kaifeng, 475004, PR China
| | - Joao Aires-de-Sousa
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
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Scheller PN, Lenz M, Hammer SC, Hauer B, Nestl BM. Imine Reductase-Catalyzed Intermolecular Reductive Amination of Aldehydes and Ketones. ChemCatChem 2015. [DOI: 10.1002/cctc.201500764] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Philipp N. Scheller
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Maike Lenz
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Stephan C. Hammer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universität Stuttgart; Allmandring 31 70569 Stuttgart Germany
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Mayr H, Ofial AR. A quantitative approach to polar organic reactivity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:619-646. [PMID: 26315811 DOI: 10.1080/1062936x.2015.1078409] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/28/2015] [Indexed: 06/04/2023]
Abstract
A method is presented which allows one to predict toxic effects which are triggered by the formation of covalent bonds between electron-deficient (electrophilic) compounds and biological electron-rich (nucleophilic) targets, as proteins or nucleic acids. It is based on our comprehensive nucleophilicity and electrophilicity scales, which we constructed as an aid for the planning of organic syntheses. For the construction of these scales, rate constants for the reactions of benzhydrylium ions (aryl2CH(+)) and structurally related quinone methides with nucleophiles have been measured and correlated by the equation lg k(20 °C) = sN(E + N), which yields absolute rate constants k (L mol(-1) s(-1)) from one parameter for electrophiles (the electrophilicity E) and two for nucleophiles (the nucleophilicity parameter N and the susceptibility sN). A freely accessible database (http://www.cup.uni-muenchen.de/oc/mayr/DBintro.html) is described, which presently comprises data for 1000 nucleophiles and 260 electrophiles and provides links to the original literature reports. The kinetic scales are complemented by a thermodynamic counterpart, which enables one to calculate association constants K (L mol(-1)) of electrophiles with nucleophiles from the empirical Lewis acidity parameters LA and Lewis basicity parameters LB by the equation lg K (20°C) = LA + LB.
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Affiliation(s)
- H Mayr
- a Department Chemie der Ludwig-Maximilians-Universität München , München , Germany
| | - A R Ofial
- a Department Chemie der Ludwig-Maximilians-Universität München , München , Germany
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9
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Chamorro E, Duque-Noreña M. Understanding the Highly Varying pKa of Arylamines. A Perspective from the Average Local Ionization Condensed-to-Atom Framework. J Phys Chem A 2015; 119:8156-62. [PMID: 26107310 DOI: 10.1021/acs.jpca.5b03252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly varying experimental pKa values for 36 arylamines spanning 7 orders of magnitude is carefully examined. Within this framework, a valence condensed-to-atom model for the average ionization energy is introduced and tested. The theoretical approach is connected to orbital Fukui functions directly mapped into semilocal or regional site-specific responses. It is revealed that the average local ionization energies associated with the amino nitrogen atom is linearly correlated to the basicity of the substituted arylamines, properly reproducing the experimental ordering of basicity. The condensed-to-atom descriptor exhibits a high predictive power, providing a new direct reactivity evaluation of significant value.
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Affiliation(s)
- Eduardo Chamorro
- Departamento de Ciencias Quimicas. Facultad de Ciencias Exactas. Nucleus Millennium of Chemical Processes and Catalysis, Universidad Andres Bello, Avenida República 275, 8370146 Santiago, Chile
| | - Mario Duque-Noreña
- Departamento de Ciencias Quimicas. Facultad de Ciencias Exactas. Nucleus Millennium of Chemical Processes and Catalysis, Universidad Andres Bello, Avenida República 275, 8370146 Santiago, Chile
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Latino DARS, Pereira F. Exploration of Quantitative StructureReactivity Relationships for the Estimation ofMayrNucleophilicity. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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On the intrinsic reactivity index for electrophilicity/nucleophilicity responses. J Mol Model 2015; 21:53. [DOI: 10.1007/s00894-015-2608-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/01/2015] [Indexed: 10/24/2022]
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Mayr H, Ammer J, Baidya M, Maji B, Nigst TA, Ofial AR, Singer T. Scales of Lewis basicities toward C-centered Lewis acids (carbocations). J Am Chem Soc 2015; 137:2580-99. [PMID: 25555037 DOI: 10.1021/ja511639b] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Equilibria for the reactions of benzhydryl cations (Ar2CH(+)) with phosphines, tert-amines, pyridines, and related Lewis bases were determined photometrically in CH2Cl2 and CH3CN solution at 20 °C. The measured equilibrium constants can be expressed by the sum of two parameters, defined as the Lewis Acidity (LA) of the benzhydrylium ions and the Lewis basicity (LB) of the phosphines, pyridines, etc. Least-squares minimization of log K = LA + LB with the definition LA = 0 for (4-MeOC6H4)2CH(+) gave a Lewis acidity scale for 18 benzhydrylium ions covering 18 orders of magnitude in CH2Cl2 as well as Lewis basicities (with respect to C-centered Lewis acids) for 56 bases. The Lewis acidities correlated linearly with the quantum chemically calculated (B3LYP/6-311++G(3df,2pd)//B3LYP/6-31G(d,p) level) methyl anion affinities of the corresponding benzhydrylium ions, which can be used as reference compounds for characterizing a wide variety of Lewis bases. The equilibrium measurements were complemented by isothermal titration calorimetry studies. Rates of SN1 solvolyses of benzhydryl chlorides, bromides, and tosylates derived from E(13-33)(+), i.e., from highly reactive carbocations, correlate excellently with the corresponding Lewis acidities and the quantum chemically calculated methyl anion affinities. This correlation does not hold for solvolyses of derivatives of the better stabilized amino-substituted benzhydrylium ions E(1-12)(+). In contrast, the correlation between electrophilic reactivities and Lewis acidities (or methyl anion affinities) is linear for all donor-substituted benzhydrylium ions E(1-21)(+), while the acceptor-substituted benzhydrylium ions E(26-33)(+) react more slowly than expected from their thermodynamic stabilities. The boundaries of linear rate-equilibrium relationships were thus defined.
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Affiliation(s)
- Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München , Butenandtstraße 5-13, Haus F, 81377 München, Germany
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Gorbunova TI, Subbotina JO, Saloutin VI, Chupakhin ON. Reactivity of polychlorinated biphenyls in nucleophilic and electrophilic substitutions. JOURNAL OF HAZARDOUS MATERIALS 2014; 278:491-499. [PMID: 25005155 DOI: 10.1016/j.jhazmat.2014.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
To explain the chemical reactivity of polychlorinated biphenyls in nucleophilic (S(N)) and electrophilic (S(E)) substitutions, quantum chemical calculations were carried out at the B3LYP/6-31G(d) level of the Density Functional Theory in gas phase. Carbon atomic charges in biphenyl structure were calculated by the Atoms-in-Molecules method. Chemical hardness and global electrophilicity index parameters were determined for congeners. A comparison of calculated descriptors and experimental data for congener reactivity in the S(N) and S(E) reactions was made. It is shown that interactions in the S(N) mechanism are reactions of the hard acid-hard base type, these are the most effective in case of highly chlorinated substrates. To explain the congener reactivity in the SE reactions, correct descriptors were not established. The obtained results can be used to carry out chemical transformations of the polychlorinated biphenyls in order to prepare them for microbiological destruction or preservation.
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Affiliation(s)
- Tatyana I Gorbunova
- I. Ya. Postovskii Institute of Organic Synthesis, Ural Branch, Russian Academy of Sciences, Kovalevskoy St., 22, Ekaterinburg 620990, Russia.
| | - Julia O Subbotina
- Ural Federal University named after the first President of Russia B.N. Yeltsin, Mira St., 19, Ekaterinburg 620002, Russia
| | - Viktor I Saloutin
- I. Ya. Postovskii Institute of Organic Synthesis, Ural Branch, Russian Academy of Sciences, Kovalevskoy St., 22, Ekaterinburg 620990, Russia
| | - Oleg N Chupakhin
- I. Ya. Postovskii Institute of Organic Synthesis, Ural Branch, Russian Academy of Sciences, Kovalevskoy St., 22, Ekaterinburg 620990, Russia
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Bondarchuk SV, Minaev BF. State-Dependent Global and Local Electrophilicity of the Aryl Cations. J Phys Chem A 2014; 118:3201-10. [DOI: 10.1021/jp501740p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sergey V. Bondarchuk
- Department
of Organic Chemistry, Bogdan Khmelnitsky Cherkasy National University, Boulevard Shevchenko 81, 18031 Cherkasy, Ukraine
| | - Boris F. Minaev
- Department
of Organic Chemistry, Bogdan Khmelnitsky Cherkasy National University, Boulevard Shevchenko 81, 18031 Cherkasy, Ukraine
- Department
of Chemistry, Tomsk State University, Prospekt Lenina 36, 634050 Tomsk, Russian Federation
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Chamorro E, Pérez P, Domingo LR. On the nature of Parr functions to predict the most reactive sites along organic polar reactions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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