1
|
Berthold C, Müller M, Ivlev SI, Andrada DM, Buchner MR. Gauging ambiphilicity of pseudo-halides via beryllium-trispyrazolylborato compounds. Dalton Trans 2023; 52:13547-13554. [PMID: 37721484 DOI: 10.1039/d3dt02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The ambiphilicity of pseudo-halides has been the object of extensive debate. Herein, we use a series of trispyrazolylborato beryllium pseudo-halido complexes [TpBe(X')] with X' = CN-, N3-, NCO- and NCS- to explore the origins of the preferred isomers. Thus, we have synthesised and characterised through NMR and IR spectroscopy as well as single crystal X-ray diffraction these complexes. A combination with quantum chemical calculations within the DFT framework enabled an in-depth understanding of the bonding modes and preferences of the investigated pseudo-halido ligands.
Collapse
Affiliation(s)
- Chantsalmaa Berthold
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Matthias Müller
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Sergei I Ivlev
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| | - Diego M Andrada
- General and Inorganic Chemistry Department, University of Saarland, Campus C4.1, 66123 Saarbruecken, Germany.
| | - Magnus R Buchner
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany.
| |
Collapse
|
2
|
Dékány AÁ, Czakó G. Exploring the versatile reactivity of the F- + SiH3Cl system on a full-dimensional coupled-cluster potential energy surface. J Chem Phys 2023; 158:2895234. [PMID: 37290077 DOI: 10.1063/5.0153083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023] Open
Abstract
We develop a full-dimensional analytical potential energy surface (PES) for the F- + SiH3Cl reaction using Robosurfer for automatically sampling the configuration space, the robust [CCSD-F12b + BCCD(T) - BCCD]/aug-cc-pVTZ composite level of theory for computing the energy points, and the permutationally invariant polynomial method for fitting. Evolution of the fitting error and the percentage of the unphysical trajectories are monitored as a function of the iteration steps/number of energy points and polynomial order. Quasi-classical trajectory simulations on the new PES reveal rich dynamics resulting in high-probability SN2 (SiH3F + Cl-) and proton-transfer (SiH2Cl- + HF) products as well as several lower-probability channels, such as SiH2F- + HCl, SiH2FCl + H-, SiH2 + FHCl-, SiHFCl- + H2, SiHF + H2 + Cl-, and SiH2 + HF + Cl-. The Walden-inversion and front-side-attack-retention SN2 pathways are found to be competitive, producing nearly racemic products at high collision energies. The detailed atomic-level mechanisms of the various reaction pathways and channels as well as the accuracy of the analytical PES are analyzed along representative trajectories.
Collapse
Affiliation(s)
- Attila Á Dékány
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| |
Collapse
|
3
|
da Silva LP, Almeida-Neto FWQ, Bezerra LL, Silva J, Monteiro NKV, Marinho MM, Dos Santos HS, Teixeira AMR, Marinho ES, de Lima-Neto P. Sulfonamide derived from anacardic acid as potential antichagasic: a theoretical approach based on molecular docking, molecular dynamics, and density functional theory calculations. J Mol Model 2023; 29:165. [PMID: 37117952 DOI: 10.1007/s00894-023-05566-9] [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: 10/24/2022] [Accepted: 04/19/2023] [Indexed: 04/30/2023]
Abstract
Chagas disease (CD) is a tropical disease caused by the parasite Trypanosoma cruzi, transmitted by the barber insect. Currently, there are approximately 7 million infected people in the world, and it is estimated that 70 million people could contract this disease. The anacardic acid (AA) showed effectiveness in in silico and in vitro tests. The antichagasic potential of five sulfonamide molecules, derived from anacardic acid, was evaluated from a molecular approach based on the density functional theory (DFT), molecular dynamics (MD), and molecular docking (docking) calculations. Methyl 2-methoxy-6- (8- (methylsulfonamide) octyl) benzoate (SA1); 2-methoxy-6- (8- (phenylsulfonamide) octyl) benzoate (SA2); methyl 2-methoxy-6- (8- (2methylphenyl sulfonamide) octyl) benzoate (SA3); methyl 2-methoxy-6- (8-(methylphenylsulfonamide)octyl)benzoate (SA4); methyl2-(8-(2,5-dimethylphenylsulfonamide)octyl)-6-methoxybenzoate (SA5) were the investigated molecules. The DFT calculations were performed using the B3LYP/6-311+G (d, p) level of theory. The global and local reactivity data showed that SA1 shows the highest molecular reactivity, while SA2 is the most stable derivative. In addition, the structures of investigated molecules were confirmed by the linear correlations higher than 0.98 displayed between the experimental and calculated spectroscopic data (IR and NMR). Molecular docking of the molecules showed a greater prominence for the SA1, SA2, and SA4 molecules in the results of distances of ligand-cruzain. In molecular dynamics, SA2 obtained better stability due to greater interactions with important amino acids of cruzain.
Collapse
Affiliation(s)
- Leonardo P da Silva
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil.
| | | | - Lucas L Bezerra
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
| | - Jacilene Silva
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
| | - Norberto K V Monteiro
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
| | - Márcia M Marinho
- Faculdade de Educação, Ciência e Letras de Iguatu, Universidade Estadual do Ceará, Iguatu, Ceará, Brazil
| | - Hélcio S Dos Santos
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
- Centro de Ciências e Tecnologia, Curso de Química, Universidade Vale do Acaraú, Sobral, Ceará, Brazil
| | - Alexandre M R Teixeira
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
- Departamento de Física, Universidade Regional do Cariri, Crato, Ceará, Brazil
| | - Emmanuel S Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Limoeiro do Norte, CE, Brazil
| | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
| |
Collapse
|
4
|
Bettens T, Alonso M, Geerlings P, De Proft F. Mechanochemical Felkin-Anh Model: Achieving Forbidden Reaction Outcomes with Mechanical Force. J Org Chem 2023; 88:2046-2056. [PMID: 36735279 DOI: 10.1021/acs.joc.2c02318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Anti-Felkin-Anh diastereoselectivity can be achieved for nucleophilic additions to α-chiral ketones upon stretching the ketone with a mechanical pulling force. Herein, a mechanochemical Felkin-Anh model is proposed for predicting the outcome of a nucleophilic addition to an α-chiral ketone. Essentially, the fully stretched chiral ketone has one substituent shielding each side of the carbonyl, in contrast to the Felkin-Anh model, in which free rotation around a bond is required to achieve the two rotamers of the ketone. Depending on the pulling scenario, either Felkin-Anh or anti-Felkin-Anh diastereoselectivity is obtained. The model is entirely based on the distance between the pulling points, which is maximized in the anti-periplanar arrangement. The major diastereomer is associated with the approach with the least steric interactions. The intuitive model is validated by means of mechanochemical density functional theory calculations. Importantly, the ketone is fully stretched in the sub 1 nN force regime, thus minimizing the risk of undesired homolytic bond rupture. Moreover, the mechanical force is not used for lowering the reaction barriers associated with the nucleophilic addition; instead, it is solely applied for locking the conformation of a molecule and provoking otherwise inaccessible reaction pathways on the force-modified potential energy surface.
Collapse
Affiliation(s)
- Tom Bettens
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050Brussels, Belgium
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050Brussels, Belgium
| |
Collapse
|
5
|
Escorihuela J, Wolf LM. Computational Study on the Co-Mediated Intramolecular Pauson–Khand Reaction of Fluorinated and Chiral N-Tethered 1,7-Enynes. Organometallics 2022; 41:2525-2534. [PMID: 36185394 PMCID: PMC9516775 DOI: 10.1021/acs.organomet.2c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 11/28/2022]
Abstract
![]()
The Co2(CO)8-mediated intramolecular
Pauson–Khand
reaction is an elegant approach to obtain cyclopentenone derivatives
containing asymmetric centers. In this work, we employed density functional
theory calculations at the M11/6-311+G(d,p) level of theory to investigate
the mechanism and reactivity for the Pauson–Khand reaction
of fluorinated and asymmetric N-tethered 1,7-enynes.
The rate-determining step was found to be the intramolecular alkene
insertion into the carbon–cobalt bond. The stereoselectivity
of the alkene insertion step was rationalized by the different transition
states showing the coordination of the alkene through the Re- and Si-face. The effects of different
fluorine groups and steric effects on both the alkenyl and alkynyl
moieties were also theoretically investigated.
Collapse
Affiliation(s)
- Jorge Escorihuela
- Departamento de Química Orgánica, Facultad de Farmacia, Universitat de València, Av. Vicent Andrés Estellés s/n, 46100Burjassot, València, Spain
| | - Lawrence M. Wolf
- Department of Chemistry, University of Massachusetts−Lowell, 1 University Avenue, Lowell, Massachusetts01854, United States
| |
Collapse
|
6
|
Cadena M, Villatoro RS, Gupta JS, Phillips C, Allen JB, Arman HD, Wherritt DJ, Clanton NA, Ruchelman AL, Simmons EM, DelMonte AJ, Coombs JR, Frantz DE. Pd-Catalyzed Chemoselective O-Benzylation of Ambident 2-Quinolinone Nucleophiles. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Melissa Cadena
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Roberto Silva Villatoro
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jyoti Shah Gupta
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Cody Phillips
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jonathan B. Allen
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Hadi D. Arman
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Daniel J. Wherritt
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Nicholas A. Clanton
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Alexander L. Ruchelman
- Chemical Process Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Eric M. Simmons
- Chemical Process Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Albert J. DelMonte
- Chemical Process Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - John R. Coombs
- Chemical Process Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Doug E. Frantz
- The Max and Minnie Tomerlin Voelcker Laboratory for Organic Chemistry, Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| |
Collapse
|
7
|
García-Aznar P, Escorihuela J. Computational insights into the inverse electron-demand Diels-Alder reaction of norbornenes with 1,2,4,5-tetrazines: norbornene substituents' effects on the reaction rate. Org Biomol Chem 2022; 20:6400-6412. [PMID: 35876298 DOI: 10.1039/d2ob01121b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of the reaction rates and mechanism of click chemistry reactions still remains an interesting challenge in organic chemistry. In this regard, the inverse electron demand Diels-Alder (IEDDA) reaction represents a promising metal-free alternative with enhanced reaction rates compared to other reactions of the click chemistry toolbox. Among the different types of dienophiles used in the IEDDA reactions, norbornenes have been widely used given their high stability and fast reaction rates. The inverse electron-demand Diels Alder reaction of 3,6-dipyridin-2-yl-1,2,4,5-tetrazine with a series of norbornene derivatives was studied with quantum mechanical calculations at the M06-2X/6-311+G(d,p) level of theory. The theoretical predictions were confirmed with the experimental data and analyzed with the use of the distortion/interaction model. The obtained results will help in obtaining a better understanding of the factors that affect the relative cycloaddition rates of norbornenes with tetrazines, which are crucial for selectively tuning their efficacy.
Collapse
Affiliation(s)
- Pablo García-Aznar
- Departamento de Química Orgánica, Facultad de Farmacia, Universitat de València, Avda. Vicente Andrés Estellés, s/n, Burjassot 46100, València, Spain.
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Facultad de Farmacia, Universitat de València, Avda. Vicente Andrés Estellés, s/n, Burjassot 46100, València, Spain.
| |
Collapse
|
8
|
Dékány AÁ, Kovács GZ, Czakó G. High-Level Systematic Ab Initio Comparison of Carbon- and Silicon-Centered S N2 Reactions. J Phys Chem A 2021; 125:9645-9657. [PMID: 34709818 PMCID: PMC8591615 DOI: 10.1021/acs.jpca.1c07574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
We characterize the
stationary points along the Walden inversion,
front-side attack, and double-inversion pathways of the X– + CH3Y and X– + SiH3Y [X,
Y = F, Cl, Br, I] SN2 reactions using chemically accurate
CCSD(T)-F12b/aug-cc-pVnZ [n = D,
T, Q] levels of theory. At the carbon center, Walden inversion dominates
and proceeds via prereaction (X–···H3CY) and postreaction (XCH3···Y–) ion-dipole wells separated by a usually submerged
transition state (X–H3C–Y)−, front-side attack occurs over high barriers, double inversion is
the lowest-energy retention pathway for X = F, and hydrogen- (F–···HCH2Y) and halogen-bonded
(X–···YCH3) complexes
exist in the entrance channel. At the silicon center, Walden inversion
proceeds through a single minimum (X–SiH3–Y)−, the front-side attack is competitive via a usually
submerged transition state separating pre- and postreaction minima
having X–Si–Y angles close to 90°, double inversion
occurs over positive, often high barriers, and hydrogen- and halogen-bonded
complexes are not found. In addition to the SN2 channels
(Y– + CH3X/SiH3X), we report
reaction enthalpies for proton abstraction (HX + CH2Y–/SiH2Y–), hydride substitution
(H– + CH2XY/SiH2XY), XH···Y– complex formation (XH···Y– + 1CH2/1SiH2), and halogen
abstraction (XY + CH3–/SiH3– and XY– + CH3/SiH3).
Collapse
Affiliation(s)
- Attila Á Dékány
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gyula Z Kovács
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| |
Collapse
|
9
|
Reddy Indukuri D, Reddy Potuganti G, Maria Cherian A, Babu Nanubolu J, Soujanya Y, Alla M. Multicomponent Domino Approaches for the Synthesis of Spirooxazolidine‐2‐thiones and Spirooxothiolane‐2‐imines. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Divakar Reddy Indukuri
- Fluoro and Agrochemicals Department CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research Ghaziabad 201002 India
| | - Gal Reddy Potuganti
- Fluoro and Agrochemicals Department CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research Ghaziabad 201002 India
| | - Arsha Maria Cherian
- Division of Polymers and Functional Materials CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
| | - Jagadeesh Babu Nanubolu
- Academy of Scientific and Innovative Research Ghaziabad 201002 India
- Center for X-ray Crystallography CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
| | - Yarasi Soujanya
- Academy of Scientific and Innovative Research Ghaziabad 201002 India
- Division of Polymers and Functional Materials CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
| | - Manjula Alla
- Fluoro and Agrochemicals Department CSIR-Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research Ghaziabad 201002 India
| |
Collapse
|
10
|
Gómez T, Fuentealba P, Robles-Navarro A, Cárdenas C. Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule. J Comput Chem 2021; 42:1681-1688. [PMID: 34121207 DOI: 10.1002/jcc.26705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 02/01/2023]
Abstract
This paper presents a brief summary of the difficulty that resides in the definition of the elusive concept of local chemical hardness. We argue that a definition of local hardness should be useful to a reactivity principle and not just as a mere definition. We then continue with a formal discussion about the benefits and difficulties of using the Fukui potential, which is interpreted as an alchemical derivative (alchemical hardness), as descriptor of local hardness of molecules. Computational evidence shows that the alchemical hardness is at least as good a descriptor as the combination of other two well-stabilized descriptors of local hardness, such as the Fukui function and grand canonical local hardness. Although our results are auspicious for the alchemical hardness as descriptor of local hardness, we finish by calling the attention of the community on the importance of discussing the raison d'être of a local hardness function and its main characteristics. We suggest that an axiomatic construction of local hardness could be they way of constructing a local hardness which is both useful and free of arbitrariness.
Collapse
Affiliation(s)
- Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago, Chile
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago, Chile
| | | | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago, Chile
| |
Collapse
|
11
|
Vermeeren P, Hamlin TA, Bickelhaupt FM. Chemical reactivity from an activation strain perspective. Chem Commun (Camb) 2021; 57:5880-5896. [PMID: 34075969 PMCID: PMC8204247 DOI: 10.1039/d1cc02042k] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.
Collapse
Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands. and Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
12
|
Deraet X, Turek J, Alonso M, Tielens F, Cottenier S, Ayers PW, Weckhuysen BM, De Proft F. Reactivity of Single Transition Metal Atoms on a Hydroxylated Amorphous Silica Surface: A Periodic Conceptual DFT Investigation. Chemistry 2021; 27:6050-6063. [PMID: 33368741 DOI: 10.1002/chem.202004660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/15/2020] [Indexed: 11/08/2022]
Abstract
The drive to develop maximal atom-efficient catalysts coupled to the continuous striving for more sustainable reactions has led to an ever-increasing interest in single-atom catalysis. Based on a periodic conceptual density functional theory (cDFT) approach, fundamental insights into the reactivity and adsorption of single late transition metal atoms supported on a fully hydroxylated amorphous silica surface have been acquired. In particular, this investigation revealed that the influence of van der Waals dispersion forces is especially significant for a silver (98 %) or gold (78 %) atom, whereas the oxophilicity of the Group 8-10 transition metals plays a major role in the interaction strength of these atoms on the irreducible SiO2 support. The adsorption energies for the less-electronegative row 4 elements (Fe, Co, Ni) ranged from -1.40 to -1.92 eV, whereas for the heavier row 5 and 6 metals, with the exception of Pd, these values are between -2.20 and -2.92 eV. The deviating behavior of Pd can be attributed to a fully filled d-shell and, hence, the absence of the hybridization effects. Through a systematic analysis of cDFT descriptors determined by using three different theoretical schemes, the Fermi weighted density of states approach was identified as the most suitable for describing the reactivity of the studied systems. The main advantage of this scheme is the fact that it is not influenced by fictitious Coulomb interactions between successive, charged reciprocal cells. Moreover, the contribution of the energy levels to the reactivity is simultaneously scaled based on their position relative to the Fermi level. Finally, the obtained Fermi weighted density of states reactivity trends show a good agreement with the chemical characteristics of the investigated metal atoms as well as the experimental data.
Collapse
Affiliation(s)
- Xavier Deraet
- Department of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Elsene, Brussels, Belgium
| | - Jan Turek
- Department of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Elsene, Brussels, Belgium
| | - Mercedes Alonso
- Department of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Elsene, Brussels, Belgium
| | - Frederik Tielens
- Department of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Elsene, Brussels, Belgium
| | - Stefaan Cottenier
- Department of Electrical Energy, Metals, Mechanical Constructions and Systems, Ghent University, Technologiepark 46, 9052, Zwijnaarde, Belgium.,Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052, Zwijnaarde, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Frank De Proft
- Department of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Elsene, Brussels, Belgium
| |
Collapse
|
13
|
Rodrigues Silva D, de Azevedo Santos L, Freitas MP, Guerra CF, Hamlin TA. Nature and Strength of Lewis Acid/Base Interaction in Boron and Nitrogen Trihalides. Chem Asian J 2020; 15:4043-4054. [PMID: 33015969 PMCID: PMC7756781 DOI: 10.1002/asia.202001127] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 11/25/2022]
Abstract
We have quantum chemically investigated the bonding between archetypical Lewis acids and bases. Our state-of-the-art computations on the X3 B-NY3 Lewis pairs have revealed the origin behind the systematic increase in B-N bond strength as X and Y are varied from F to Cl, Br, I, H. For H3 B-NY3 , the bonding trend is driven by the commonly accepted mechanism of donor-acceptor [HOMO(base)-LUMO(acid)] interaction. Interestingly, for X3 B-NH3 , the bonding mechanism is determined by the energy required to deform the BX3 to the pyramidal geometry it adopts in the adduct. Thus, Lewis acids that can more easily pyramidalize form stronger bonds with Lewis bases. The decrease in the strain energy of pyramidalization on going from BF3 to BI3 is directly caused by the weakening of the B-X bond strength, which stems primarily from the bonding in the plane of the molecule (σ-like) and not in the π system, at variance with the currently accepted mechanism.
Collapse
Affiliation(s)
- Daniela Rodrigues Silva
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Departamento de QuímicaUniversidade Federal de Lavras37200-900Lavras–MGBrazil
| | - Lucas de Azevedo Santos
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Departamento de QuímicaUniversidade Federal de Lavras37200-900Lavras–MGBrazil
| | - Matheus P. Freitas
- Departamento de QuímicaUniversidade Federal de Lavras37200-900Lavras–MGBrazil
| | - Célia Fonseca Guerra
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
- Leiden Institute of ChemistryGorlaeus LaboratoriesLeiden UniversityEinsteinweg 552333 CCLeiden (TheNetherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
| |
Collapse
|
14
|
Hoffmann G, Balcilar M, Tognetti V, Héroux P, Gaüzère B, Adam S, Joubert L. Predicting experimental electrophilicities from quantum and topological descriptors: A machine learning approach. J Comput Chem 2020. [DOI: 10.1002/jcc.26376] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Guillaume Hoffmann
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
| | | | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
| | - Pierre Héroux
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Benoît Gaüzère
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Sébastien Adam
- Normandie Univ., UNIROUEN, UNIHAVRE, INSA Rouen, LITIS Rouen France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS Mont St Aignan France
| |
Collapse
|
15
|
Hansen T, Vermeeren P, Haim A, van Dorp MJH, Codée JDC, Bickelhaupt FM, Hamlin TA. Regioselectivity of Epoxide Ring-Openings via SN
2 Reactions Under Basic and Acidic Conditions. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000590] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Anissa Haim
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Maarten J. H. van Dorp
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Jeroen D. C. Codée
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry; Amsterdam Institute of Molecular and Life Sciences (AIMMS); Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| |
Collapse
|
16
|
Stuyver T, De Proft F, Geerlings P, Shaik S. How Do Local Reactivity Descriptors Shape the Potential Energy Surface Associated with Chemical Reactions? The Valence Bond Delocalization Perspective. J Am Chem Soc 2020; 142:10102-10113. [PMID: 32366103 PMCID: PMC7304891 DOI: 10.1021/jacs.0c02390] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Indexed: 01/11/2023]
Abstract
How do local reactivity descriptors, such as the Fukui function and the local spin density distribution, shape the potential energy surface (PES) associated with chemical reactions and thus govern reactivity trends and regioselective preferences? This is the question that is addressed here through a qualitative valence bond (VB) analysis. We demonstrate that common density functional theory (DFT)-based local reactivity descriptors can essentially be regarded-in one way or another-as indirect measures of delocalization, i.e., resonance stabilization, of the reactants within VB theory. The inherent connection between (spatial) delocalization and (energetic) resonance stabilization embedded in VB theory provides a natural and elegant framework for analyzing and comprehending the impact of individual local reactivity descriptors on the global PES. Our analysis provides new insights into the role played by local reactivity descriptors and illustrates under which conditions they can sometimes fail to predict reactivity trends and regioselective preferences, e.g., in the case of ambident reactivity. This treatment constitutes a first step toward a unification of VB theory and conceptual DFT.
Collapse
Affiliation(s)
- Thijs Stuyver
- Institute
of Chemistry, The Hebrew University, Jerusalem 91904, Israel
- Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Frank De Proft
- Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Paul Geerlings
- Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sason Shaik
- Institute
of Chemistry, The Hebrew University, Jerusalem 91904, Israel
| |
Collapse
|
17
|
Bettens T, Alonso M, De Proft F, Hamlin TA, Bickelhaupt FM. Ambident Nucleophilic Substitution: Understanding Non-HSAB Behavior through Activation Strain and Conceptual DFT Analyses. Chemistry 2020; 26:3884-3893. [PMID: 31957943 PMCID: PMC7154642 DOI: 10.1002/chem.202000272] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 01/31/2023]
Abstract
The ability to understand and predict ambident reactivity is key to the rational design of organic syntheses. An approach to understand trends in ambident reactivity is the hard and soft acids and bases (HSAB) principle. The recent controversy over the general validity of this principle prompted us to investigate the competing gas-phase SN 2 reaction channels of archetypal ambident nucleophiles CN- , OCN- , and SCN- with CH3 Cl (SN 2@C) and SiH3 Cl (SN 2@Si), using DFT calculations. Our combined analyses highlight the inability of the HSAB principle to correctly predict the reactivity trends of these simple, model reactions. Instead, we have successfully traced reactivity trends to the canonical orbital-interaction mechanism and the resulting nucleophile-substrate interaction energy. The HOMO-LUMO orbital interactions set the trend in both SN 2@C and SN 2@Si reactions. We provide simple rules for predicting the ambident reactivity of nucleophiles based on our Kohn-Sham molecular orbital analysis.
Collapse
Affiliation(s)
- Tom Bettens
- Eenheid Algemene Chemie (ALGC)Vrije Universiteit BrusselPleinlaan 21050BrusselsBelgium
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC)Vrije Universiteit BrusselPleinlaan 21050BrusselsBelgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC)Vrije Universiteit BrusselPleinlaan 21050BrusselsBelgium
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081HVAmsterdamThe Netherlands
- Institute for Molecules and Materials (IMM)Radboud University NijmegenHeyendaalseweg 1356525AJNijmegenThe Netherlands
| |
Collapse
|