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Norjmaa G, Rebek J, Himo F. Modeling Amine Methylation in Methyl Ester Cavitand. Chemistry 2024:e202303911. [PMID: 38224206 DOI: 10.1002/chem.202303911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 01/16/2024]
Abstract
Methylation of amines inside an introverted resorcinarene-based deep methyl ester cavitand is investigated by means of molecular dynamics simulations and quantum chemical calculations. Experimentally, the cavitand has been shown to bind a number of amines and accelerate the methylation reaction by more than four orders of magnitude for some of them. Eight different amines are considered in the present study, and the geometries and energies of their binding to the cavitand are first characterized and analyzed. Next, the methyl transfer reactions are investigated and the calculated barriers are found to be in generally good agreement with experimental results. In particular, the experimentally-observed rate acceleration in the cavitand as compared to the solution reaction is well reproduced by the calculations. The origins of this rate acceleration are analyzed by computational modifications made to the structure of the cavitand, and the role of the solvent is discussed.
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Affiliation(s)
- Gantulga Norjmaa
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, California, United States
- Center for Supramolecular Chemistry and Catalysis, Shanghai University, 200444, Shanghai, P. R. China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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2
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Study on geometry and chemical activity of twisted cucurbit[13]uril based on density functional theory. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02146-8] [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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Robles-Navarro A, Cárdenas C, Fuentealba P. Electronegativity under Confinement. Molecules 2021; 26:molecules26226924. [PMID: 34834015 PMCID: PMC8620044 DOI: 10.3390/molecules26226924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree–Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures.
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Affiliation(s)
- Andrés Robles-Navarro
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Estación Central, Santiago 9170124, Chile
- Correspondence: (C.C.); (P.F.)
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Estación Central, Santiago 9170124, Chile
- Correspondence: (C.C.); (P.F.)
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Pal R, Poddar A, Chattaraj PK. Atomic Clusters: Structure, Reactivity, Bonding, and Dynamics. Front Chem 2021; 9:730548. [PMID: 34485247 PMCID: PMC8415529 DOI: 10.3389/fchem.2021.730548] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Atomic clusters lie somewhere in between isolated atoms and extended solids with distinctly different reactivity patterns. They are known to be useful as catalysts facilitating several reactions of industrial importance. Various machine learning based techniques have been adopted in generating their global minimum energy structures. Bond-stretch isomerism, aromatic stabilization, Rener-Teller effect, improved superhalogen/superalkali properties, and electride characteristics are some of the hallmarks of these clusters. Different all-metal and nonmetal clusters exhibit a variety of aromatic characteristics. Some of these clusters are dynamically stable as exemplified through their fluxional behavior. Several of these cluster cavitands are found to be agents for effective confinement. The confined media cause drastic changes in bonding, reactivity, and other properties, for example, bonding between two noble gas atoms, and remarkable acceleration in the rate of a chemical reaction under confinement. They have potential to be good hydrogen storage materials and also to activate small molecules for various purposes. Many atomic clusters show exceptional opto-electronic, magnetic, and nonlinear optical properties. In this Review article, we intend to highlight all these aspects.
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Affiliation(s)
- Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Arpita Poddar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
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Pal R, Chattaraj PK. Possible effects of fluxionality of a cavitand on its catalytic activity through confinement. Phys Chem Chem Phys 2021; 23:15817-15834. [PMID: 34169304 DOI: 10.1039/d1cp01826d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The discovery of fullerenes was a huge milestone in the scientific community, and with it came the urge to discover and analyze various small and large atomic and molecular clusters having a cavity. These cavitands of varied shapes and sizes have wide applications in the encapsulation of rare gas atoms to induce bond formation between them, storage of hydrogen and hydrocarbons to be used as alternative sources of fuel, catalyzation of otherwise slow reactions without using a catalyst, activation of small gas molecules, etc. Various cavitands like fullerenes, [ExBox]4+, cucurbit[n]urils, borospherenes, octa acid, etc. have been used for this purpose. Some clusters including cavitands exhibit fluxional behaviour. Systems in a confined environment often manifest interesting variations in their properties and behaviour, compared to their unconfined counterparts, facilitating the aforementioned applications. In this perspective article, we explore the possibility of making use of this extra degree of freedom, viz., the fluxionality, in changing the catalytic activity of the cavitand.
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Affiliation(s)
- Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, 721302, India
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Daver H, Rebek J, Himo F. Modeling the Reaction of Carboxylic Acids and Isonitriles in a Self-Assembled Capsule. Chemistry 2020; 26:10861-10870. [PMID: 32428333 PMCID: PMC7522688 DOI: 10.1002/chem.202001735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/11/2020] [Indexed: 11/10/2022]
Abstract
Quantum chemical calculations were used to study the reaction of carboxylic acids with isonitriles inside a resorcinarene-based self-assembled capsule. Experimentally, it has been shown that the reactions between p-tolylacetic acid and n-butyl isonitrile or isopropyl isonitrile behave differently in the presence of the capsule compared both with each other and also with their solution counterparts. Herein, the reasons for these divergent behaviors are addressed by comparing the detailed energy profiles for the reactions of the two isonitriles inside and outside the capsule. An energy decomposition analysis was conducted to quantify the different factors affecting the reactivity. The calculations reproduce the experimental findings very well. Thus, encapsulation leads to lowering of the energy barrier for the first step of the reaction, the concerted α-addition and proton transfer, which in solution is rate-determining, and this explains the rate acceleration observed in the presence of the capsule. The barrier for the final step of the reaction, the 1,3 O→N acyl transfer, is calculated to be higher with the isopropyl substituent inside the capsule compared with n-butyl. With the isopropyl substituent, the transition state and the product of this step are significantly shorter than the preceding intermediate, and this results in energetically unfavorable empty spaces inside the capsule, which cause a higher barrier. With the n-butyl substituent, on the other hand, the carbon chain can untwine and hence uphold an appropriate guest length.
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Affiliation(s)
- Henrik Daver
- Department of Organic ChemistryArrhenius LaboratoryStockholm University106 91StockholmSweden
- Present address: Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology and Department of ChemistryThe Scripps Research Institute10550 North Torrey Pines RoadLa JollaCalifornia92037USA
- Center for Supramolecular Chemistry and CatalysisShanghai UniversityShanghai200444P.R. China
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University106 91StockholmSweden
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Levi S, Zhang Q, Major DT. Thermodynamic and Kinetic Control Determine the Sesquiterpene Reaction Pathways Inside Nanocapsules. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Qi Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan 610064, P.R. China
| | - Dan T. Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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Caramori GF, Østrøm I, Ortolan AO, Nagurniak GR, Besen VM, Muñoz-Castro A, Orenha RP, Parreira RLT, Galembeck SE. The usefulness of energy decomposition schemes to rationalize host–guest interactions. Dalton Trans 2020; 49:17457-17471. [DOI: 10.1039/d0dt03518a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The findings reported here reveal the robustness and practical application of EDA-NOCV in rationalizing molecular recognition situations in host–guest systems.
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Affiliation(s)
| | - Ina Østrøm
- Department of Chemistry
- Federal University of Santa Catarina
- Florianópolis
- Brazil
| | | | | | - Vitor M. Besen
- Department of Chemistry
- Federal University of Santa Catarina
- Florianópolis
- Brazil
| | - Alvaro Muñoz-Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares
- Facultad de Ingeniería
- Universidad Autonoma de Chile
- Santiago
- Chile
| | - Renato P. Orenha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
| | - Renato L. T. Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
| | - Sérgio E. Galembeck
- Departamento de Química
- Faculdade de Filosofia
- Ciências e Letras de Ribeirão Preto
- Universidade de São Paulo
- Ribeirão Preto
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Chakraborty D, Chattaraj PK. Bonding, Reactivity, and Dynamics in Confined Systems. J Phys Chem A 2019; 123:4513-4531. [DOI: 10.1021/acs.jpca.9b00830] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Confinement induced catalytic activity in a Diels-Alder reaction: comparison among various CB[n], n = 6–8, cavitands. J Mol Model 2018; 24:228. [PMID: 30097736 DOI: 10.1007/s00894-018-3765-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/27/2018] [Indexed: 11/27/2022]
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Venkataramanan NS, Suvitha A, Kawazoe Y. Unravelling the nature of binding of cubane and substituted cubanes within cucurbiturils: A DFT and NCI study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.03.071] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Goehry C, Besora M, Maseras F. Computational Description of a Huisgen Cycloaddition Inside a Self-Assembled Nanocapsule. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Charles Goehry
- Institute of Chemical Research of Catalonia (ICIQ); The Barcelona Institute of Science and Technology; Avgda. Paı̈sos Catalans 16 43007 Tarragona Catalonia Spain
| | - Maria Besora
- Institute of Chemical Research of Catalonia (ICIQ); The Barcelona Institute of Science and Technology; Avgda. Paı̈sos Catalans 16 43007 Tarragona Catalonia Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ); The Barcelona Institute of Science and Technology; Avgda. Paı̈sos Catalans 16 43007 Tarragona Catalonia Spain
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Catalonia Spain
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Chakraborty D, Chattaraj PK. Host-guest interactions between octa acid and cations/nucleobases. J Comput Chem 2018; 39:161-175. [PMID: 29105789 DOI: 10.1002/jcc.25097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022]
Abstract
The nature of host-guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li+ , Na+ , K+ , Be+2 , Mg+2 , Ca+2 , Li3 O+ , Na3 O+ , K3 O+ ) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)-based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298.15 K temperature and one atmospheric pressure. OA exhibits high selectivity in binding the lighter cations/metal cluster cations as compared to the heavier congeners along each given series. Moreover, OA exhibits enhanced affinity as well as selectivity in binding A/G/TTF molecules as compared to C/T/U. Noncovalent interaction and energy decomposition analyses reveal that in addition to the van der Waals interaction, significant contribution from electrostatic as well as orbital interactions dictate the outcome in all the host-guest complexes. Time dependent DFT calculations have been carried out to assess the role of the guests in tuning the electronic properties as well as absorption spectrum of OA. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
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Chakraborty D, Chattaraj PK. Confinement induced thermodynamic and kinetic facilitation of some Diels-Alder reactions inside a CB[7] cavitand. J Comput Chem 2017; 39:151-160. [PMID: 29094421 DOI: 10.1002/jcc.25094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
The effect of geometrical confinement on the Diels-Alder reactions between some model dienes viz. furan, thiophene, cyclopentadiene, benzene, and a classic dienophile, ethylene has been explored by performing density functional theory-based calculations. The effect of confinement has been imposed by a rigid macrocyclic molecule cucurbit[7]uril (CB[7]). Results indicate that all the reactions become thermodynamically more favorable at 298.15 K temperature and one atmospheric pressure inside CB[7] as compared to the corresponding free gaseous state reactions. Moreover, the rate constants associated with the reactions experience manifold enhancement inside CB[7] as compared to the "unconfined" reactions. Suitable contribution from the entropy factor makes the concerned reactions more facile inside CB[7]. The energy gap between the frontier molecular orbitals of the dienes and dienophiles decrease inside CB[7] as compared to that in the free state reactions thereby allowing facile orbital interactions. The nature of interaction as well as bonding has been analyzed with the help of atoms-in-molecules, noncovalent interaction, natural bond orbital as well as energy decomposition analyses. Results suggest that all the guests bind with CB[7] in an attractive fashion. Primarily, noncovalent interactions stabilize the host-guest systems. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
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Chakraborty D, Das R, Chattaraj PK. Change in optoelectronic properties of ExBox+4 on functionalization and guest encapsulation. Phys Chem Chem Phys 2017; 19:23373-23385. [DOI: 10.1039/c7cp02433a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
High non-linear optical properties could be derived from the ExBox+4 moiety due to functionalization as well as suitable guest encapsulation.
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Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Ranjita Das
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies
- Indian Institute of Technology
- Kharagpur 721302
- India
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