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Saha J, Banerjee S, Malo S, Das AK, Das I. A Torquoselective Thermal 6π-Electrocyclization Approach to 1,4-Cyclohexadienes via Solvent-Aided Proton Transfer: Experimental and Theoretical Studies. Chemistry 2024; 30:e202304009. [PMID: 38179806 DOI: 10.1002/chem.202304009] [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: 12/01/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/06/2024]
Abstract
The thermal 6π-electrocyclization of hexatriene typically delivers 1,3-cyclohexadiene (1,3-CHD). However, there is only limited success in directly synthesizing 1,4-cyclohexadiene (1,4-CHD) using such an approach, probably due to the difficulty in realizing thermally-forbidden 1,3-hydride shift after electrocyclic ring closure. The present study shows that by heating (2E,4E,6E)-hexatrienes bearing ester or ketone substituents at the C1-position in a mixture of toluene/MeOH or EtOH (2 : 1) solvents at 90-100 °C, 1,4-CHDs can be selectively synthesized. This is achieved through a torquoselective disrotatory 6π-electrocyclic ring closure followed by a proton-transfer process. The success of this method depends on the polar protic solvent-assisted intramolecular proton transfer from 1,3-CHD to 1,4-CHD, which has been confirmed by deuterium-labeling experiments. There are no reports to date for such a solvent-assisted isomerization. Density functional theory (DFT) studies have suggested that forming 1,3-CHD and subsequent isomerization is a thermodynamically feasible process, regardless of the functional groups involved. Two possible successive polar solvent-assisted proton-transfer pathways have been identified for isomerization.
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Affiliation(s)
- Jayanta Saha
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Soumadip Banerjee
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science Jadavpur, Kolkata, 700032, India
| | - Sidhartha Malo
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhijit Kumar Das
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science Jadavpur, Kolkata, 700032, India
| | - Indrajit Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical BiologyJadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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2
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Mohiti M, Lu Y, He H, Ni SF, Somfai P. Regio- and Enantioselective Synthesis of 1,2-Diamines by Formal Hydroamination of Enamines: Scope, Mechanism, and Asymmetric Synthesis of Orthogonally Protected Bis-Piperazines as a Privileged Scaffold. Chemistry 2024; 30:e202303078. [PMID: 38205968 DOI: 10.1002/chem.202303078] [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: 09/22/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/12/2024]
Abstract
We have previously reported the first formal hydroamination of enamines for the synthesis of chiral 1,2-diamines. Here, we describe: (i) the discovery, optimization, and substrate expansion of this reaction; (ii) a novel and straightforward protocol for the "click-type" synthesis of enamines in quantitative yield utilizing sodium sulfate in a dual role as an ancillary and dehydrating agent without the need for workup or purification; (iii) the application of this methodology to the first enantioselective synthesis of orthogonally protected 1,1'-(1-(4-fluorophenyl)ethane-1,2-diyl) piperazines, a scaffold for rapid lead optimization in drug discovery; (iv) a computational investigation into the mechanism and rationalization of the enantioselectivities of the reaction.
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Affiliation(s)
- Maziar Mohiti
- Center for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 22100, Lund, Sweden
| | - Yu Lu
- Center for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 22100, Lund, Sweden
| | - Hui He
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Shao-Fei Ni
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Peter Somfai
- Center for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 22100, Lund, Sweden
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3
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Saha J, Banerjee S, Malo S, Das AK, Das I. Thermally Activated Geometrical Regioselective E→Z Isomerization-Enabled Cascade Sequences of Conjugated Dienals: Experimental and DFT Studies. Chemistry 2023; 29:e202302335. [PMID: 37555389 DOI: 10.1002/chem.202302335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 08/10/2023]
Abstract
The geometrical regioselective E→Z isomerization of a conjugated alkene under thermal activation pose a challenge due to microscopic reversibility. Herein we report that such reversibility issues can be circumvented by integrating E→Z isomerization with subsequent cyclization cascade, particularly in the absence of commonly employed light, acids, or metal-catalysts. Thus, linearly conjugated dienals in a mixture of toluene-alcohol (2 : 1) solvents or only with alcohol at 60-70 °C can be converted to γ-alkoxybutenolides in moderate to good yields. The intermediary 2Z,4E-isomer can be isolated, which includes the first example of isolating the regioselective isomerization product under thermal conditions. Density functional theory (DFT) studies have been employed to shed light on the feasibility of geometrical alkene isomerization and ensuing cascade sequences. It has been observed that the regioselective 2E,4E→2Z,4E isomerization of dienal is a thermodynamically facile (ΔG <0) process. Structural elucidation further reveals that the presence of a certain charge transfer and a non-covalent interaction may be the primary reasons for the enhanced stability of the 2Z,4E-isomer. The thermodynamic plausibility of the subsequent cascade reaction from the Z-isomer to the anticipated product in the presence of a polar protic solvent (here MeOH) is also explicated. Out of the two probable pathways, the "hemiacetal pathway" involving a relay proton transfer is kinetically more feasible due to the diminished activation barrier than the "conjugate addition pathway".
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Affiliation(s)
- Jayanta Saha
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Soumadip Banerjee
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Sidhartha Malo
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhijit Kumar Das
- School of Mathematical and Computational Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Indrajit Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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4
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Uranga J, Mata RA. The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis. J Chem Inf Model 2023; 63:3118-3127. [PMID: 37127583 DOI: 10.1021/acs.jcim.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The enzyme acetoacetate decarboxylase (AAD) has a crucial function in the process of decarboxylating the substrate acetoacetate (AA). It has been extensively studied over the years, but its exact catalytic mechanism has remained partly unsolved due to the difficulty in assessing reaction intermediates. In this study, we combine molecular dynamics and electronic structure calculations to rediscover its catalytic mechanism. Our results show that the presence of the substrate, the acetoacetate, significantly influences the electrostatic potential of the active site. Furthermore, our simulations show that the decarboxylation reaction can take place by means of a direct proton transfer instead of via an enamine intermediate, which is thought to be strictly necessary. This work provides new insights into the role of the electrostatic interactions on the catalytic activity of AAD and for the first time connects it to the catalytic mechanism of other decarboxylases.
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Affiliation(s)
- Jon Uranga
- Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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5
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Smolobochkin AV, Gazizov AS, Yakhshilikova LJ, Sidlyaruk NA, Khamatgalimov AR, Burilov AR, Pudovik MA. Synthesis of substituted tetrahydropyrimidin-2-ones through nucleophilic cyclization / electrophilic substitution of 1-(3,3-diethoxypropyl)urea with C-nucleophiles. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Biesemans B, De Clercq J, Stevens CV, Thybaut JW, Lauwaert J. Recent advances in amine catalyzed aldol condensations. CATALYSIS REVIEWS 2022. [DOI: 10.1080/01614940.2022.2048570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bert Biesemans
- Laboratory for Chemical Technology (LCT), Department of Materials, Textiles, and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Ghent, Belgium
| | - Jeriffa De Clercq
- Industrial Catalysis and Adsorption Technology (INCAT), Department of Materials, Textiles, and Chemical Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Christian V. Stevens
- SynBioC Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Joris W. Thybaut
- Laboratory for Chemical Technology (LCT), Department of Materials, Textiles, and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Ghent, Belgium
| | - Jeroen Lauwaert
- Industrial Catalysis and Adsorption Technology (INCAT), Department of Materials, Textiles, and Chemical Engineering, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
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8
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Das M, Gogoi AR, Sunoj RB. Molecular Insights on Solvent Effects in Organic Reactions as Obtained through Computational Chemistry Tools. J Org Chem 2021; 87:1630-1640. [PMID: 34752092 DOI: 10.1021/acs.joc.1c02222] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Molecular understanding of the role of protic solvents in a gamut of organic transformations can be developed using density functional and ab initio computational studies focused on the reaction mechanism. Inclusion of explicit solvent molecules in the vital TSs has been proven to be valuable toward improving the energetic estimates of organocatalytic as well as transition-metal-catalyzed organic reactions. Herein, we provide an overview of the importance of an explicit-implicit solvation model using a number of interesting examples.
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Affiliation(s)
- Manajit Das
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achyut Ranjan Gogoi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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9
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Unnikrishnan A, Sunoj RB. Iridium-Catalyzed Regioselective Borylation through C-H Activation and the Origin of Ligand-Dependent Regioselectivity Switching. J Org Chem 2021; 86:15618-15630. [PMID: 34598435 DOI: 10.1021/acs.joc.1c02126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Research efforts in catalytic regioselective borylation using C-H bond activation of arenes have gained considerable recent attention. The ligand-enabled regiocontrol, such as in the borylation of benzaldehyde, the selectivity could be switched from the ortho to meta position, under identical conditions, by just changing the external ligand (L) from 8-aminoquinoline (8-AQ) to tetramethylphenanthroline (TMP). The DFT(B3LYP-D3) computations helped us learn that the energetically preferred catalytic pathway includes the formation of an Ir-π-complex between the active catalyst [Ir(L)(Bpin)3] and benzaldimine, a C-H bond oxidative addition (OA) to form an Ir(V)aryl-hydride intermediate, and a reductive elimination to furnish the borylated benzaldehyde as the final product. The lowest energetic span (δEortho = 26 kcal/mol with 8-AQ) is noted in the ortho borylation pathway, with the OA transition state (TS) as the turnover-determining TS. The change in regiochemical preference to the meta borylation (δEmeta = 26) with TMP is identified. A hemilabile mode of 8-AQ participation is found to exhibit a δEortho of 24 kcal/mol for the ortho borylation, relative to that in the chelate mode (δEortho = 26 kcal/mol). The predicted regioselectivity switching is in good agreement with the earlier experimental observations.
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Affiliation(s)
- Anju Unnikrishnan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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10
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Kirschtowski S, Jameel F, Stein M, Seidel-Morgenstern A, Hamel C. Kinetics of the reductive amination of 1-undecanal in thermomorphic multicomponent system. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Huxoll F, Jameel F, Bianga J, Seidensticker T, Stein M, Sadowski G, Vogt D. Solvent Selection in Homogeneous Catalysis—Optimization of Kinetics and Reaction Performance. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04431] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabian Huxoll
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Froze Jameel
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Jonas Bianga
- Laboratory of Industrial Chemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Thomas Seidensticker
- Laboratory of Industrial Chemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Gabriele Sadowski
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Dieter Vogt
- Laboratory of Industrial Chemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
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12
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Lu Z, Hammond GB, Xu B. Revisiting the role of acids and hydrogen bond acceptors in enamine formation. Org Biomol Chem 2020; 18:6849-6852. [PMID: 32852003 DOI: 10.1039/d0ob01579b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A systematic investigation into the effects of acids and hydrogen bond acceptors on the reaction rates and equilibria of enamine formation is reported. Acids can accelerate the reaction but do not change the reaction equilibria. In comparison, hydrogen bond acceptors facilitate the enamine formation via their strong hydrogen bonding interaction with the water generated in the reaction.
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Affiliation(s)
- Zhichao Lu
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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13
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Abstract
The proline-catalysed asymmetric aldol reaction is usually carried out in highly dipolar aprotic solvents (dimethylsulfoxide, dimethylformamide, acetonitrile) where proline presents an acceptable solubility. Protic solvents are generally characterized by poor stereocontrol (e.g., methanol) or poor reactivity (e.g., water). Here, we report that water/methanol mixtures are exceptionally simple and effective reaction media for the intermolecular organocatalytic aldol reaction using the simple proline as the catalyst.
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14
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Saa JM, Frontera A. On the Role of Water as a Catalyst in Prebiotic Chemistry. Chemphyschem 2020; 21:313-320. [PMID: 31904135 DOI: 10.1002/cphc.201901069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/17/2019] [Indexed: 12/20/2022]
Abstract
In this manuscript we provide computational support to the catalytic role of water in all kinds of pseudopericyclic reactions operating in the reductive acid cycle, as well as in other metabolic processes. Water catalysis is not limited to those reactions where simple translocation of hydrogen atoms occurs, such as those represented by NuH+E→Nu-EH general equation. Indeed, water catalysis is more general and extremely important in tautomerization reactions of the type HX-Y=Z→X=Y-ZH, which operate in the reductive citric acid cycle and metabolic processes. Moreover, the comprehensive theoretical study reported herein illustrates that these reactions appear to behave as authentic enzyme-catalyzed reactions showing Michaelis-Menten behavior, however with the abnormal singularity that the concentration of the catalytic "water clusters" of different length and nature must be taken as a huge number. Overall, the results presented are suggestive of the workability of the so-called "metabolism first" proposal in a hot water world, as water catalysis eliminates the dilution problem frequently associated to this proposal.
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Affiliation(s)
- José M Saa
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
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15
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Keshavarz F, Shcherbacheva A, Kubečka J, Vehkamäki H, Kurtén T. Computational Study of the Effect of Mineral Dust on Secondary Organic Aerosol Formation by Accretion Reactions of Closed-Shell Organic Compounds. J Phys Chem A 2019; 123:9008-9018. [PMID: 31556608 DOI: 10.1021/acs.jpca.9b06331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The effect of dust aerosols on accretion reactions of water, formaldehyde, and formic acid was studied in the conditions of earth's troposphere at the DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97X-D/6-31++G** level of theory. A detailed analysis of the reaction mechanisms in the gas phase and on the surface of mineral dust, represented by mono- and trisilicic acid, revealed that mineral dust has the potential of decreasing reaction barrier heights. Specifically, at 0 K, mineral dust can lower the apparent energy barrier of the reaction of formaldehyde with formic acid to zero. However, when the entropic contributions to the reaction free energies were accounted for, mineral dust was found to selectively enhance the reaction of water with formaldehyde, while inhibiting the reaction of formaldehyde and formic acid, in the lower parts of the troposphere (with temperatures around 298 K). In the upper troposphere (with temperatures closer to 198 K), mineral dust catalyzes both reactions and also the reaction of methanol with formic acid. Despite the intrinsic potential of mineral dust, calculation of the catalytic enhancement parameter for a likely range of dust aerosol concentrations suggested that dust aerosols will not contribute to secondary organic aerosol formation via dimerization of closed-shell organic compounds. The main reason for this is the relatively low absolute concentration of tropospheric dust aerosol and its inefficiency in increasing the effective reaction rate coefficients.
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16
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Faveere W, Mihaylov T, Pelckmans M, Moonen K, Gillis-D’Hamers F, Bosschaerts R, Pierloot K, Sels BF. Glycolaldehyde as a Bio-Based C2 Platform Chemical: Catalytic Reductive Amination of Vicinal Hydroxyl Aldehydes. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02437] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- William Faveere
- Center for Sustainable Catalysis and Engineering (CSCE), Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Tzvetan Mihaylov
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Michiel Pelckmans
- Center for Sustainable Catalysis and Engineering (CSCE), Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Kristof Moonen
- Eastman Chemical Company, Technologiepark 21, 9052 Zwijnaarde, Belgium
| | - Frederik Gillis-D’Hamers
- Center for Sustainable Catalysis and Engineering (CSCE), Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Bert F. Sels
- Center for Sustainable Catalysis and Engineering (CSCE), Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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17
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Biçer E, Pehlivan V, Bekiroğlu YG. Synthesis, Characterization, in vitro Antifungal Activities and Calf Thymus DNA Interactions of Two Different Hydroxy Benzaldehyde Derivative Schiff Bases from Sulfamethizole: Electrochemical, Spectroscopic and Biological Study. RUSS J ELECTROCHEM+ 2019. [DOI: 10.1134/s1023193519050045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Apel C, Hartmann SS, Lentz D, Christmann M. Dienamine‐Induced Divinylcyclopropane–Cycloheptadiene Rearrangements. Angew Chem Int Ed Engl 2019; 58:5075-5079. [DOI: 10.1002/anie.201813880] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/11/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Caroline Apel
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Sven Sören Hartmann
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Dieter Lentz
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Mathias Christmann
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
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19
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Apel C, Hartmann SS, Lentz D, Christmann M. Dienamine‐Induced Divinylcyclopropane–Cycloheptadiene Rearrangements. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Caroline Apel
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Sven Sören Hartmann
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Dieter Lentz
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
| | - Mathias Christmann
- Freie Universität BerlinInstitute of Chemistry and Biochemistry Takustr. 3 14195 Berlin Germany
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20
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Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0040-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Pelckmans M, Mihaylov T, Faveere W, Poissonnier J, Van Waes F, Moonen K, Marin GB, Thybaut JW, Pierloot K, Sels BF. Catalytic Reductive Aminolysis of Reducing Sugars: Elucidation of Reaction Mechanism. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00619] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Michiel Pelckmans
- Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Tzvetan Mihaylov
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - William Faveere
- Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Jeroen Poissonnier
- Laboratory for Chemical Technology, Universiteit Gent, Technologiepark 914, 9052 Gent, Belgium
| | | | - Kristof Moonen
- Eastman Chemical Company, Technologiepark 21, 9000 Ghent, Belgium
| | - Guy B. Marin
- Laboratory for Chemical Technology, Universiteit Gent, Technologiepark 914, 9052 Gent, Belgium
| | - Joris W. Thybaut
- Laboratory for Chemical Technology, Universiteit Gent, Technologiepark 914, 9052 Gent, Belgium
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Bert F. Sels
- Department M2S, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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22
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Hirvonen V, Myllys N, Kurtén T, Elm J. Closed-Shell Organic Compounds Might Form Dimers at the Surface of Molecular Clusters. J Phys Chem A 2018; 122:1771-1780. [PMID: 29364673 DOI: 10.1021/acs.jpca.7b11970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of covalently bound dimer formation is studied using high-level quantum chemical methods. Reaction free energy profiles for dimer formation between common oxygen-containing functional groups are calculated, and based on the Gibbs free energy differences between transition states and reactants, we show that none of the studied two-component gas-phase reactions are kinetically feasible at 298.15 K and 1 atm. Therefore, the catalyzing effect of water, base, or acid molecules is calculated, and sulfuric acid is identified to lower the activation free energies significantly. We find that the reactions yielding hemiacetal, peroxyhemiacetal, α-hydroxyester, and geminal diol products occur with activation free energies of less than 10 kcal/mol with sulfuric acid as a catalyst, indicating that these reactions could potentially take place on the surface of sulfuric acid clusters. Additionally, the formed dimer products bind stronger onto the pre-existing cluster than the corresponding reagent monomers do. This implies that covalent dimerization reactions stabilize the existing cluster thermodynamically and make it less likely to evaporate. However, the studied small organic compounds, which contain only one functional group, are not able to form dimer products that are stable against evaporation at atmospheric conditions. Calculations of dimer formation onto a cluster surface and the clustering ability of dimer products should be extended to large terpene oxidation products in order to estimate the real atmospheric significance.
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Affiliation(s)
- Viivi Hirvonen
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Nanna Myllys
- Department of Physics, University of Helsinki , 00100 Helsinki, Finland
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki , 00100 Helsinki, Finland
| | - Jonas Elm
- Department of Chemistry, Aarhus University , 8000 Aarhus C, Denmark
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23
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Boz E, Tüzün NŞ, Stein M. Computational investigation of the control of the thermodynamics and microkinetics of the reductive amination reaction by solvent coordination and a co-catalyst. RSC Adv 2018; 8:36662-36674. [PMID: 35558904 PMCID: PMC9088820 DOI: 10.1039/c8ra08135b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022] Open
Abstract
Amines are among the most important and frequently used chemical compounds due to their biological activity and a wide range of applications in industry. Reductive amination reactions are an efficient and facile route to synthesize long chain amines from sustainable sources by using a different available aldehydes and ketones, and a large variety of amines including primary, secondary and tertiary forms. The pathway of the reaction process is critically dependent on reaction parameters such as the pH of the reaction medium, choice of solvent (explicitly coordinating solvent) and process conditions. These parameters are affecting the reaction performance and the selectivity but are still not fully rationalized. Here, we investigate the microkinetics and thermodynamics of the individual steps of the reductive amination reaction by exploring the systems' parameters. Explicit water coordination to the aldehyde leads to a stepwise rather than concerted nucleophilic addition with a lower activation barrier by 6–10 kcal mol−1. At low pH, the pathway is changed by a direct protonation of the amine substrate. This protonation does not strongly affect the kinetics of the reaction, but the thermodynamic equilibria. The presence of an acid as a co-catalyst leads to the formation of an iminium intermediate and this drives the reaction forward. Thus, the presence of an acid as a co-catalyst clearly renders this pathway the thermodynamically preferred one. Consequently, altering the reaction parameters does not only influence the reaction kinetics, but also the thermodynamic profile of the pathways in all cases. Further understanding of the reaction dynamics is essential to develop a microkinetic model of the reaction to then control and engineer the process in order to rationally design routes to tailor-made products. Green production of tertiary amine from sustainable sources can be controlled by appropriate choice of reaction parameters identified by computational means.![]()
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Affiliation(s)
- Esra Boz
- Max Planck Institute for Dynamics of Complex Technical Systems
- Molecular Simulations and Design Group
- Magdeburg
- Germany
- Istanbul Technical University
| | - Nurcan Ş. Tüzün
- Istanbul Technical University
- Department of Chemistry
- Istanbul
- Turkey
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems
- Molecular Simulations and Design Group
- Magdeburg
- Germany
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24
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Renzi P, Hioe J, Gschwind RM. Enamine/Dienamine and Brønsted Acid Catalysis: Elusive Intermediates, Reaction Mechanisms, and Stereoinduction Modes Based on in Situ NMR Spectroscopy and Computational Studies. Acc Chem Res 2017; 50:2936-2948. [PMID: 29172479 PMCID: PMC6300316 DOI: 10.1021/acs.accounts.7b00320] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
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Over the years, the field of enantioselective organocatalysis has
seen unparalleled growth in the development of novel synthetic applications
with respect to mechanistic investigations. Reaction optimization
appeared to be rather empirical than rational. This offset between
synthetic development and mechanistic understanding was and is generally
due to the difficulties in detecting reactive intermediates and the
inability to experimentally evaluate transition states. Thus, the
first key point for mechanistic studies is detecting elusive intermediates
and characterizing them in terms of their structure, stability, formation
pathways, and kinetic properties. The second key point is evaluating
the importance of these intermediates and their properties in the
transition state. In the past 7 years, our group has addressed
the problems with
detecting elusive intermediates in organocatalysis by means of NMR
spectroscopy and eventually theoretical calculations. Two main activation
modes were extensively investigated: secondary amine catalysis and,
very recently, Brønsted acid catalysis. Using these examples,
we discuss potential methods to stabilize intermediates via intermolecular
interactions; to elucidate their structures, formation pathways and
kinetics; to change the kinetics of the reactions; and to address
their relevance in transition states. The elusive enamine in proline-catalyzed
aldol reactions is used as an example of the stabilization of intermediates
via inter- and intramolecular interactions; the determination of kinetics
on its formation pathway is discussed. Classical structural characterization
of intermediates is described using prolinol and prolinol ether enamines
and dienamines. The Z/E dilemma
for the second double bond of the dienamines shows how the kinetics
of a reaction can be changed to allow for the detection of reaction
intermediates. We recently started to investigate substrate–catalyst
complexes in the field of Brønsted acid catalysis. These studies
on imine/chiral phosphoric acid complexes show that an appropriate
combination of highly developed NMR and theoretical methods can provide
detailed insights into the complicated structures, exchange kinetics,
and H-bonding properties of chiral ion pairs. Furthermore, the merging
of these structural investigations and photoisomerization even allowed
the active transition state combinations to be determined for the
first time on the basis of experimental data only, which is the gold
standard in mechanistic investigations and was previously thought
to be exclusively the domain of theoretical calculations. Thus,
this Account summarizes our recent mechanistic work in the
field of organocatalysis and explains the potential methods for addressing
the central questions in mechanistic studies: stabilization of intermediates,
elucidation of structures and formation pathways, and addressing transition
state combinations experimentally.
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Affiliation(s)
- Polyssena Renzi
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
| | - Johnny Hioe
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
| | - Ruth M. Gschwind
- Institut für Organische Chemie, Universität Regensburg, D-95053 Regensburg, Germany
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25
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Duce S, Alonso I, Lamsabhi AM, Rodrigo E, Morales S, García Ruano JL, Poveda A, Mauleón P, Cid MB. The Acidity of a Carbon Nucleophile Dictates Enantioselectivity and Reactivity in Michael Additions to Aromatic and Aliphatic Enals via Iminium Activation. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02806] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sara Duce
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Alonso
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Al Mokhtar Lamsabhi
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eduardo Rodrigo
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sara Morales
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José Luis García Ruano
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ana Poveda
- Chemical
Glycobiology Lab, CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio-Bizkaia, Spain
| | - Pablo Mauleón
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - M. Belén Cid
- Departamento
de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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26
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Myllys N, Olenius T, Kurtén T, Vehkamäki H, Riipinen I, Elm J. Effect of Bisulfate, Ammonia, and Ammonium on the Clustering of Organic Acids and Sulfuric Acid. J Phys Chem A 2017; 121:4812-4824. [DOI: 10.1021/acs.jpca.7b03981] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nanna Myllys
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
| | - Tinja Olenius
- Department of Environmental Science and Analytical Chemistry & Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, Helsinki FI-00014, Finland
| | - Hanna Vehkamäki
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
| | - Ilona Riipinen
- Department of Environmental Science and Analytical Chemistry & Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Jonas Elm
- Department
of Physics, University of Helsinki, Helsinki FI-00014, Finland
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27
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Novel family of fused tricyclic [1,4]diazepines: Design, synthesis, crystal structures and molecular docking studies. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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28
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Dalessandro EV, Collin HP, Guimarães LGL, Valle MS, Pliego JR. Mechanism of the Piperidine-Catalyzed Knoevenagel Condensation Reaction in Methanol: The Role of Iminium and Enolate Ions. J Phys Chem B 2017; 121:5300-5307. [DOI: 10.1021/acs.jpcb.7b03191] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ellen V. Dalessandro
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Hugo P. Collin
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Luiz Gustavo L. Guimarães
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Marcelo S. Valle
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
| | - Josefredo R. Pliego
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil
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29
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Manzano R, Datta S, Paton RS, Dixon DJ. Enantioselective Silver and Amine Co-catalyzed Desymmetrizing Cycloisomerization of Alkyne-Linked Cyclohexanones. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rubén Manzano
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Swarup Datta
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Robert S. Paton
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
| | - Darren J. Dixon
- Department of Chemistry, Chemistry Research Laboratory; University of Oxford; Mansfield Road Oxford OX1 3TA UK
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30
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Manzano R, Datta S, Paton RS, Dixon DJ. Enantioselective Silver and Amine Co-catalyzed Desymmetrizing Cycloisomerization of Alkyne-Linked Cyclohexanones. Angew Chem Int Ed Engl 2017; 56:5834-5838. [PMID: 28429384 DOI: 10.1002/anie.201612048] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 03/02/2017] [Indexed: 01/23/2023]
Abstract
A silver(I) and amine co-catalyzed desymmetrization of 4-propargylamino cyclohexanones for the direct enantioselective synthesis of 2-azabicyclo[3.3.1]nonanes is described. Exploiting reactivity arising from dual activation of the pendant terminal alkyne by silver(I) and the ketone moiety through transient enamine formation, this synthetically relevant transformation is easy to perform, efficient and broad in scope. High enantioselectivity (up to 96 % ee) was achieved by exploiting a significant matching effect between the chirality of a cinchona alkaloid-derived aminophosphine ligand for the silver(I) salt and the 2-bis(aryl)methylpyrrolidine catalyst which was rationalized by DFT calculations. This allowed for the preparation of both enantiomers of the bicyclic product with near-identical stereocontrol.
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Affiliation(s)
- Rubén Manzano
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Swarup Datta
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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31
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de Lima Batista AP, Zahariev F, Slowing II, Braga AAC, Ornellas FR, Gordon MS. Silanol-Assisted Carbinolamine Formation in an Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation by Fragmentation Methods. J Phys Chem B 2015; 120:1660-9. [PMID: 26670797 DOI: 10.1021/acs.jpcb.5b08446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aldol reaction catalyzed by an amine-substituted mesoporous silica nanoparticle (amine-MSN) surface was investigated using a large molecular cluster model (Si392O958C6NH361) combined with the surface integrated molecular orbital/molecular mechanics (SIMOMM) and fragment molecular orbital (FMO) methods. Three distinct pathways for the carbinolamine formation, the first step of the amine-catalyzed aldol reaction, are proposed and investigated in order to elucidate the role of the silanol environment on the catalytic capability of the amine-MSN material. The computational study reveals that the most likely mechanism involves the silanol groups actively participating in the reaction, forming and breaking covalent bonds in the carbinolamine step. Therefore, the active participation of MSN silanol groups in the reaction mechanism leads to a significant reduction in the overall energy barrier for the carbinolamine formation. In addition, a comparison between the findings using a minimal cluster model and the Si392O958C6NH361 cluster suggests that the use of larger models is important when heterogeneous catalysis problems are the target.
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Affiliation(s)
- Ana P de Lima Batista
- Departamento de Química Fundamental, Instituto de Química , São Paulo, São Paulo 05508-000, Brazil
| | - Federico Zahariev
- Ames Laboratory and Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
| | - Igor I Slowing
- Ames Laboratory and Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
| | - Ataualpa A C Braga
- Departamento de Química Fundamental, Instituto de Química , São Paulo, São Paulo 05508-000, Brazil
| | - Fernando R Ornellas
- Departamento de Química Fundamental, Instituto de Química , São Paulo, São Paulo 05508-000, Brazil
| | - Mark S Gordon
- Ames Laboratory and Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
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32
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Morales S, Guijarro FG, Alonso I, García Ruano JL, Cid MB. Dual Role of Pyrrolidine and Cooperative Pyrrolidine/Pyrrolidinium Effect in Nitrone Formation. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01726] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sara Morales
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Fernando G. Guijarro
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Inés Alonso
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - José Luis García Ruano
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - M. Belén Cid
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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33
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Asari AH, Lam YH, Tius MA, Houk KN. Origins of the Stereoselectivity in a Thiourea–Primary Amine-Catalyzed Nazarov Cyclization. J Am Chem Soc 2015; 137:13191-9. [DOI: 10.1021/jacs.5b08969] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Austin H. Asari
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yu-hong Lam
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Marcus A. Tius
- Department
of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
- The Cancer Research Center of Hawaii, Honolulu, Hawaii 96813, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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34
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Han J, Lu Z, Flach AL, Paton RS, Hammond GB, Xu B. Role of Hydrogen-Bonding Acceptors in Organo-Enamine Catalysis. Chemistry 2015; 21:11687-91. [DOI: 10.1002/chem.201502407] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 11/09/2022]
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35
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Gammack Yamagata AD, Datta S, Jackson KE, Stegbauer L, Paton RS, Dixon DJ. Enantioselective desymmetrization of prochiral cyclohexanones by organocatalytic intramolecular Michael additions to α,β-unsaturated esters. Angew Chem Int Ed Engl 2015; 54:4899-903. [PMID: 25727215 PMCID: PMC4678487 DOI: 10.1002/anie.201411924] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 01/09/2023]
Abstract
A new catalytic asymmetric desymmetrization reaction for the synthesis of enantioenriched derivatives of 2-azabicyclo[3.3.1]nonane, a key motif common to many alkaloids, has been developed. Employing a cyclohexanediamine-derived primary amine organocatalyst, a range of prochiral cyclohexanone derivatives possessing an α,β-unsaturated ester moiety linked to the 4-position afforded the bicyclic products, which possess three stereogenic centers, as single diastereoisomers in high enantioselectivity (83-99% ee) and in good yields (60-90%). Calculations revealed that stepwise C-C bond formation and proton transfer via a chair-shaped transition state dictate the exclusive endo selectivity and enabled the development of a highly enantioselective primary amine catalyst.
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Affiliation(s)
- Adam D Gammack Yamagata
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - Swarup Datta
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - Kelvin E Jackson
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - Linus Stegbauer
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - Robert S Paton
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
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36
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Scavenger mechanism of methylglyoxal by metformin. A DFT study. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1649-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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37
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de Gracia Retamosa M, de Cózar A, Sánchez M, Miranda JI, Sansano JM, Castelló LM, Nájera C, Jiménez AI, Sayago FJ, Cativiela C, Cossío FP. Remote Substituent Effects on the Stereoselectivity and Organocatalytic Activity of Densely Substituted Unnatural Proline Esters in Aldol Reactions. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500160] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Gammack Yamagata AD, Datta S, Jackson KE, Stegbauer L, Paton RS, Dixon DJ. Enantioselective Desymmetrization of Prochiral Cyclohexanones by Organocatalytic Intramolecular Michael Additions to α,β-Unsaturated Esters. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411924] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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39
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Cheng GJ, Zhang X, Chung LW, Xu L, Wu YD. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. J Am Chem Soc 2015; 137:1706-25. [PMID: 25568962 DOI: 10.1021/ja5112749] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.
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Affiliation(s)
- Gui-Juan Cheng
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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40
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Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Frau J, Muñoz F. A DFT study of the carboxymethyl-phosphatidylethanolamine formation from glyoxal and phosphatidylethanolamine surface. Comparison with the formation of N(ε)-(carboxymethyl)lysine from glyoxal and l-lysine. Phys Chem Chem Phys 2015; 17:8210-22. [DOI: 10.1039/c4cp05360e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mechanisms of the generation of CML and CM-PE from the reactions between glyoxal and l-lysine, and glyoxal and phosphatidylethanolamine (PE) were studied using the DFT method.
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Affiliation(s)
- C. Solís-Calero
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - J. Ortega-Castro
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | | | - J. Frau
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - F. Muñoz
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
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Willoughby PH, Niu D, Wang T, Haj MK, Cramer CJ, Hoye TR. Mechanism of the reactions of alcohols with o-benzynes. J Am Chem Soc 2014; 136:13657-65. [PMID: 25232890 PMCID: PMC4183651 DOI: 10.1021/ja502595m] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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We
have studied reactions of secondary and primary alcohols with
benzynes generated by the hexadehydro-Diels–Alder (HDDA) reaction.
These alcohols undergo competitive addition vs dihydrogen transfer
to produce aryl ethers vs reduced benzenoid products, respectively.
During the latter process, an equivalent amount of oxidized ketone
(or aldehyde) is formed. Using deuterium labeling studies, we determined
that (i) it is the carbinol C–H and adjacent O–H hydrogen
atoms that are transferred during this process and (ii) the mechanism
is consistent with a hydride-like transfer of the C–H. Substrates
bearing an internal trap attached to the reactive, HDDA-derived benzyne
intermediate were used to probe the kinetic order of the alcohol trapping
agent in the H2-transfer as well as in the alcohol addition
process. The H2-transfer reaction is first order in alcohol.
Our results are suggestive of a concerted H2-transfer process,
which is further supported by density functional theory (DFT) computational
studies and results of a kinetic isotope effect experiment. In contrast,
alcohol addition to the benzyne is second order in alcohol, a previously
unrecognized phenomenon. Additional DFT studies were used to further
probe the mechanistic aspects of the alcohol addition process.
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Affiliation(s)
- Patrick H Willoughby
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Armstrong A, Boto RA, Dingwall P, Contreras-García J, Harvey MJ, Mason NJ, Rzepa HS. The Houk–List transition states for organocatalytic mechanisms revisited. Chem Sci 2014. [DOI: 10.1039/c3sc53416b] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ten year old Houk–List model for rationalising the origin of stereoselectivity in the organocatalysed intermolecular aldol addition is revisited, using a variety of computational techniques that have been introduced or improved since the original study.
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Affiliation(s)
- Alan Armstrong
- Department of Chemistry
- Imperial College London
- South Kensington Campus
- London, UK
| | - Roberto A. Boto
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7616
- Laboratoire de Chimie Théorique
- Paris, France
| | - Paul Dingwall
- Department of Chemistry
- Imperial College London
- South Kensington Campus
- London, UK
| | - Julia Contreras-García
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR 7616
- Laboratoire de Chimie Théorique
- Paris, France
| | - Matt J. Harvey
- High Performance Computing
- ICT services
- Imperial College London
- UK
| | - Nicholas J. Mason
- Department of Chemistry
- Imperial College London
- South Kensington Campus
- London, UK
| | - Henry S. Rzepa
- Department of Chemistry
- Imperial College London
- South Kensington Campus
- London, UK
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43
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Gan L, Chang Q, Zhou J. Transformations and Tautomeric Equilibrium among Different Intermediates in Proline‐Catalyzed Reactions of Aldehydes or Ketones. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/01/54-60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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44
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A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Liu L, Sarkisian R, Xu Z, Wang H. Asymmetric Michael Addition of Ketones to Alkylidene Malonates and Allylidene Malonates via Enamine–Metal Lewis Acid Bifunctional Catalysis. J Org Chem 2012; 77:7693-9. [DOI: 10.1021/jo301070s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu Liu
- Department of Chemistry and
Biochemistry, Miami University, Oxford,
Ohio 45056, United States
| | - Ryan Sarkisian
- Department of Chemistry and
Biochemistry, Miami University, Oxford,
Ohio 45056, United States
| | - Zhenghu Xu
- Department of Chemistry and
Biochemistry, Miami University, Oxford,
Ohio 45056, United States
- Key Lab of Colloid and Interface
Chemistry of Ministry of Education, School of Chemistry and Chemical
Engineering, Shandong University, No. 27
South Shanda Road, Jinan, Shandong 250100, China
| | - Hong Wang
- Department of Chemistry and
Biochemistry, Miami University, Oxford,
Ohio 45056, United States
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46
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Sunoj RB, Anand M. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. Phys Chem Chem Phys 2012; 14:12715-36. [PMID: 22893252 DOI: 10.1039/c2cp41719g] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.
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Affiliation(s)
- Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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47
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Anand M, Sunoj RB. Role of Explicit Solvents in Palladium(II)-Catalyzed Alkoxylation of Arenes: An Interesting Paradigm for Preferred Outer-Sphere Reductive Elimination over Inner-Sphere Pathway. Organometallics 2012. [DOI: 10.1021/om300681e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Megha Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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48
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Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
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Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
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Reddi Y, Sunoj RB. Origin of Stereoselectivity in a Chiral N-Heterocyclic Carbene-Catalyzed Desymmetrization of Substituted Cyclohexyl 1,3-Diketones. Org Lett 2012; 14:2810-3. [DOI: 10.1021/ol301036u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yernaidu Reddi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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50
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Chen X, Jin J, Wang N, Lu P, Wang Y. Palladium-Catalyzed Selective Synthesis of Naphthalenes and Indenones and Their Luminescent Properties. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101506] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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