51
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Pahima E, Zhang Q, Tiefenbacher K, Major DT. Discovering Monoterpene Catalysis Inside Nanocapsules with Multiscale Modeling and Experiments. J Am Chem Soc 2019; 141:6234-6246. [PMID: 30907083 DOI: 10.1021/jacs.8b13411] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Large-scale production of natural products, such as terpenes, presents a significant scientific and technological challenge. One promising approach to tackle this problem is chemical synthesis inside nanocapsules, although enzyme-like control of such chemistry has not yet been achieved. In order to better understand the complex chemistry inside nanocapsules, we design a multiscale nanoreactor simulation approach. The nanoreactor simulation protocol consists of hybrid quantum mechanics-molecular mechanics-based high temperature Langevin molecular dynamics simulations. Using this approach we model the tail-to-head formation of monoterpenes inside a resorcin[4]arene-based capsule (capsule I). We provide a rationale for the experimentally observed kinetics of monoterpene product formation and product distribution using capsule I, and we explain why additional stable monoterpenes, like camphene, are not observed. On the basis of the in-capsule I simulations, and mechanistic insights, we propose that feeding the capsule with pinene can yield camphene, and this proposal is verified experimentally. This suggests that the capsule may direct the dynamic reaction cascades by virtue of π-cation interactions.
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Affiliation(s)
- Efrat Pahima
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Qi Zhang
- Department of Chemistry , University of Basel , Mattenstrasse 24a , 4058 Basel , Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry , University of Basel , Mattenstrasse 24a , 4058 Basel , Switzerland.,Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 24 , 4058 Basel , Switzerland
| | - Dan T Major
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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52
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Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products. Nature 2019; 568:122-126. [PMID: 30867595 DOI: 10.1038/s41586-019-1021-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
Pericyclic reactions are powerful transformations for the construction of carbon-carbon and carbon-heteroatom bonds in organic synthesis. Their role in biosynthesis is increasingly apparent, and mechanisms by which pericyclases can catalyse reactions are of major interest1. [4+2] cycloadditions (Diels-Alder reactions) have been widely used in organic synthesis2 for the formation of six-membered rings and are now well-established in biosynthesis3-6. [6+4] and other 'higher-order' cycloadditions were predicted7 in 1965, and are now increasingly common in the laboratory despite challenges arising from the generation of a highly strained ten-membered ring system8,9. However, although enzyme-catalysed [6+4] cycloadditions have been proposed10-12, they have not been proven to occur. Here we demonstrate a group of enzymes that catalyse a pericyclic [6+4] cycloaddition, which is a crucial step in the biosynthesis of streptoseomycin-type natural products. This type of pericyclase catalyses [6+4] and [4+2] cycloadditions through a single ambimodal transition state, which is consistent with previous proposals11,12. The [6+4] product is transformed to a less stable [4+2] adduct via a facile Cope rearrangement, and the [4+2] adduct is converted into the natural product enzymatically. Crystal structures of three pericyclases, computational simulations of potential energies and molecular dynamics, and site-directed mutagenesis establish the mechanism of this transformation. This work shows how enzymes are able to catalyse concerted pericyclic reactions involving ambimodal transition states.
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53
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Schroeder S, Strauch C, Gaelings N, Niggemann M. Vinyl Triflimides-A Case of Assisted Vinyl Cation Formation. Angew Chem Int Ed Engl 2019; 58:5119-5123. [PMID: 30694004 DOI: 10.1002/anie.201810916] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/28/2018] [Indexed: 12/31/2022]
Abstract
A new concept for selectivity control in carbocation-driven reactions has been identified which allows for the chemo-, regio-, and stereoselective addition of nucleophiles to alkynes-assisted vinyl cation formation-enabled by a Li+ -based supramolecular framework. Mechanistic analysis of a model complex (Li2 NTf2 + ⋅3 H2 O) confirms that solely the formation of a complex between the incoming nucleophile and the transition state of the alkyne protonation is responsible for the resulting selective N addition to the vinyl cation. Into the bargain, a general, operationally simple synthetic procedure to previously inaccessible vinyl triflimides is provided.
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Affiliation(s)
- Sebastian Schroeder
- Institute of Organic Chemistry, RWTH Aachen, Landoltweg 1, 52072, Aachen, Germany
| | - Christina Strauch
- Institute of Organic Chemistry, RWTH Aachen, Landoltweg 1, 52072, Aachen, Germany
| | - Niklas Gaelings
- Institute of Organic Chemistry, RWTH Aachen, Landoltweg 1, 52072, Aachen, Germany
| | - Meike Niggemann
- Institute of Organic Chemistry, RWTH Aachen, Landoltweg 1, 52072, Aachen, Germany
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54
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Schroeder S, Strauch C, Gaelings N, Niggemann M. Vinyltriflimide – ein Fall von assistierter Vinylkationenbildung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810916] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sebastian Schroeder
- Institute of Organic ChemistryRWTH Aachen Landoltweg 1 52072 Aachen Deutschland
| | - Christina Strauch
- Institute of Organic ChemistryRWTH Aachen Landoltweg 1 52072 Aachen Deutschland
| | - Niklas Gaelings
- Institute of Organic ChemistryRWTH Aachen Landoltweg 1 52072 Aachen Deutschland
| | - Meike Niggemann
- Institute of Organic ChemistryRWTH Aachen Landoltweg 1 52072 Aachen Deutschland
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55
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Castiñeira Reis M, López CS, Nieto Faza O, Tantillo DJ. Pushing the limits of concertedness. A waltz of wandering carbocations. Chem Sci 2019; 10:2159-2170. [PMID: 30881640 PMCID: PMC6385557 DOI: 10.1039/c8sc03567a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Among the array of complex terpene-forming carbocation cyclization/rearrangement reactions, the so-called "triple shift" reactions are among the most unexpected. Such reactions involve the asynchronous combination of three 1,n-shifts into a concerted process, e.g., a 1,2-alkyl shift followed by a 1,3-hydride shift followed by a second 1,2-alkyl shift. This type of reaction so far has been proposed to occur during the biosynthesis of diterpenes and the sidechains of sterols. Here we describe efforts to push the limits of concertedness in this type of carbocation reaction by designing, and characterizing with quantum chemical computations, systems that could couple additional 1,n-shift events to a triple shift leading, in principle to quadruple, pentuple, etc. shifts. While our designs did not lead to clear-cut examples of quadruple, etc. shifts, they did lead to reactions with surprisingly flat energy surfaces where more than five chemical events connect reactants and plausible products. Ab initio molecular dynamics simulations demonstrate that the formal minima on these surfaces interchange on short timescales, both with each other and with additional unexpected structures, allowing us a glimpse into a very complex manifold that allows ready access to great structural diversity.
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Affiliation(s)
- Marta Castiñeira Reis
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Carlos Silva López
- Departamento de Química Orgánica , Universidade de Vigo , Lagoas-Marcosende , 36310 , Vigo , Spain
| | - Olalla Nieto Faza
- Departamento de Química Orgánica , Universidade de Vigo , As Lagoas , 32004 , Ourense , Spain .
| | - Dean J Tantillo
- Department of Chemistry , University of California , One Shields Ave , Davis , CA 95616 , USA .
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56
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Tang B, Paton RS. Biosynthesis of Providencin: Understanding Photochemical Cyclobutane Formation with Density Functional Theory. Org Lett 2019; 21:1243-1247. [DOI: 10.1021/acs.orglett.8b03838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bencan Tang
- Department of Chemical and Environment Engineering, Science and Engineering Building, The University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China
| | - Robert S. Paton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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57
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Burns JM, Boittier ED. Pathway Bifurcation in the (4 + 3)/(5 + 2)-Cycloaddition of Butadiene and Oxidopyrylium Ylides: The Significance of Molecular Orbital Isosymmetry. J Org Chem 2019; 84:5997-6005. [DOI: 10.1021/acs.joc.8b03236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jed M. Burns
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
| | - Eric D. Boittier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, 4067 Queensland, Australia
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58
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Xue XS, Jamieson CS, Garcia-Borràs M, Dong X, Yang Z, Houk KN. Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity. J Am Chem Soc 2019; 141:1217-1221. [DOI: 10.1021/jacs.8b12674] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiao-Song Xue
- State Key Laboratory
of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Cooper S. Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Xiaofei Dong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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59
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Hare SR, Li A, Tantillo DJ. Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions. Chem Sci 2018; 9:8937-8945. [PMID: 30627409 PMCID: PMC6296359 DOI: 10.1039/c8sc02653j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
A post-transition state bifurcation (PTSB) involved in a Pummerer-type rearrangement is characterized using density functional theory (DFT) calculations on potential energy stationary points and direct dynamics simulations. A sensitivity of the ratio of products produced via this PTSB to solvent dielectric constant is revealed and implications of such a dependence for selectivity control of organic reactions are discussed.
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Affiliation(s)
| | - Ang Li
- Shanghai Institute of Organic Chemistry , China
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60
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61
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62
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Pu M, Heshmat M, Privalov T. Liberation of H 2 from (o-C 6H 4Me) 3P-H (+) + (-)H-B(p-C 6F 4H) 3 ion-pair: A transition-state in the minimum energy path versus the transient species in Born-Oppenheimer molecular dynamics. J Chem Phys 2018; 147:014303. [PMID: 28688388 DOI: 10.1063/1.4989672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using Born-Oppenheimer molecular dynamics (BOMD) with density functional theory, transition-state (TS) calculations, and the quantitative energy decomposition analysis (EDA), we examined the mechanism of H2-liberation from LB-H(+) + (-)H-LA ion-pair, 1, in which the Lewis base (LB) is (o-C6H4Me)3P and the Lewis acid (LA) is B(p-C6F4H)3. BOMD simulations indicate that the path of H2 liberation from the ion-pair 1 goes via the short-lived transient species, LB⋯H2⋯LA, which are structurally reminiscent of the TS-structure in the minimum-energy-path describing the reversible reaction between H2 and (o-C6H4Me)3P/B(p-C6F4H)3 frustrated Lewis pair (FLP). With electronic structure calculations performed on graphics processing units, our BOMD data-set covers more than 1 ns of evolution of the ion-pair 1 at temperature T ≈ 400 K. BOMD simulations produced H2-recombination events with various durations of H2 remaining fully recombined as a molecule within a LB/LA attractive "pocket"-from very short vibrational-time scale to time scales in the range of a few hundred femtoseconds. With the help of perturbational approach to trajectory-propagation over a saddle-area, we directly examined dynamics of H2-liberation. Using EDA, we elucidated interactions between the cationic and anionic fragments in the ion-pair 1 and between the molecular fragments in the TS-structure. We have also considered a model that qualitatively takes into account the potential energy characteristics of H-H recombination and H2-release plus inertia of molecular motion of the (o-C6H4Me)3P/B(p-C6F4H)3 FLP.
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Affiliation(s)
- Maoping Pu
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Mojgan Heshmat
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Timofei Privalov
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
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63
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O’Brien TE, Bertolani SJ, Zhang Y, Siegel JB, Tantillo DJ. Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case. ACS Catal 2018; 8:3322-3330. [PMID: 30034923 PMCID: PMC6049084 DOI: 10.1021/acscatal.8b00342] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Terpene synthases comprise a family of enzymes that convert acyclic oligo-isoprenyl diphosphates to terpene natural products with complex, polycyclic carbon backbones via the generation and protection of carbocation intermediates. To accommodate this chemistry, terpene synthase active sites generally are lined with alkyl and aromatic, i.e., nonpolar, sidechains. Predicting the correct, mechanistically relevant binding modes for entire terpene synthase reaction pathways remains an unsolved challenge. Here we describe a method for identifying such modes: TerDockin, a series of protocols to predict the orientation of carbon skeletons of substrates and derived carbocations relative to the bound diphosphate group in terpene synthase active sites. Using this recipe for bornyl diphosphate synthase, we have predicted binding modes that are consistent with all current experimental observations, including the results of isotope labeling experiments and known stereoselectivity. In addition, the predicted binding modes recapitulate key findings of a seminal study involving more computationally demanding QM/MM molecular dynamics methods on part of this pathway. This work illustrates the value of the TerDockin approach as a starting point for more involved calculations and sets the stage for the rational engineering of this family of enzymes.
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Affiliation(s)
- Terrence E. O’Brien
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Steven J. Bertolani
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Yue Zhang
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Justin B. Siegel
- Department of Chemistry, University of California Davis, Davis, California, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Dean J. Tantillo
- Department of Chemistry, University of California Davis, Davis, California, USA
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64
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Hong YJ, Tantillo DJ. A Maze of Dyotropic Rearrangements and Triple Shifts: Carbocation Rearrangements Connecting Stemarene, Stemodene, Betaerdene, Aphidicolene, and Scopadulanol. J Org Chem 2018; 83:3780-3793. [PMID: 29494166 DOI: 10.1021/acs.joc.8b00138] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Results of quantum chemical investigations shed new light on the mechanisms of formation of the stemarene, stemodene, betaerdene, aphidicolene, and scopadulanol diterpenes from syn-copalyl diphosphate ( syn-CPP). These terpenes are shown to be connected by a complex network of reaction pathways involving concerted but asynchronous dyotropic rearrangements and triple shift rearrangements. The interconnection of these pathways leads to multiple routes for formation of each diterpene, which could lead to different origins for some carbon atoms in a given diterpenes under different conditions.
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Affiliation(s)
- Young J Hong
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
| | - Dean J Tantillo
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
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65
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Hazra CK, Jeong J, Kim H, Baik MH, Park S, Chang S. Reductive Carbocyclization of Homoallylic Alcohols to syn
-Cyclobutanes by a Boron-Catalyzed Dual Ring-Closing Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chinmoy Kumar Hazra
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Jinhoon Jeong
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Hyunjoong Kim
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Mu-Hyun Baik
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Sehoon Park
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Sukbok Chang
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
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66
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Hazra CK, Jeong J, Kim H, Baik MH, Park S, Chang S. Reductive Carbocyclization of Homoallylic Alcohols to syn
-Cyclobutanes by a Boron-Catalyzed Dual Ring-Closing Pathway. Angew Chem Int Ed Engl 2018; 57:2692-2696. [DOI: 10.1002/anie.201713285] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Chinmoy Kumar Hazra
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Jinhoon Jeong
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Hyunjoong Kim
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Mu-Hyun Baik
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Sehoon Park
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
| | - Sukbok Chang
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 South Korea
- Department of Chemistry; Korea Advanced Institute of Science & Technology (KAIST); Daejeon 305-701 South Korea
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67
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Huang AC, Hong YJ, Bond AD, Tantillo DJ, Osbourn A. Diverged Plant Terpene Synthases Reroute the Carbocation Cyclization Path towards the Formation of Unprecedented 6/11/5 and 6/6/7/5 Sesterterpene Scaffolds. Angew Chem Int Ed Engl 2018; 57:1291-1295. [PMID: 29194888 PMCID: PMC5814883 DOI: 10.1002/anie.201711444] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 11/16/2022]
Abstract
Sesterterpenoids are a relatively rare class of plant terpenes. Sesterterpene synthase (STS)-mediated cyclization of the linear C25 isoprenoid precursor geranylfarnesyl diphosphate (GFPP) defines sesterterpene scaffolds. So far only a very limited number of STSs have been characterized. The discovery of three new plant STSs is reported that produce a suite of sesterterpenes with unprecedented 6/11/5 and 6/6/7/5 fused ring systems when transiently co-expressed with a GFPP synthase in Nicotiana benthamiana. Structural elucidation, feeding experiments, and quantum chemical calculations suggest that these STSs catalyze an unusual cyclization path involving reprotonation, intramolecular 1,6 proton transfer, and concerted but asynchronous bicyclization events. The cyclization is diverted from those catalyzed by the characterized plant STSs by forming unified 15/5 bicyclic sesterterpene intermediates. Mutagenesis further revealed a conserved amino acid residue implicated in reprotonation.
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Affiliation(s)
- Ancheng C. Huang
- Department of Metabolic BiologyJohn Innes CentreColney Lane, Norwich Research ParkNorwichNR4 7UHUK
| | - Young J. Hong
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Andrew D. Bond
- Department of ChemistryUniversity of CambridgeLensfield RdCambridgeCB2 1EWUK
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California, DavisDavisCA95616USA
| | - Anne Osbourn
- Department of Metabolic BiologyJohn Innes CentreColney Lane, Norwich Research ParkNorwichNR4 7UHUK
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68
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Burns JM. Computational evidence for a reaction pathway bifurcation in Sasaki-type (4 + 3)-cycloadditions. Org Biomol Chem 2018; 16:1828-1836. [DOI: 10.1039/c8ob00075a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Evidence for a post-transition state bifurcation in a (4 + 3)-cycloaddition is presented.
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Affiliation(s)
- Jed M. Burns
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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69
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Huang AC, Hong YJ, Bond AD, Tantillo DJ, Osbourn A. Diverged Plant Terpene Synthases Reroute the Carbocation Cyclization Path towards the Formation of Unprecedented 6/11/5 and 6/6/7/5 Sesterterpene Scaffolds. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201711444] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ancheng C. Huang
- Department of Metabolic Biology; John Innes Centre; Colney Lane, Norwich Research Park Norwich NR4 7UH UK
| | - Young J. Hong
- Department of Chemistry; University of California, Davis; Davis CA 95616 USA
| | - Andrew D. Bond
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
| | - Dean J. Tantillo
- Department of Chemistry; University of California, Davis; Davis CA 95616 USA
| | - Anne Osbourn
- Department of Metabolic Biology; John Innes Centre; Colney Lane, Norwich Research Park Norwich NR4 7UH UK
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70
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Freud Y, Ansbacher T, Major DT. Catalytic Control in the Facile Proton Transfer in Taxadiene Synthase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02824] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yehoshua Freud
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tamar Ansbacher
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im
Street, Jerusalem 9101001, Israel
| | - Dan Thomas Major
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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71
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SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis. Nature 2017; 549:502-506. [PMID: 28902839 PMCID: PMC5679075 DOI: 10.1038/nature23882] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations to make multiple regioselective and stereoselective carbon-carbon bonds1. These reactions have been widely applied for the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centers2–6. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples, intramolecular Diels-Alder (IMDA) reaction7, Cope8 and Claisen rearrangements9, have been characterized. Here, we report the discovery of a S-adenosyl-L-methionine (SAM) dependent enzyme LepI that can catalyse stereoselective dehydration, bifurcating IMDA/hetero-DA (HDA) reactions via an ambimodal transition state, and a [3,3]-sigmatropic retro-Claisen rearrangement leading to the formation of dihydopyran core in the fungal natural product leporin10. Combined in vitro enzymatic characterization and computational studies provide evidence and mechanistic insight about how the O-methyltransferase-like protein LepI regulates the bifurcating biosynthetic reaction pathways (“direct” HDA and “byproduct recycle” IMDA/retro-Claisen reaction pathways) by utilizing SAM as the cofactor in order to converge to the desired biosynthetic end product. This work highlights that LepI is the first example of an enzyme catalysing a (SAM-dependent) retro-Claisen rearrangement. We suggest that more pericyclic biosynthetic enzymatic transformations are yet to be discovered in the intriguing enzyme toolboxes in Nature11, and propose an ever expanding role of the versatile cofactor SAM in enzyme catalysis.
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Abstract
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The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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73
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Hare SR, Tantillo DJ. Post-transition state bifurcations gain momentum – current state of the field. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0104] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. For example, the distribution of products seen in simulations has been found to be extremely sensitive to the local environment of the reacting system (i.e. the presence of a catalyst, enzyme, or explicit solvent molecules). The outlook for the future of this field is discussed, with an eye towards the application of the principles discussed here by experimental chemists to design a reaction setup to efficiently generate desired products.
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Affiliation(s)
- Stephanie R. Hare
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J. Tantillo
- University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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74
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Palazzo TA, Mose R, Jørgensen KA. Cycloadditionen: Warum ist der Übergang von sechs zu zehn Elektronen so schwer? Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Rasmus Mose
- Department of Chemistry; Aarhus University; DK-8000 Aarhus C Dänemark
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75
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Cycloaddition Reactions: Why Is It So Challenging To Move from Six to Ten Electrons? Angew Chem Int Ed Engl 2017; 56:10033-10038. [DOI: 10.1002/anie.201701085] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/06/2017] [Indexed: 12/26/2022]
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76
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Santalla H, Faza ON, Gómez G, Fall Y, Silva López C. From Hydrindane to Decalin: A Mild Transformation through a Dyotropic Ring Expansion. Org Lett 2017. [PMID: 28641016 DOI: 10.1021/acs.orglett.7b01621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An unexpected ring expansion converting hydrindane cores into decalins has been observed. The process occurs under very mild conditions and with exquisite transfer of chiral information. The ring expansion provides access to decorated decalins with complete stereocontrol. The reaction mechanism is studied in order to gain insight into the underlying causes for the low thermal requirements in this reaction and the nature of the chirality transfer process. Interestingly, both result from an unprecedented dyotropic reaction involving a mesylate group.
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Affiliation(s)
- Hugo Santalla
- Departamento de Química Orgánica, Campus Lagoas-Marcosende , 36310 Vigo, Spain
| | - Olalla Nieto Faza
- Departamento de Química Orgánica, Campus Lagoas-Marcosende , 36310 Vigo, Spain
| | - Generosa Gómez
- Departamento de Química Orgánica and Instituto de Investigación Sanitaria Galicia Sur (IISGS), Campus Lagoas-Marcosende , 36310 Vigo, Spain
| | - Yagamare Fall
- Departamento de Química Orgánica and Instituto de Investigación Sanitaria Galicia Sur (IISGS), Campus Lagoas-Marcosende , 36310 Vigo, Spain
| | - Carlos Silva López
- Departamento de Química Orgánica, Campus Lagoas-Marcosende , 36310 Vigo, Spain
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77
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Pan LL, Song LF, Miao Y, Yang Y, Merz KM. Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots? Biochemistry 2017; 56:2995-3007. [PMID: 28570807 DOI: 10.1021/acs.biochem.7b00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction. Single-point electronic structure calculations were also used to explore the performance of the self-consistent charge density functional tight-binding method to model specific reaction steps. Importantly, we observe that the two reaction pathways have comparable activation parameters and propose that the origin of the novel product is predicated, at least in part, on the topology of the potential energy surface as revealed by reaction dynamics studies.
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Affiliation(s)
- Li-Li Pan
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Yipu Miao
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Yue Yang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , 578 South Shaw Lane, East Lansing, Michigan 48824, United States.,Institute for Cyber Enabled Research, Michigan State University , 567 Wilson Road, Room 1440, East Lansing, Michigan 48824, United States
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78
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Hare SR, Pemberton RP, Tantillo DJ. Navigating Past a Fork in the Road: Carbocation-π Interactions Can Manipulate Dynamic Behavior of Reactions Facing Post-Transition-State Bifurcations. J Am Chem Soc 2017; 139:7485-7493. [PMID: 28504880 DOI: 10.1021/jacs.7b01042] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dynamics calculations are described for carbocation rearrangements involving product-forming pathways with post-transition-state bifurcations. We show that noncovalent interactions with associated benzene rings (a simple model of aromatic amino acid side chains) can switch inherent dynamical tendencies for competing modes of disrotation, establishing that meaningful changes in dynamically controlled product selectivity can be achieved with few weak noncovalent interactions.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Ryan P Pemberton
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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79
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Spezia R, Martínez-Nuñez E, Vazquez S, Hase WL. Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20170035. [PMID: 28320909 PMCID: PMC5360905 DOI: 10.1098/rsta.2017.0035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
| | - Emilio Martínez-Nuñez
- Departamento de Química Física and Centro Singular de Investigación en Química, Biológica y Materiales Moleculares (CIQUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Saulo Vazquez
- Departamento de Química Física and Centro Singular de Investigación en Química, Biológica y Materiales Moleculares (CIQUS), Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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80
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Martin-Somer A, Spezia R, Yáñez M. Gas-phase reactivity of [Ca(formamide)] 2+ complex: an example of different dynamical behaviours. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0196. [PMID: 28320901 PMCID: PMC5360897 DOI: 10.1098/rsta.2016.0196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)]2+ complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Ana Martin-Somer
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, CEA CNRS Université Paris Saclay, 91025 Evry, France
- LAMBE, Université d'Evry, 91025 Evry, France
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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81
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Pelot KA, Hagelthorn LM, Addison JB, Zerbe P. Biosynthesis of the oxygenated diterpene nezukol in the medicinal plant Isodon rubescens is catalyzed by a pair of diterpene synthases. PLoS One 2017; 12:e0176507. [PMID: 28445526 PMCID: PMC5405970 DOI: 10.1371/journal.pone.0176507] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/11/2017] [Indexed: 01/09/2023] Open
Abstract
Plants produce an immense diversity of natural products (i.e. secondary or specialized metabolites) that offer a rich source of known and potentially new pharmaceuticals and other desirable bioproducts. The Traditional Chinese Medicinal plant Isodon rubescens (Lamiaceae) contains an array of bioactive labdane-related diterpenoid natural products. Of these, the ent-kauranoid oridonin is the most prominent specialized metabolite that has been extensively studied for its potent antimicrobial and anticancer efficacy. Mining of a previously established transcriptome of I. rubescens leaf tissue identified seven diterpene synthase (diTPSs) candidates. Here we report the functional characterization of four I. rubescens diTPSs. IrTPS5 and IrTPS3 were identified as an ent-copalyl diphosphate (CPP) synthase and a (+)-CPP synthase, respectively. Distinct transcript abundance of IrTPS5 and the predicted ent-CPP synthase IrTPS1 suggested a role of IrTPS5 in specialized ent-kaurene metabolism possibly en route to oridonin. Nicotiana benthamiana co-expression assays demonstrated that IrTPS4 functions sequentially with IrTPS3 to form miltiradiene. In addition, IrTPS2 converted the IrTPS3 product (+)-CPP into the hydroxylated tricyclic diterpene nezukol not previously identified in I. rubescens. Metabolite profiling verified the presence of nezukol in I. rubescens leaf tissue. The proposed IrTPS2-catalyzed reaction mechanism proceeds via the common ionization of the diphosphate group of (+)-CPP, followed by formation of an intermediary pimar-15-en-8-yl+ carbocation and neutralization of the carbocation by water capture at C-8 to yield nezukol, as confirmed by nuclear magnetic resonance (NMR) analysis. Oxygenation activity is rare for the family of class I diTPSs and offers new catalysts for developing metabolic engineering platforms to produce a broader spectrum of bioactive diterpenoid natural products.
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Affiliation(s)
- Kyle A. Pelot
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - Lynne M. Hagelthorn
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - J. Bennett Addison
- Department of Chemistry, University of California-Davis, Davis, California, United States of America
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
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82
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dos Passos Gomes G, Alabugin IV. Drawing Catalytic Power from Charge Separation: Stereoelectronic and Zwitterionic Assistance in the Au(I)-Catalyzed Bergman Cyclization. J Am Chem Soc 2017; 139:3406-3416. [DOI: 10.1021/jacs.6b11054] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Gabriel dos Passos Gomes
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-439, United States
| | - Igor V. Alabugin
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-439, United States
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83
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Cheema J, Faraldos JA, O'Maille PE. REVIEW: Epistasis and dominance in the emergence of catalytic function as exemplified by the evolution of plant terpene synthases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 255:29-38. [PMID: 28131339 DOI: 10.1016/j.plantsci.2016.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/17/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes. Using the emergence of terpene cyclization in specialized metabolism as an excellent example, this review describes the process of discovery and interpretation of dominance and epistasis in relation to current efforts. Specifically, we outline experimental approaches to isolating epistatic networks of mutations in protein structure, formally quantifying epistatic interactions, then building biochemical models with chemical mechanisms in efforts to achieve an understanding of the physical basis for epistasis. From these models we describe informed conjectures about past evolutionary events that underlie the emergence, divergence and specialization of terpene synthases to illustrate key principles of the constraining forces of epistasis in enzyme function.
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Affiliation(s)
- Jitender Cheema
- John Innes Centre, Computational and Systems Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Juan A Faraldos
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Paul E O'Maille
- John Innes Centre, Department of Metabolic Biology, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Food Research, Food & Health Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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84
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McFadden TR, Fang C, Geib SJ, Merling E, Liu P, Curran DP. Synthesis of Boriranes by Double Hydroboration Reactions of N-Heterocyclic Carbene Boranes and Dimethyl Acetylenedicarboxylate. J Am Chem Soc 2017; 139:1726-1729. [DOI: 10.1021/jacs.6b09873] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Timothy R. McFadden
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Cheng Fang
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Steven J. Geib
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Everett Merling
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peng Liu
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Dennis P. Curran
- Department of Chemistry and ‡Computational Modeling & Simulation Program, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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85
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Bhattacharyya K, Karmakar S, Datta A. External electric field control: driving the reactivity of metal-free azide–alkyne click reactions. Phys Chem Chem Phys 2017; 19:22482-22486. [DOI: 10.1039/c7cp04202g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An external electric field is demonstrated as an efficient catalyst to accelerate click reactions.
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Affiliation(s)
| | - Sharmistha Karmakar
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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86
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Abstract
[4 + 2]-Cycloadditions are increasingly being recognized in the biosynthetic pathways of many structurally complex natural products. A relatively small collection of enzymes from these pathways have been demonstrated to increase rates of cyclization and impose stereochemical constraints on the reactions. While mechanistic investigation of these enzymes is just beginning, recent studies have provided new insights with implications for understanding their biosynthetic roles, mechanisms of catalysis, and evolutionary origin.
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Affiliation(s)
- Byung-Sun Jeon
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
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87
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Nieves-Quinones Y, Singleton DA. Dynamics and the Regiochemistry of Nitration of Toluene. J Am Chem Soc 2016; 138:15167-15176. [PMID: 27794598 DOI: 10.1021/jacs.6b07328] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The regiochemistry of the nitration of toluene by NO2+BF4- in dichloromethane is accurately predicted from trajectories in explicit solvent. Simpler models and approaches based on transition state theory fail to account for the selectivity. Potential of mean force calculations find no free-energy barrier for reaction of the toluene/NO2+BF4- encounter complex, yet the trajectories require an extraordinary 3 ps to descend an exergonic slope. The selectivity is decided late in long trajectories because their completion requires solvent and counterion reorganization. The normal descriptive understanding of the regiochemistry based on transition-state energies is unsupported.
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Affiliation(s)
- Yexenia Nieves-Quinones
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Daniel A Singleton
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
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88
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Wedler HB, Newman T, Tantillo DJ. Decarboxylation Facilitated by Carbocation Formation and Rearrangement during Steam Distillation of Vetiver Oil. JOURNAL OF NATURAL PRODUCTS 2016; 79:2744-2748. [PMID: 27676594 DOI: 10.1021/acs.jnatprod.6b00348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Density functional theory (DFT) calculations are used to probe the validity of mechanistic proposals for the conversion of isozizanoic acid to 12-norisoziza-5-ene, a reaction that occurs during steam distillation of vetiver oil. While this conversion corresponds overall to a simple decarboxylation, a multistep mechanism involving carbocation intermediates is supported by the computational results.
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Affiliation(s)
- Henry B Wedler
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - T Newman
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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89
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Hare SR, Tantillo DJ. Cryptic post-transition state bifurcations that reduce the efficiency of lactone-forming Rh-carbenoid C-H insertions. Chem Sci 2016; 8:1442-1449. [PMID: 28451284 PMCID: PMC5390789 DOI: 10.1039/c6sc03745c] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/18/2016] [Indexed: 11/21/2022] Open
Abstract
Post-transition state bifurcations are described that lead to unexpected byproducts in Rh-promoted C–H insertion reactions.
Byproducts of chemical reactions are generally thought to result from the competition between two reaction pathways, each with its own rate-determining transition state structure. We show here, however, that pathways with a single transition state structure followed by a post-transition state bifurcation may also be a source of undesired products, especially those whose appearance is unexpected. The viability of this scenario for intramolecular C–H insertion reactions affording β-lactones via Rh-carbenoid intermediates is assessed through quantum chemical calculations on potential energy surfaces and quasi-classical molecular dynamics simulations. It appears that, in these cases, the rhodium catalyst is to blame for the accessibility of a second, unintended, pathway following the transition state structure for β-lactone formation that leads to fragmentation to a ketene and carbonyl compound. If an unexpected product is formed via a post-transition state bifurcation, conventional strategies for suppressing its formation are unlikely to succeed. Guidelines for recognizing the presence of a post-transition state bifurcation are described here, along with hints at means for controlling product distributions.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry , University of California - Davis , One Shields Ave Davis , CA 95616 , USA .
| | - Dean J Tantillo
- Department of Chemistry , University of California - Davis , One Shields Ave Davis , CA 95616 , USA .
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90
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Gilmore K, Mohamed RK, Alabugin IV. The Baldwin rules: revised and extended. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1261] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kerry Gilmore
- Department of Biomolecular Systems; Max Planck Institute of Colloids and Interfaces; Potsdam Germany
| | - Rana K. Mohamed
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL USA
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL USA
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91
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Purino M, Ardiles AE, Callies O, Jiménez IA, Bazzocchi IL. Montecrinanes A–C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from
Celastrus vulcanicola
. Insights into Triterpenoid Biosynthesis Based on DFT Calculations. Chemistry 2016; 22:7582-91. [DOI: 10.1002/chem.201600294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Martín Purino
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Alejandro E. Ardiles
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
- Departamento de Química Facultad de Ciencias Universidad de Chile Las Palmeras 3425 Ñuñoa, Santiago Chile
| | - Oliver Callies
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Ignacio A. Jiménez
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
| | - Isabel L. Bazzocchi
- Instituto Universitario de Bio-Orgánica “Antonio González” and Departamento de Química Universidad de La Laguna C/Astrofísico Francisco Sánchez 2 38206 La Laguna, Tenerife Spain
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92
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Patel A, Chen Z, Yang Z, Gutiérrez O, Liu HW, Houk KN, Singleton DA. Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A. J Am Chem Soc 2016; 138:3631-4. [PMID: 26909570 PMCID: PMC5367884 DOI: 10.1021/jacs.6b00017] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SpnF, an enzyme involved in the biosynthesis of spinosyn A, catalyzes a transannular Diels-Alder reaction. Quantum mechanical computations and dynamic simulations now show that this cycloaddition is not well described as either a concerted or stepwise process, and dynamical effects influence the identity and timing of bond formation. The transition state for the reaction is ambimodal and leads directly to both the observed Diels-Alder and an unobserved [6+4] cycloadduct. The potential energy surface bifurcates and the cycloadditions occur by dynamically stepwise modes featuring an "entropic intermediate". A rapid Cope rearrangement converts the [6+4] adduct into the observed [4+2] adduct. Control of nonstatistical dynamical effects may serve as another way by which enzymes control reactions.
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Affiliation(s)
- Ashay Patel
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Zhuo Chen
- Department of Chemistry, Texas A & M University, College Station, Texas 77843-3255, United States
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Osvaldo Gutiérrez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Hung-wen Liu
- College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Daniel A. Singleton
- Department of Chemistry, Texas A & M University, College Station, Texas 77843-3255, United States
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93
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Hare SR, Tantillo DJ. Dynamic behavior of rearranging carbocations - implications for terpene biosynthesis. Beilstein J Org Chem 2016; 12:377-90. [PMID: 27340434 PMCID: PMC4902080 DOI: 10.3762/bjoc.12.41] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout.
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Affiliation(s)
- Stephanie R Hare
- Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California–Davis, 1 Shields Avenue, Davis, CA 95616, USA
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94
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Martín-Sómer A, Yáñez M, Hase WL, Gaigeot MP, Spezia R. Post-Transition State Dynamics in Gas Phase Reactivity: Importance of Bifurcations and Rotational Activation. J Chem Theory Comput 2016; 12:974-82. [DOI: 10.1021/acs.jctc.5b01135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Martín-Sómer
- Departamento
de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
- Université d’Evry Val d’Essonne, UMR
8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587, F-91025 Evry Cedex, France
| | - Manuel Yáñez
- Departamento
de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, E-28049 Madrid, Spain
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Marie-Pierre Gaigeot
- Université d’Evry Val d’Essonne, UMR
8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587, F-91025 Evry Cedex, France
- Institut Universitaire de France (IUF), 103 Blvd. St. Michel, 75005 Paris, France
| | - Riccardo Spezia
- Université d’Evry Val d’Essonne, UMR
8587 LAMBE, Boulevard F. Mitterrand, 91025 Evry Cedex, France
- CNRS, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587, F-91025 Evry Cedex, France
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95
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"Cation-Stitching Cascade": exquisite control of terpene cyclization in cyclooctatin biosynthesis. Sci Rep 2015; 5:18471. [PMID: 26681256 PMCID: PMC4683443 DOI: 10.1038/srep18471] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
Terpene cyclization is orchestrated by terpene cyclases, which are involved in the biosynthesis of various cyclic natural products, but understanding the origin and mechanism of the selectivity of terpene cyclization is challenging. In this work, we describe an in-depth mechanistic study on cyclooctatin biosynthesis by means of theoretical calculations combined with experimental methods. We show that the main framework of cyclooctatin is formed through domino-type carbocation transportation along the terpene chain, which we call a “cation-stitching cascade”, including multiple hydrogen-shifts and a ring rearrangement that elegantly determine the stereoselectivity.
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96
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Yang Z, Doubleday C, Houk KN. QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels–Alder Reaction. J Chem Theory Comput 2015; 11:5606-12. [DOI: 10.1021/acs.jctc.5b01029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhongyue Yang
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Charles Doubleday
- Department
of Chemistry, Columbia University, 3000 Broadway,
MC 3142, New York, New York 10027, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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97
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Pu M, Privalov T. Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two-Step Pathway in the Frustrated Lewis Pair Reaction. Chemistry 2015; 21:17708-20. [DOI: 10.1002/chem.201502926] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Indexed: 11/06/2022]
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98
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Song L, Zhu G, Liu Y, Liu B, Qin S. Total Synthesis of Atisane-Type Diterpenoids: Application of Diels–Alder Cycloadditions of Podocarpane-Type Unmasked ortho-Benzoquinones. J Am Chem Soc 2015; 137:13706-14. [DOI: 10.1021/jacs.5b08958] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Liqiang Song
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Guili Zhu
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yongjiang Liu
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Bo Liu
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- State
Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Song Qin
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
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99
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Zhang L, Wang Y, Yao ZJ, Wang S, Yu ZX. Kinetic or Dynamic Control on a Bifurcating Potential Energy Surface? An Experimental and DFT Study of Gold-Catalyzed Ring Expansion and Spirocyclization of 2-Propargyl-β-tetrahydrocarbolines. J Am Chem Soc 2015; 137:13290-300. [DOI: 10.1021/jacs.5b05971] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lei Zhang
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yi Wang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
College of Chemistry, Peking University, Beijing 100871, China
| | - Zhu-Jun Yao
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Shaozhong Wang
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Zhi-Xiang Yu
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
College of Chemistry, Peking University, Beijing 100871, China
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100
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Hoeven R, Heyes DJ, Hay S, Scrutton NS. Does the pressure dependence of kinetic isotope effects report usefully on dynamics in enzyme H-transfer reactions? FEBS J 2015; 282:3243-55. [PMID: 25581554 PMCID: PMC4949571 DOI: 10.1111/febs.13193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/15/2014] [Accepted: 01/08/2015] [Indexed: 11/30/2022]
Abstract
The temperature dependence of kinetic isotope effects (KIEs) has emerged as the main experimental probe of enzymatic H-transfer by quantum tunnelling. Implicit in the interpretation is a presumed role for dynamic coupling of H-transfer chemistry to the protein environment, the so-called 'promoting motions/vibrations hypothesis'. This idea remains contentious, and others have questioned the importance and/or existence of promoting motions/vibrations. New experimental methods of addressing this problem are emerging, including use of mass-modulated enzymes and time-resolved spectroscopy. The pressure dependence of KIEs has been considered as a potential probe of quantum tunnelling reactions, because semi-classical KIEs, which are defined by differences in zero-point vibrational energy, are relatively insensitive to kbar changes in pressure. Reported combined pressure and temperature (p-T) dependence studies of H-transfer reactions are, however, limited. Here, we extend and review the available p-T studies that have utilized well-defined experimental systems in which quantum mechanical tunnelling is established. These include flavoproteins, quinoproteins, light-activated enzymes and chemical model systems. We show that there is no clear general trend between the p-T dependencies of the KIEs in these systems. Given the complex nature of p-T studies, we conclude that computational simulations using determined (e.g. X-ray) structures are also needed alongside experimental measurements of reaction rates/KIEs to guide the interpretation of p-T effects. In providing new insight into H-transfer/environmental coupling, combined approaches that unite both atomistic understanding with experimental rate measurements will require careful evaluation on a case-by-case basis. Although individually informative, we conclude that p-T studies do not provide the more generalized insight that has come from studies of the temperature dependence of KIEs.
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Affiliation(s)
- Robin Hoeven
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, UK
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