1
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McCann S, Roe WE, Agnew HE, Knipe PC. Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers. Angew Chem Int Ed Engl 2023; 62:e202307180. [PMID: 37414732 PMCID: PMC10952507 DOI: 10.1002/anie.202307180] [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: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.
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Affiliation(s)
- Sinead McCann
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - William E. Roe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Hannah E. Agnew
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Peter C. Knipe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
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2
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Roe WE, Warnock TMC, Knipe PC. A spirocyclic backbone accesses new conformational space in an extended, dipole-stabilized foldamer. Commun Chem 2023; 6:71. [PMID: 37069245 PMCID: PMC10110530 DOI: 10.1038/s42004-023-00868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Most aromatic foldamers adopt uniform secondary structures, offering limited potential for the exploration of conformational space and the formation of tertiary structures. Here we report the incorporation of spiro bis-lactams to allow controlled rotation of the backbone of an iteratively synthesised foldamer. This enables precise control of foldamer shape along two orthogonal directions, likened to the aeronautical yaw and roll axes. XRD, NMR and computational data suggest that homo-oligomers adopt an extended right-handed helix with a pitch of over 30 Å, approximately that of B-DNA. Compatibility with extant foldamers to form hetero-oligomers is demonstrated, allowing greater structural complexity and function in future hybrid foldamer designs.
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Affiliation(s)
- William Edward Roe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Toyah Mary Catherine Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Peter Clarke Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK.
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3
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De Oliveira Silva A, Harper JL, Fuhr KN, Lalancette RA, Cheong PHY, Brenner-Moyer SE. DyKAT by DiCat: Stereoconvergent Dienamine-Catalyzed Claisen Rearrangements. J Org Chem 2022; 87:10105-10113. [PMID: 35881006 DOI: 10.1021/acs.joc.2c01079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Claisen rearrangement establishes the feasibility of DyKAT of γ-epimeric enals via dienamine formation to afford enantioenriched products. γ-Aryl and -alkyl enals, and exocyclic enals that introduce quaternary centers, are all amenable substrates. Products are readily converted into pyrrolidines or cyclopentenols. Notably, a reactive dienamine intermediate has been isolated from a catalytic reaction, fully characterized, and converted to product upon reexposure to reaction conditions. Product configuration arises from a directing C-H···π interaction in the transition state.
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Affiliation(s)
- Ana De Oliveira Silva
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Jordan L Harper
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Katherine N Fuhr
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Roger A Lalancette
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Paul Ha-Yeon Cheong
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Stacey E Brenner-Moyer
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
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4
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Xie Y, Luo D, Wiener J, Tang S, Chepyshev S, Schafmeister C. Development of Fmoc-Protected Bis-Amino Acids toward Automated Synthesis of Highly Functionalized Spiroligomers. Org Lett 2022; 24:3421-3425. [PMID: 35499925 PMCID: PMC9113113 DOI: 10.1021/acs.orglett.2c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report the fluorenylmethoxycarbonyl (Fmoc) protection of functionalized bis-amino acid building blocks using a temporary Cu2+ complexation strategy, together with an efficient multikilogram-scale synthesis of bis-amino acid precursors. This allows the synthesis of stereochemically and functionally diverse spiroligomers utilizing solid-phase Fmoc/tBu chemistry to facilitate the development of applications. Four tetramers were assembled on a semiautomated microwave peptide synthesizer. We determined their secondary structures with two-dimensional nuclear magnetic resonance spectroscopy.
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5
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Abstract
Computational methods have emerged as a powerful tool to augment traditional experimental molecular catalyst design by providing useful predictions of catalyst performance and decreasing the time needed for catalyst screening. In this perspective, we discuss three approaches for computational molecular catalyst design: (i) the reaction mechanism-based approach that calculates all relevant elementary steps, finds the rate and selectivity determining steps, and ultimately makes predictions on catalyst performance based on kinetic analysis, (ii) the descriptor-based approach where physical/chemical considerations are used to find molecular properties as predictors of catalyst performance, and (iii) the data-driven approach where statistical analysis as well as machine learning (ML) methods are used to obtain relationships between available data/features and catalyst performance. Following an introduction to these approaches, we cover their strengths and weaknesses and highlight some recent key applications. Furthermore, we present an outlook on how the currently applied approaches may evolve in the near future by addressing how recent developments in building automated computational workflows and implementing advanced ML models hold promise for reducing human workload, eliminating human bias, and speeding up computational catalyst design at the same time. Finally, we provide our viewpoint on how some of the challenges associated with the up-and-coming approaches driven by automation and ML may be resolved.
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Affiliation(s)
- Ademola Soyemi
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
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6
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Hurley MFD, Northrup JD, Ge Y, Schafmeister CE, Voelz VA. Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. J Chem Inf Model 2021; 61:2818-2828. [PMID: 34125519 DOI: 10.1021/acs.jcim.1c00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to preorganize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies to predict and design conformational and binding properties of macrocycles as functional scaffolds for peptidomimetics. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly preorganized all-trans amide conformation, whose formation is likely limited by the slow rate of cis/trans isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na+ has a higher affinity to the macrocycle than K+, with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.
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Affiliation(s)
- Matthew F D Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Justin D Northrup
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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7
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Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. J Am Chem Soc 2021; 143:785-797. [PMID: 33395523 DOI: 10.1021/jacs.0c09423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report here on the salient role of protein mobility in accessing conformational landscapes that enable efficient enzyme catalysis. We are focused on yeast enolase, a highly conserved lyase with a TIM barrel domain and catalytic loop, as part of a larger study of the relationship of site selective protein motions to chemical reactivity within superfamilies. Enthalpically hindered variants were developed by replacement of a conserved hydrophobic side chain (Leu 343) with smaller side chains. Leu343 is proximal to the active site base in enolase, and comparative pH rate profiles for the valine and alanine variants indicate a role for side chain hydrophobicity in tuning the pKa of the catalytic base. However, the magnitude of a substrate deuterium isotope effect is almost identical for wild-type (WT) and Leu343Ala, supporting an unchanged rate-determining proton abstraction step. The introduced hydrophobic side chains at position 343 lead to a discontinuous break in both activity and activation energy as a function of side chain volume. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments were performed as a function of time and temperature for WT and Leu343Ala, and provide a spatially resolved map of changes in protein flexibility following mutation. Impacts on protein flexibility are localized to specific networks that arise at the protein-solvent interface and terminate in a loop that has been shown by X-ray crystallography to close over the active site. These interrelated effects are discussed in the context of long-range, solvent-accessible and thermally activated networks that play key roles in tuning the precise distances and interactions among reactants.
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Affiliation(s)
- Emily J Thompson
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Adhayana Paul
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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8
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Affiliation(s)
- Zebediah C. Girvin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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An X, Du J, Jia Z, Zhang Q, Yu K, Zhang Y, Zhao X, Fang R, Fan C. Asymmetric Catalytic [4+5] Annulation of
ortho
‐Quinone Methides with Vinylethylene Carbonates and its Extension to Stereoselective Tandem Rearrangement. Chemistry 2020; 26:3803-3809. [DOI: 10.1002/chem.201904903] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Xian‐Tao An
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Ji‐Yuan Du
- College of Chemistry and Chemical EngineeringLiaocheng University 1 Hunan Road Liaocheng 252059 China
| | - Zhi‐Long Jia
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Qing Zhang
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Ke‐Yin Yu
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Yi‐Zhou Zhang
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Xian‐He Zhao
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Ran Fang
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
| | - Chun‐An Fan
- State Key Laboratory of Applied Organic ChemistryCollege of Chemistry and Chemical EngineeringLanzhou University 222 Tianshui Nanlu Lanzhou 730000 China
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10
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Nothling MD, Xiao Z, Bhaskaran A, Blyth MT, Bennett CW, Coote ML, Connal LA. Synthetic Catalysts Inspired by Hydrolytic Enzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03326] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mitchell D. Nothling
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zeyun Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
| | - Ayana Bhaskaran
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mitchell T. Blyth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher W. Bennett
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michelle L. Coote
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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11
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Utilization of the p-nitrobenzyloxycarbonyl (pNZ) amine protecting group and pentafluorophenyl (Pfp) esters for the solid phase synthesis of spiroligomers. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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12
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Ge Y, Voelz VA. Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization. J Phys Chem B 2018. [PMID: 29518328 DOI: 10.1021/acs.jpcb.7b11871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Bayesian Inference of Conformational Populations (BICePs) algorithm reconciles theoretical predictions of conformational state populations with sparse and/or noisy experimental measurements. Among its key advantages is its ability to perform objective model selection through a quantity we call the BICePs score, which reflects the integrated posterior evidence in favor of a given model, computed through free energy estimation methods. Here, we explore how the BICePs score can be used for force field validation and parametrization. Using a 2D lattice protein as a toy model, we demonstrate that BICePs is able to select the correct value of an interaction energy parameter given ensemble-averaged experimental distance measurements. We show that if conformational states are sufficiently fine-grained, the results are robust to experimental noise and measurement sparsity. Using these insights, we apply BICePs to perform force field evaluations for all-atom simulations of designed β-hairpin peptides against experimental NMR chemical shift measurements. These tests suggest that BICePs scores can be used for model selection in the context of all-atom simulations. We expect this approach to be particularly useful for the computational foldamer design as a tool for improving general-purpose force fields given sparse experimental measurements.
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Affiliation(s)
- Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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13
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Theoretical study of Lewis acid activation models for hypervalent fluoroiodane reagent: The generality of “F-coordination” activation model. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Northrup JD, Purcell CR, Schafmeister CE. One-Pot Synthesis of Chiral, Spirocyclic 4-Hydantoin-Proline Derivatives for Incorporation into Spiroligomer-Based Macromolecules. J Org Chem 2017; 82:3223-3231. [PMID: 27690253 DOI: 10.1021/acs.joc.6b01773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Derivatives of 4-hydantoin-proline have been synthesized via a direct two-step alkylation method. This method is valuable in the development of applications of N,N'-disubstituted hydantoin bearing α-amino acids by improving yields, reducing the time and number of steps required to synthesize these substituted molecules, and enabling late stage functionalization of spiroligomer termini. Over 20 unique electrophiles have been tested, highlighting the inherent versatility of this chemistry.
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Affiliation(s)
- J D Northrup
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Claire R Purcell
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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15
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Krenske EH, Burns JM, McGeary RP. Claisen rearrangements of benzyl vinyl ethers: theoretical investigation of mechanism, substituent effects, and regioselectivity. Org Biomol Chem 2017; 15:7887-7893. [DOI: 10.1039/c7ob01666b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical calculations are reported which examine the mechanisms of Claisen rearrangements of benzyl vinyl ethers and the ways in which substituents influence reactivity and regioselectivity.
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Affiliation(s)
- Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Jed M. Burns
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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16
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Zhou B, Yan T, Xue XS, Cheng JP. Mechanism of Silver-Mediated Geminal Difluorination of Styrenes with a Fluoroiodane Reagent: Insights into Lewis-Acid-Activation Model. Org Lett 2016; 18:6128-6131. [PMID: 27934395 DOI: 10.1021/acs.orglett.6b03134] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorination mediated by the cyclic hypervalent fluoroiodane reagent (1) often requires an exogenous Lewis acid. The widely accepted Lewis-acid-activation model is that a given Lewis acid binds to the oxygen atom of 1 (O-coordination) to polarize the I-O bond. Computational studies of silver-mediated geminal difluorination of styrenes with 1 reveal a new "F-coordination" model that is energetically much preferred over the commonly accepted "O-coordination" model. The calculations rationalize the regioselective formation of the geminal difluorination product.
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Affiliation(s)
| | | | | | - Jin-Pei Cheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University , Beijing 100084, China
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17
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Cheong JE, Pfeiffer CT, Northrup JD, Parker MF, Schafmeister CE. An improved, scalable synthesis of bis-amino acids. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis. Angew Chem Int Ed Engl 2015; 54:12772-6. [DOI: 10.1002/anie.201506793] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 12/15/2022]
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20
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Abstract
We demonstrate the synthesis and characterization of the solution conformations of a collection of functionalized spiroligomer-based macrocycles. These macrocycles contain 14 independently controllable stereocenters and four independently controllable functional groups on a highly preorganized scaffold. These molecules are being developed to display complex, preorganized surfaces for binding proteins and to create enzyme-like active sites. In this work, we demonstrate the convergent synthetic approach to this new class of macrocycles and demonstrate that the conformational properties of these molecules can be changed by altering the configuration stereocenters within the backbone.
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Affiliation(s)
- Qingquan Zhao
- Department of Chemistry, Temple University , 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Christian E Schafmeister
- Department of Chemistry, Temple University , 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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21
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Panigrahi K, Applegate GA, Malik G, Berkowitz DB. Combining a Clostridial enzyme exhibiting unusual active site plasticity with a remarkably facile sigmatropic rearrangement: rapid, stereocontrolled entry into densely functionalized fluorinated phosphonates for chemical biology. J Am Chem Soc 2015; 137:3600-9. [PMID: 25719907 DOI: 10.1021/jacs.5b00022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C-O stereochemistry in the substrate into the δ-C-S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93-99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the "L"-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters ("D"), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure-reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS(‡) = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH(‡) = -2.3 kcal/mol) and entropic (ΔΔS(‡) = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.
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Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Gregory A Applegate
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Guillaume Malik
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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22
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Walvoord RR, Huynh PNH, Kozlowski MC. Quantification of electrophilic activation by hydrogen-bonding organocatalysts. J Am Chem Soc 2014; 136:16055-65. [PMID: 25325850 PMCID: PMC4235367 DOI: 10.1021/ja5086244] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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A spectrophotometric sensor is described
that provides a useful
assessment of the LUMO-lowering provided by catalysts in Diels–Alder
and Friedel–Crafts reactions. A broad range of 33 hydrogen-bonding
catalysts was assessed with the sensor, and the relative rates in
the above reactions spanned 5 orders of magnitude as determined via 1H- and 2H NMR spectroscopic measurements, respectively.
The differences between the maximum wavelength shift of the sensor
with and without catalyst (Δλmax–1) were found to correlate linearly with ln(krel) values for both reactions, even though the substrate feature
that interacts with the catalyst differs significantly (ketone vs
nitro). The sensor provides an assessment of both the inherent
reactivity of a catalyst architecture as well as the sensitivity of the reaction to changes within an architecture.
In contrast, catalyst pKa values are a
poor measure of reactivity, although correlations have been identified
within catalyst classes.
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Affiliation(s)
- Ryan R Walvoord
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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