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Angera IJ, Wright MM, Del Valle JR. Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides. Acc Chem Res 2024; 57:1287-1297. [PMID: 38626119 DOI: 10.1021/acs.accounts.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.
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Affiliation(s)
- Isaac J Angera
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Starnes SK, Del Valle JR. Synthesis, derivatization, and conformational scanning of peptides containing N-Aminoglycine. Methods Enzymol 2024; 698:1-26. [PMID: 38886028 DOI: 10.1016/bs.mie.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
N-alkylated glycine residues are the main constituent of peptoids and peptoid-peptide hybrids that are employed across the biomedical and materials sciences. While the impact of backbone N-alkylation on peptide conformation has been extensively studied, less is known about the effect of N-amination on the secondary structure propensity of glycine. Here, we describe a convenient protocol for the incorporation of N-aminoglycine into host peptides on solid support. Amide-to-hydrazide substitution also affords a nucleophilic handle for further derivatization of the backbone. To demonstrate the utility of late-stage hydrazide modification, we synthesized and evaluated the stability of polyproline II helix and β-hairpin model systems harboring N-aminoglycine derivatives. The described procedures provide facile entry into peptidomimetic libraries for conformational scanning.
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Dolenc J, Haywood EJ, Zhu T, Smith LJ. Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds. J Chem Inf Model 2022; 62:6704-6714. [PMID: 35816656 PMCID: PMC9795546 DOI: 10.1021/acs.jcim.2c00516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular dynamics (MD) simulations have been used to characterize the effects of backbone N-amination of residues in a model β-hairpin peptide. This modification is of considerable interest as N-aminated peptides have been shown to inhibit amyloid-type aggregation. Six derivatives of the β-hairpin peptide, which contain one, two, or four N-aminated residues, have been studied. For each peptide 100 ns MD simulations starting from the folded β-hairpin structure were performed. The effects of the N-amination prove to be very sequence dependent. N-Amination of a residue involved in interstrand hydrogen bonding (Val3) leads to unfolding of the β-hairpin, whereas N-amination of a residue toward the C-terminus (Leu11) gives fraying at the termini of the peptide. In the other derivatives the peptide remains folded, with increasing levels of N-amination reducing the right-handed twist of the β-hairpin and favoring population of a type II' rather than a type I' β-turn. MD simulations (100 ns) have also been run for each peptide starting from an unfolded extended chain. Here, the peptide with four N-aminated residues shows the most folding into the β-hairpin (34%). Analysis of the simulations shows that N-amination favors the population of β (φ, ψ) conformations by the preceding residue due to, at least in part, a network of weak NH2(i)-CO(i) and NH2(i)-CO(i-2) hydrogen bonds. It also leads to a reduction of misfolding because of changes in the hydrogen-bonding potential. Both of these features help funnel the peptide to the folded β-hairpin structure. The conformational insights provided through this work give a firm foundation for the design of N-aminated peptide inhibitors for modulating protein-protein interactions and aggregation.
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Affiliation(s)
- Jožica Dolenc
- Chemistry
- Biology
- Pharmacy Information Center, ETH Zurich, Zurich CH-8093, Switzerland
| | - Esme J. Haywood
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Tingting Zhu
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Lorna J. Smith
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, (L.J.S.)
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4
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Rathman BM, Rowe JL, Del Valle JR. Synthesis and conformation of backbone N-aminated peptides. Methods Enzymol 2021; 656:271-294. [PMID: 34325790 DOI: 10.1016/bs.mie.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The chemical modification of peptides is a promising approach for the design of protein-protein interaction inhibitors and peptide-based drug candidates. Among several peptidomimetic strategies, substitution of the amide backbone maintains side-chain functionality that may be important for engagement of biological targets. Backbone amide substitution has been largely limited to N-alkylation, which can promote cis amide geometry and disrupt important H-bonding interactions. In contrast, N-amination of peptides induces distinct backbone geometries and maintains H-bond donor capacity. In this chapter we discuss the conformational characteristics of designed N-amino peptides and present a detailed protocol for their synthesis on solid support. The described methods allow for backbone N-amino scanning of biologically active parent sequences.
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5
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Elbatrawi YM, Pedretty KP, Giddings N, Woodcock HL, Del Valle JR. δ-Azaproline and Its Oxidized Variants. J Org Chem 2020; 85:4207-4219. [DOI: 10.1021/acs.joc.9b03384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassin M. Elbatrawi
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle P. Pedretty
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Giddings
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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6
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Howard EH, Cain CF, Kang C, Del Valle JR. Synthesis of Enantiopure ε-Oxapipecolic Acid. J Org Chem 2019; 85:1680-1686. [DOI: 10.1021/acs.joc.9b02382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evan H. Howard
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher F. Cain
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Changwon Kang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Kang CW, Sarnowski MP, Elbatrawi YM, Del Valle JR. Access to Enantiopure α-Hydrazino Acids for N-Amino Peptide Synthesis. J Org Chem 2017; 82:1833-1841. [DOI: 10.1021/acs.joc.6b02718] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chang Won Kang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Matthew P. Sarnowski
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yassin M. Elbatrawi
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Juan R. Del Valle
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017; 56:2083-2086. [DOI: 10.1002/anie.201609395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/12/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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Revilla-López G, Rodríguez-Ropero F, Curcó D, Torras J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database. Proteins 2011; 79:1841-52. [PMID: 21491493 PMCID: PMC3092812 DOI: 10.1002/prot.23009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/22/2011] [Accepted: 01/28/2011] [Indexed: 01/16/2023]
Abstract
Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Francisco Rodríguez-Ropero
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EEI, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Phys Biol 2006; 3:S54-62. [PMID: 16582465 DOI: 10.1088/1478-3975/3/1/s06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Physically building complex multi-molecular structures from naturally occurring biological macromolecules has aroused a great deal of interest. Here we focus on nanostructures composed of re-engineered, natural 'foldamer' building blocks. Our aim is to provide some of the underlying concepts and schemes for crafting structures utilizing such conformationally relatively stable molecular components. We describe how, via chemical biology strategies, it is further possible to chemically manipulate the foldamer building blocks toward specific shape-driven structures, which in turn could be used toward potential-designed functions. We outline the criteria in choosing candidate foldamers from the vast biological repertoire, and how to enhance their stability through selected targeted replacements by non-proteinogenic conformationally constrained amino acids. These approaches combine bioinformatics, high performance computations and mathematics with synthetic organic chemistry. The resulting artificially engineered self-organizing molecular scale structures take advantage of nature's nanobiology toolkit and at the same time improve on it, since their new targeted function differs from that optimized by evolution. The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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12
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Sivaguru J, Sunoj RB, Wada T, Origane Y, Inoue Y, Ramamurthy V. Enhanced Diastereoselectivity via Confinement: Photoisomerization of 2,3-Diphenylcyclopropane-1-carboxylic Acid Derivatives within Zeolites. J Org Chem 2004; 69:6533-47. [PMID: 15387575 DOI: 10.1021/jo049365i] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From the perspective of asymmetric induction, the photochemistry of 24 chiral esters and amides of cis-2,3-diphenylcyclopropane-1-carboxylic acid from excited singlet and triplet states has been investigated within zeolites. The chiral auxiliaries placed at a remote location from the isomerization site functioned far better within a zeolite than in solution. Generally, chiral auxiliaries with an aromatic or a carbonyl substituent performed better than the ones containing only alkyl substituents. A model based on cation-binding-dependent flexibility of the chiral auxiliary accounts for the observed variation in de between aryl (and carbonyl) and alkyl chiral auxiliaries within zeolites. Cation-dependent diastereomer switch was also observed in select examples.
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Affiliation(s)
- J Sivaguru
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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Sivaguru J, Sunoj RB, Wada T, Origane Y, Inoue Y, Ramamurthy V. Enhanced Diastereoselectivity via Confinement: Diastereoselective Photoisomerization of 2,3-Diphenyl-1-benzoylcyclopropane Derivatives within Zeolites. J Org Chem 2004; 69:5528-36. [PMID: 15307720 DOI: 10.1021/jo049697n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photochemistry of optically pure trans-2,3-diphenyl-1-benzoylcyclopropane has been examined in isotropic solution and within zeolites. Results suggest that it isomerizes by cleavage of either the C1-C2 or C1-C3 bond. From the perspective of chiral induction, photoisomerization of cis-2,3-diphenyl-1-benzoylcyclopropane derivatives with chiral auxiliaries placed at the meta and para positions of the benzoyl group have been examined both in isotropic solution and within zeolites. Whereas in isotropic solution the chiral auxiliaries placed at the meta position exhibit very little influence during the conversion of triplet cis-2,3-diphenyl-1-benzoylcyclopropane derivatives, they have significant influence within zeolites. For example, alpha-methyl benzylamine placed at the meta position of the benzoyl group (via an amide bond) yields the trans isomer with a diastereoselectivity (de) of 71% within NaY zeolite, whereas in solution no de is obtained. The chiral induction process within zeolites depends on the nature of the alkali ion and on the presence of water. Results suggest that the chiral auxiliary is able to control the bond being cleaved (C1-C2 vs. C1-C3 bond) within a zeolite, but it is unable to do so in an isotropic solution.
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Affiliation(s)
- J Sivaguru
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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Alemán C, Casanovas J. Analysis of the oxalamide functionality as hydrogen bonding former: geometry, energetics, cooperative effects, NMR chemical characterization and implications in molecular engineering. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Watson TM, Hirst JD. Density Functional Theory Vibrational Frequencies of Amides and Amide Dimers. J Phys Chem A 2002. [DOI: 10.1021/jp025551l] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tim M. Watson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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