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Harris BS, Bejagam KK, Baer MD. Development of a Systematic and Extensible Force Field for Peptoids (STEPs). J Phys Chem B 2023; 127:6573-6584. [PMID: 37462325 DOI: 10.1021/acs.jpcb.3c01424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Peptoids (N-substituted glycines) are a class of biomimetic polymers that have attracted significant attention due to their accessible synthesis and enzymatic and thermal stability relative to their naturally occurring counterparts (polypeptides). While these polymers provide the promise of more robust functional materials via hierarchical approaches, they present a new challenge for computational structure prediction for material design. The reliability of calculations hinges on the accuracy of interactions represented in the force field used to model peptoids. For proteins, structure prediction based on sequence and de novo design has made dramatic progress in recent years; however, these models are not readily transferable for peptoids. Current efforts to develop and implement peptoid-specific force fields are spread out, leading to replicated efforts and a fragmented collection of parameterized sidechains. Here, we developed a peptoid-specific force field containing 70 different side chains, using GAFF2 as starting point. The new model is validated based on the generation of Ramachandran-like plots from DFT optimization compared against force field reproduced potential energy and free energy surfaces as well as the reproduction of equilibrium cis/trans values for some residues experimentally known to form helical structures. Equilibrium cis/trans distributions (Kct) are estimated for all parameterized residues to identify which residues have an intrinsic propensity for cis or trans states in the monomeric state.
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Affiliation(s)
- Bradley S Harris
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Karteek K Bejagam
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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2
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Lenstra DC, Wolf JJ, Mecinović J. Catalytic Staudinger Reduction at Room Temperature. J Org Chem 2019; 84:6536-6545. [PMID: 31050295 DOI: 10.1021/acs.joc.9b00831] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report an efficient catalytic Staudinger reduction at room temperature that enables the preparation of a structurally diverse set of amines from azides in excellent yields. The reaction is based on the use of catalytic amounts of triphenylphosphine as a phosphine source and diphenyldisiloxane as a reducing agent. Our catalytic Staudinger reduction exhibits a high chemoselectivity, as exemplified by reduction of azides over other common functionalities, including nitriles, alkenes, alkynes, esters, and ketones.
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Affiliation(s)
- Danny C Lenstra
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , Nijmegen 6525 AJ , The Netherlands
| | - Joris J Wolf
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , Nijmegen 6525 AJ , The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , Nijmegen 6525 AJ , The Netherlands.,Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , Odense 5230 , Denmark
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Jin H, Jian T, Ding YH, Chen Y, Mu P, Wang L, Chen CL. Solid-phase synthesis of three-armed star-shaped peptoids and their hierarchical self-assembly. Biopolymers 2019; 110:e23258. [PMID: 30676654 DOI: 10.1002/bip.23258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 12/19/2022]
Abstract
Due to the branched structure feature and unique properties, a variety of star-shaped polymers have been designed and synthesized. Despite those advances, solid-phase synthesis of star-shaped sequence-defined synthetic polymers that exhibit hierarchical self-assembly remains a significant challenge. Hence, we present an effective strategy for the solid-phase synthesis of three-armed star-shaped peptoids, in which ethylenediamine was used as the centric star pivot. Based on the sequence of monomer addition, a series of AA'A''-type and ABB'-type peptoids were synthesized and characterized by UPLC-MS (ultrahigh performance liquid chromatography-mass spectrometry). By taking advantage of the easy-synthesis and large side-chain diversity, we synthesized star-shaped peptoids with tunable functions. We further demonstrated the aqueous self-assembly of some representative peptoids into biomimetic nanomaterials with well-defined hierarchical structures, such as nanofibers and nanotubes. These results indicate that star-shaped peptoids offer the potential in self-assembly of biomimetic nanomaterials with tunable chemistries and functions.
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Affiliation(s)
- Haibao Jin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
| | - Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
| | - Yan-Huai Ding
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
- Institute of Rheological Mechanics, Xiangtan University, Xiangtan, Hunan, China
| | - Yulin Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
- Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, New York
| | - Lei Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia
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Zhang S, Hu B, Zheng Z, Walsh PJ. Palladium-Catalyzed Triarylation of sp 3 C-H Bonds in Heteroarylmethanes: Synthesis of Triaryl(heteroaryl)methanes. Adv Synth Catal 2018; 360:1493-1498. [PMID: 30093851 PMCID: PMC6078434 DOI: 10.1002/adsc.201701347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A straightforward method for the palladium-catalyzed triarylation of heteroarylmethanes at the methyl group has been developed. The reaction works with a variety of aryl halides, enabling the rapid synthesis of triaryl(heteroaryl)methanes in moderate to excellent yields.
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Affiliation(s)
- Shuguang Zhang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, People’s Republic of China
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Bowen Hu
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Zhipeng Zheng
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Patrick J. Walsh
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, People’s Republic of China
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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5
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Martens S, Holloway JO, Du Prez FE. Click and Click-Inspired Chemistry for the Design of Sequence-Controlled Polymers. Macromol Rapid Commun 2017; 38. [PMID: 28990247 DOI: 10.1002/marc.201700469] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/18/2017] [Indexed: 01/09/2023]
Abstract
During the previous decade, many popular chemical reactions used in the area of "click" chemistry and similarly efficient "click-inspired" reactions have been applied for the design of sequence-defined and, more generally, sequence-controlled structures. This combination of topics has already made quite a significant impact on scientific research to date and has enabled the synthesis of highly functionalized and complex oligomeric and polymeric structures, which offer the prospect of many exciting further developments and applications in the near future. This minireview highlights the fruitful combination of these two topics for the preparation of sequence-controlled oligomeric and macromolecular structures and showcases the vast number of publications in this field within a relatively short span of time. It is divided into three sections according to the click-(inspired) reaction that has been applied: copper-catalyzed azide-alkyne cycloaddition, thiol-X, and related thiolactone-based reactions, and finally Diels-Alder-chemistry-based routes are outlined, respectively.
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Affiliation(s)
- Steven Martens
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
| | - Joshua O Holloway
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Centre of Macromolecular Chemistry (CMaC), Ghent University, Krijgslaan 281 S4-bis, B-9000, Ghent, Belgium
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Zhang S, Kim BS, Wu C, Mao J, Walsh PJ. Palladium-catalysed synthesis of triaryl(heteroaryl)methanes. Nat Commun 2017; 8:14641. [PMID: 28290445 PMCID: PMC5355892 DOI: 10.1038/ncomms14641] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/19/2017] [Indexed: 12/19/2022] Open
Abstract
Tetraarylmethane derivatives are desirable for a variety of applications, but difficult to access with modern C-C bond-forming reactions. Here we report a straightforward method for palladium-catalysed arylation of aryl(heteroaryl)methanes and diaryl(heteroaryl)methanes with aryl chlorides. This reaction enables introduction of various aryl groups to construct triaryl(heteroaryl)methanes via a C-H functionalization in good to excellent yield, and represents the first step towards a general transition metal catalysed synthesis of tetraarylmethanes.
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Affiliation(s)
- Shuguang Zhang
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
| | - Byeong-Seon Kim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
| | - Chen Wu
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
| | - Jianyou Mao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211816, China
| | - Patrick J Walsh
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, 30 South Puzhu Road, Nanjing 211816, China
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Gangloff N, Ulbricht J, Lorson T, Schlaad H, Luxenhofer R. Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering. Chem Rev 2015; 116:1753-802. [DOI: 10.1021/acs.chemrev.5b00201] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Niklas Gangloff
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Juliane Ulbricht
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Thomas Lorson
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Helmut Schlaad
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Robert Luxenhofer
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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Knight AS, Zhou EY, Francis MB, Zuckermann RN. Sequence Programmable Peptoid Polymers for Diverse Materials Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5665-5691. [PMID: 25855478 DOI: 10.1002/adma.201500275] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/13/2015] [Indexed: 06/04/2023]
Abstract
Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.
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Affiliation(s)
- Abigail S Knight
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Effie Y Zhou
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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Arseneault M, Wafer C, Morin JF. Recent advances in click chemistry applied to dendrimer synthesis. Molecules 2015; 20:9263-94. [PMID: 26007183 PMCID: PMC6272213 DOI: 10.3390/molecules20059263] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/12/2015] [Indexed: 11/16/2022] Open
Abstract
Dendrimers are monodisperse polymers grown in a fractal manner from a central point. They are poised to become the cornerstone of nanoscale devices in several fields, ranging from biomedicine to light-harvesting. Technical difficulties in obtaining these molecules has slowed their transfer from academia to industry. In 2001, the arrival of the "click chemistry" concept gave the field a major boost. The flagship reaction, a modified Hüisgen cycloaddition, allowed researchers greater freedom in designing and building dendrimers. In the last five years, advances in click chemistry saw a wider use of other click reactions and a notable increase in the complexity of the reported structures. This review covers key developments in the click chemistry field applied to dendrimer synthesis from 2010 to 2015. Even though this is an expert review, basic notions and references have been included to help newcomers to the field.
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Affiliation(s)
- Mathieu Arseneault
- Chimie, Université Laval, 1045 avenue de la Médecine, Pavillon Alexandre-Vachon, QC G1V 0A6, Canada.
| | - Caroline Wafer
- Chimie, Université Laval, 1045 avenue de la Médecine, Pavillon Alexandre-Vachon, QC G1V 0A6, Canada.
| | - Jean-François Morin
- Chimie, Université Laval, 1045 avenue de la Médecine, Pavillon Alexandre-Vachon, QC G1V 0A6, Canada.
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