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Hwang IC, Rick SW. The pH Response of a Peptoid Oligomer. J Phys Chem B 2023; 127:2872-2878. [PMID: 36926948 DOI: 10.1021/acs.jpcb.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Polypeptoids are N-substituted glycine polymers, which differ from peptides in the placement of the side chain on the amide nitrogen rather than the Cα carbon. A peptoid with a chiral side chain containing both an aromatic group and carboxylic acid has a structure that responds to pH changes. All-atom molecular dynamics simulations using a force field specifically tuned for peptoids were carried out with an advanced sampling method for the peptoid (S)-N-(1-carboxy-2-phenylethyl)glycine in the high and low pH limits. The simulations show that the structure changes from mostly cis amide bonds at low pH to mostly trans bonds at high pH. The structural changes are driven by side chain-backbone hydrogen bonds at low pH and side chain repulsions and increased water contact at high pH.
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Affiliation(s)
- In Chul Hwang
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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2
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Dhabal D, Jiang Z, Pallath A, Patel AJ. Characterizing the Interplay between Polymer Solvation and Conformation. J Phys Chem B 2021; 125:5434-5442. [PMID: 33978411 DOI: 10.1021/acs.jpcb.1c02191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhitong Jiang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Akash Pallath
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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3
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Ziolek RM, Smith P, Pink DL, Dreiss CA, Lorenz CD. Unsupervised Learning Unravels the Structure of Four-Arm and Linear Block Copolymer Micelles. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02523] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert M. Ziolek
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Paul Smith
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Demi L. Pink
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
| | - Cécile A. Dreiss
- Institute of Pharmaceutical Science, King’s College London, London SE1 9NH, U.K
| | - Christian D. Lorenz
- Biological Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, U.K
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4
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Carr AC, Piunova VA, Maarof H, Rice JE, Swope WC. Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers. J Phys Chem B 2018; 122:5356-5367. [PMID: 29385796 DOI: 10.1021/acs.jpcb.7b10539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.
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Affiliation(s)
- Amber C Carr
- IBM Almaden Research Center, IBM Research , 650 Harry Road , San Jose , California 95120 , United States
| | - Victoria A Piunova
- IBM Almaden Research Center, IBM Research , 650 Harry Road , San Jose , California 95120 , United States
| | - Hasmerya Maarof
- Department of Chemistry , Universiti Teknologi Malaysia , Johor Bahru , 81310 Johor , Malaysia
| | - Julia E Rice
- IBM Almaden Research Center, IBM Research , 650 Harry Road , San Jose , California 95120 , United States
| | - William C Swope
- IBM Almaden Research Center, IBM Research , 650 Harry Road , San Jose , California 95120 , United States
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Mella M, La Rocca MV, Miele Y, Izzo L. On the origin and consequences of high DMAEMA reactivity ratio in ATRP copolymerization with MMA: An experimental and theoretical study#. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.29017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia; Università degli Studi dell'Insubria, via Valleggio 9; Como 22100 Italy
| | - Mario Vincenzo La Rocca
- Dipartimento di Scienza ed Alta Tecnologia; Università degli Studi dell'Insubria, via Valleggio 9; Como 22100 Italy
| | - Ylenia Miele
- Dipartimento di Chimica e Biologia; Università degli Studi di Salerno, Via Giovanni Paolo II, 132; 84084 Fisciano Italy
| | - Lorella Izzo
- Dipartimento di Chimica e Biologia; Università degli Studi di Salerno, Via Giovanni Paolo II, 132; 84084 Fisciano Italy
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6
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Abstract
Abstract
The nature of chemical product design problems is diverse and multidisciplinary. It involves many design issues such as project management, market study, product design, process design, and economic analysis for better organizing the product design project and achieving better products. This article provides an overview of chemical product design with a multidisciplinary hierarchical framework including all the design issues and tasks. Each of the design issues and tasks are introduced and discussed, methods and tools are summarized and compared, challenges and perspectives are presented to help the chemical product design researchers on finding more novel, innovative and sustainable products, by the combined effort from academia and industry to develop a systematic generic framework, and tools including product simulator, process simulator, database manager, modeling tool, and templates for design problems.
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Affiliation(s)
- Lei Zhang
- Department of Chemical and Biomolecular Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Hong Kong
- Institute of Process Systems Engineering, School of Chemical Engineering, Dalian University of Technology , Dalian 116012 , China
| | - Ka Yip Fung
- Department of Chemical and Biomolecular Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Hong Kong
| | - Christianto Wibowo
- ClearWaterBay Technology, 4000 Valley Blvd., Suite 100 , Pomona, CA 91789 , USA
| | - Rafiqul Gani
- Department of Chemical and Biochemical Engineering , Technical University of Denmark , Lyngby DK-2800 , Denmark
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Kubo T, Bentz KC, Powell KC, Figg CA, Swartz JL, Tansky M, Chauhan A, Savin DA, Sumerlin BS. Modular and rapid access to amphiphilic homopolymers via successive chemoselective post-polymerization modification. Polym Chem 2017. [DOI: 10.1039/c7py01585b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A modular and simplified post-polymerization modification strategy is developed for the synthesis of amphiphilic homopolymers.
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Affiliation(s)
- Tomohiro Kubo
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Kyle C. Bentz
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Kristin C. Powell
- Department of Chemical Engineering
- University of Florida
- Gainesville
- USA
| | - C. Adrian Figg
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Jeremy L. Swartz
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Maxym Tansky
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Anuj Chauhan
- Department of Chemical Engineering
- University of Florida
- Gainesville
- USA
| | - Daniel A. Savin
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
| | - Brent S. Sumerlin
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville
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