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Title: Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide

Abstract

Coarse-grained model of DMA, containing the basic motif of the peptoid backbone, based on short ranged many-body ranged interactions.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]
  1. Department of Chemistry; Louisiana State University; Baton Rouge; USA
  2. Department of Chemistry; University of New Orleans; New Orleans; USA
Publication Date:
Research Org.:
Louisiana State Univ., Baton Rouge, LA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1540017
DOE Contract Number:  
SC0012432
Resource Type:
Journal Article
Journal Name:
Physical Chemistry Chemical Physics. PCCP (Print)
Additional Journal Information:
Journal Volume: 20; Journal Issue: 36; Journal ID: ISSN 1463-9076
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
Chemistry; Physics

Citation Formats

Du, Pu, Rick, Steven W., and Kumar, Revati. Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide. United States: N. p., 2018. Web. doi:10.1039/c8cp03283a.
Du, Pu, Rick, Steven W., & Kumar, Revati. Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide. United States. doi:10.1039/c8cp03283a.
Du, Pu, Rick, Steven W., and Kumar, Revati. Mon . "Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide". United States. doi:10.1039/c8cp03283a.
@article{osti_1540017,
title = {Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide},
author = {Du, Pu and Rick, Steven W. and Kumar, Revati},
abstractNote = {Coarse-grained model of DMA, containing the basic motif of the peptoid backbone, based on short ranged many-body ranged interactions.},
doi = {10.1039/c8cp03283a},
journal = {Physical Chemistry Chemical Physics. PCCP (Print)},
issn = {1463-9076},
number = 36,
volume = 20,
place = {United States},
year = {2018},
month = {1}
}

Works referenced in this record:

Block Copolymer Membranes for Aqueous Solution Applications
journal, March 2016


Block Copolymers: Synthesis, Self-Assembly, and Applications
journal, October 2017


Peptoid Polymers: A Highly Designable Bioinspired Material
journal, May 2013


Polypeptoids from N -Substituted Glycine N -Carboxyanhydrides: Hydrophilic, Hydrophobic, and Amphiphilic Polymers with Poisson Distribution
journal, September 2011

  • Fetsch, Corinna; Grossmann, Arlett; Holz, Lisa
  • Macromolecules, Vol. 44, Issue 17
  • DOI: 10.1021/ma201015y

Polypeptoids: a model system to study the effect of monomer sequence on polymer properties and self-assembly
journal, January 2013

  • Rosales, Adrianne M.; Segalman, Rachel A.; Zuckermann, Ronald N.
  • Soft Matter, Vol. 9, Issue 35
  • DOI: 10.1039/c3sm51421h

Polypeptoid Materials: Current Status and Future Perspectives
journal, May 2012

  • Zhang, Donghui; Lahasky, Samuel H.; Guo, Li
  • Macromolecules, Vol. 45, Issue 15
  • DOI: 10.1021/ma202319g

Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering
journal, December 2015


Self-assembly of block copolymers
journal, May 2001


Self-Assembly of Amphiphilic Block Copolypeptoids – Micelles, Worms and Polymersomes
journal, September 2016

  • Fetsch, Corinna; Gaitzsch, Jens; Messager, Lea
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep33491

Solution Self-Assemblies of Sequence-Defined Ionic Peptoid Block Copolymers
journal, February 2018

  • Sternhagen, Garrett L.; Gupta, Sudipta; Zhang, Yueheng
  • Journal of the American Chemical Society, Vol. 140, Issue 11
  • DOI: 10.1021/jacs.8b00461

Highly Defined Multiblock Copolypeptoids: Pushing the Limits of Living Nucleophilic Ring-Opening Polymerization
journal, June 2012

  • Fetsch, Corinna; Luxenhofer, Robert
  • Macromolecular Rapid Communications, Vol. 33, Issue 19
  • DOI: 10.1002/marc.201200189

Determination of the persistence length of helical and non-helical polypeptoids in solution
journal, January 2012

  • Rosales, Adrianne M.; Murnen, Hannah K.; Kline, Steven R.
  • Soft Matter, Vol. 8, Issue 13
  • DOI: 10.1039/c2sm07092h

Development and use of an atomistic CHARMM-based forcefield for peptoid simulation
journal, November 2013

  • Mirijanian, Dina T.; Mannige, Ranjan V.; Zuckermann, Ronald N.
  • Journal of Computational Chemistry, Vol. 35, Issue 5
  • DOI: 10.1002/jcc.23478

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation
journal, January 2018


The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
journal, March 1988

  • Jorgensen, William L.; Tirado-Rives, Julian
  • Journal of the American Chemical Society, Vol. 110, Issue 6
  • DOI: 10.1021/ja00214a001

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
journal, January 1996

  • Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
  • Journal of the American Chemical Society, Vol. 118, Issue 45
  • DOI: 10.1021/ja9621760

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
journal, April 2016


Coarse-Graining Methods for Computational Biology
journal, May 2013


Multiscale Modeling of Coarse-Grained Macromolecular Liquids
journal, September 2009

  • McCarty, J.; Lyubimov, I. Y.; Guenza, M. G.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 35
  • DOI: 10.1021/jp905071w

Coarse-Grained Protein Models and Their Applications
journal, June 2016


Bridging scales through multiscale modeling: a case study on protein kinase A
journal, September 2015


Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems
journal, May 2011


Coarse-Graining in Interaction Space:  A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials
journal, April 2008

  • Izvekov, Sergei; Swanson, Jessica M. J.; Voth, Gregory A.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 15
  • DOI: 10.1021/jp710339n

Multiscale Modeling of Proteins
journal, February 2010

  • Tozzini, Valentina
  • Accounts of Chemical Research, Vol. 43, Issue 2
  • DOI: 10.1021/ar9001476

Computer simulation of protein folding
journal, February 1975

  • Levitt, Michael; Warshel, Arieh
  • Nature, Vol. 253, Issue 5494
  • DOI: 10.1038/253694a0

The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

Perspective on the Martini model
journal, January 2013

  • Marrink, Siewert J.; Tieleman, D. Peter
  • Chemical Society Reviews, Vol. 42, Issue 16
  • DOI: 10.1039/c3cs60093a

Pair potentials in disordered many-particle systems: A study for liquid gallium
journal, December 1983


Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
journal, June 1994


A Multiscale Coarse-Graining Method for Biomolecular Systems
journal, February 2005

  • Izvekov, Sergei; Voth, Gregory A.
  • The Journal of Physical Chemistry B, Vol. 109, Issue 7
  • DOI: 10.1021/jp044629q

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
journal, June 2004

  • Izvekov, Sergei; Parrinello, Michele; Burnham, Christian J.
  • The Journal of Chemical Physics, Vol. 120, Issue 23
  • DOI: 10.1063/1.1739396

Systematic coarse-graining of molecular models by the Newton inversion method
journal, January 2010

  • Lyubartsev, Alexander; Mirzoev, Alexander; Chen, LiJun
  • Faraday Discuss., Vol. 144
  • DOI: 10.1039/B901511F

Coarse-Grained Models of Aqueous and Pure Liquid Alkanes
journal, June 2017

  • Gyawali, Gaurav; Sternfield, Samuel; Kumar, Revati
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 8
  • DOI: 10.1021/acs.jctc.7b00389

Coarse-Grained Simulations of Aqueous Thermoresponsive Polyethers
journal, April 2018


Implicit-Solvent Coarse-Grained Simulation with a Fluctuating Interface Reveals a Molecular Mechanism for Peptoid Monolayer Buckling
journal, December 2015

  • Haxton, Thomas K.; Zuckermann, Ronald N.; Whitelam, Stephen
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 1
  • DOI: 10.1021/acs.jctc.5b00910

Tunable peptoid microspheres: effects of side chain chemistry and sequence
journal, January 2013

  • Hebert, Melissa L.; Shah, Dhaval S.; Blake, Phillip
  • Organic & Biomolecular Chemistry, Vol. 11, Issue 27
  • DOI: 10.1039/c3ob40561c

Computer simulation of local order in condensed phases of silicon
journal, April 1985


Water Simulation Model with Explicit Three-Molecule Interactions
journal, July 2008

  • Kumar, R.; Skinner, J. L.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 28
  • DOI: 10.1021/jp8009468

Water Modeled As an Intermediate Element between Carbon and Silicon
journal, April 2009

  • Molinero, Valeria; Moore, Emily B.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 13
  • DOI: 10.1021/jp805227c

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


The Nose–Hoover thermostat
journal, October 1985

  • Evans, D. J.; Holian, B. L.
  • The Journal of Chemical Physics, Vol. 83, Issue 8
  • DOI: 10.1063/1.449071

Constant pressure molecular dynamics algorithms
journal, September 1994

  • Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
  • The Journal of Chemical Physics, Vol. 101, Issue 5
  • DOI: 10.1063/1.467468

Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions
journal, January 1996

  • Luty, Brock A.; van Gunsteren, Wilfred F.
  • The Journal of Physical Chemistry, Vol. 100, Issue 7
  • DOI: 10.1021/jp9518623

Guidelines for the analysis of free energy calculations
journal, March 2015

  • Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
  • Journal of Computer-Aided Molecular Design, Vol. 29, Issue 5
  • DOI: 10.1007/s10822-015-9840-9

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations
journal, August 2011

  • Steinbrecher, Thomas; Joung, InSuk; Case, David A.
  • Journal of Computational Chemistry, Vol. 32, Issue 15
  • DOI: 10.1002/jcc.21909

Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
journal, June 1994


GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015


A Methane−Water Model for Coarse-Grained Simulations of Solutions and Clathrate Hydrates
journal, June 2010

  • Jacobson, Liam C.; Molinero, Valeria
  • The Journal of Physical Chemistry B, Vol. 114, Issue 21
  • DOI: 10.1021/jp1013576

Isothermal compressibility of SPC/E water
journal, October 1990

  • Motakabbir, Kazi A.; Berkowitz, M.
  • The Journal of Physical Chemistry, Vol. 94, Issue 21
  • DOI: 10.1021/j100384a067

Molecular dynamics simulation of the orthobaric densities and surface tension of water
journal, March 1995

  • Alejandre, José; Tildesley, Dominic J.; Chapela, Gustavo A.
  • The Journal of Chemical Physics, Vol. 102, Issue 11
  • DOI: 10.1063/1.469505

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models
journal, March 2011

  • Sakamaki, Ryuji; Sum, Amadeu K.; Narumi, Tetsu
  • The Journal of Chemical Physics, Vol. 134, Issue 12
  • DOI: 10.1063/1.3574038

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
journal, April 2010

  • Shivakumar, Devleena; Williams, Joshua; Wu, Yujie
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 5
  • DOI: 10.1021/ct900587b