scholarly journals Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2764
Author(s):  
Utkarsh Kapoor ◽  
Arjita Kulshreshtha ◽  
Arthi Jayaraman
Keyword(s):  
Hydrogen Bonding ◽  
Bond Angle ◽  
Persistence Length ◽  
Distance Distribution ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Implicit Solvent ◽  
End Distance ◽  
End To End ◽  
Chain Lengths

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

END-TO-END DISTANCE DISTRIBUTION OF FORCE STRETCHED CHAINS RECONSTRUCTION BY MAXIMUM-ENTROPY METHOD

2004 ◽  
Vol 18 (17n19) ◽  
pp. 2365-2375
Author(s):  
LURU DAI ◽  
FEI LIU ◽  
ZHONG-CAN OU-YANG
Keyword(s):  
Secondary Structure ◽  
Maximum Entropy ◽  
Single Molecule ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Distance Distribution ◽  
Extension Force ◽  
End Distance ◽  
Force Curves ◽  
End To End

Using the maximum-entropy method, the end-to-end distance distribution of the force stretched chain is calculated from the moments of the distribution, which can be obtained from the extension-force curves recorded in single-molecule experiments. If one knows force expansion of the extension through the (n-1)th power of force, it is enough information to calculate the n moments of the distribution. The method is examined with force stretched chain models, Gaussian chain and excluded-volume chain on two-dimension lattice. The method reconstructs all distributions precisely. The method also is applied to force stretched complex chain molecules: the hairpin and secondary structure conformations. We find that the distributions of homogeneous chains of two conformations are very different: there are two independent peaks in hairpin distribution; while only one peak is observed in the distribution of secondary structure conformations. Our discussion also shows that the end-to-end distance distribution may discover more critical physical information than the simpler extension-force curves can give.

scholarly journals Semiflexible Polymer Enclosed in a 3D Compact Domain

2021 ◽  
Vol 9 ◽  
Author(s):  
Pavel Castro-Villarreal ◽  
J. E. Ramírez
Keyword(s):  
Persistence Length ◽  
Compact Domain ◽  
Mean Square ◽  
Shape Transition ◽  
Conformational States ◽  
Semiflexible Polymer ◽  
End Distance ◽  
The Mean ◽  
End To End ◽  
Polymer Shape

The conformational states of a semiflexible polymer enclosed in a volume V:=ℓ3 are studied as stochastic realizations of paths using the stochastic curvature approach developed in [Rev. E 100, 012503 (2019)], in the regime whenever 3ℓ/ℓp>1, where ℓp is the persistence length. The cases of a semiflexible polymer enclosed in a cube and sphere are considered. In these cases, we explore the Spakowitz–Wang–type polymer shape transition, where the critical persistence length distinguishes between an oscillating and a monotonic phase at the level of the mean-square end-to-end distance. This shape transition provides evidence of a universal signature of the behavior of a semiflexible polymer confined in a compact domain.

Influence of long-range interactions on the end-to-end distance distribution and cyclization probability of short chains

1991 ◽  
Vol 24 (18) ◽  
pp. 5167-5170 ◽  
Author(s):  
Ana M. Rubio ◽  
Juan J. Freire ◽  
Arturo Horta ◽  
Ines Fernandez de Pierola
Keyword(s):  
Long Range ◽  
Distance Distribution ◽  
Long Range Interactions ◽  
End Distance ◽  
End To End

scholarly journals Coarse-Grained Simulations of the Effects of Chain Length, Solvent Quality, and Chemical Defects on the Solution-Phase Morphology of MEH-PPV Conjugated Polymers

2012 ◽  
Vol 65 (5) ◽  
pp. 463 ◽  
Author(s):  
Ming Chiu ◽  
Tak W. Kee ◽  
David M. Huang
Keyword(s):  
Polymer Chains ◽  
Coarse Grained ◽  
Radius Of Gyration ◽  
Implicit Solvent ◽  
Coarse Grained Model ◽  
Solvent Quality ◽  
Defect Content ◽  
Coarse Grained Simulations ◽  
Chain Lengths ◽  
Poor Solvent

A mesoscale coarse-grained model of the conjugated polymer poly(2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) in implicit solvent is developed. The model is parametrized to reproduce the local structure and dynamics of an atomistic simulation model and accounts for the effects of solvent quality and saturation chemical defects on the polymer structure. Polymers with defect concentrations of 0 to 10 % are simulated using Langevin dynamics in tetrahydrofuran (THF) and in a model poor solvent for chain lengths and solution concentrations used experimentally. The polymer chains are extended in THF and collapse into compact structures in the poor solvent. The radius of gyration decreases with defect content in THF and agrees quantitatively with experiment. The structures formed in poor solvent by chains with 300 monomer units change from toroidal to cylindrical with increasing defect content, while chains containing 1000 monomers form cylinders regardless of defect content. These results have implications for energy transfer in MEH-PPV.

scholarly journals Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein

2016 ◽  
Vol 110 (2) ◽  
pp. 362-371 ◽  
Author(s):  
Alexander F. Chin ◽  
Dmitri Toptygin ◽  
W. Austin Elam ◽  
Travis P. Schrank ◽  
Vincent J. Hilser
Keyword(s):  
Tau Protein ◽  
Persistence Length ◽  
End Distance ◽  
End To End
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