MCDP: an advanced tool to simulate comb-like polymers

León, Salvador; Alemán, Carlos; Escalé, Francesc; Laso, Manuel

doi:10.1002/1096-987x(20010130)22:2<162::aid-jcc3>3.0.co;2-o

Cited by 14 publications

(6 citation statements)

References 37 publications

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“…Monte Carlo Simulations. MC simulations were performed using the parallelized version of the MCDP (Monte Carlo simulations of Dense Polymers) computer program, which was explicitly designed to simulate the crystal structure of synthetic polymers. The atomistic model consisted of eight independent chains, which were packed in an orthorhombic box with the helix axes oriented parallel to the c -axis at the positions indicated in Figure .…”

Section: Methodsmentioning

confidence: 99%

Crystal Structure of the α-Form of Poly(l-lactide)

2001

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Study on the molecular packing of the R-form of poly(L-lactide) has been attempted taking into account packing energy calculations, refinement against new electron diffraction data, and Monte Carlo simulations. Packing energy has been evaluated for a fixed 107 conformation and an antiparallel arrangement of molecular chains. The energetically allowed space seems to be quite restricted, but with several minima of similar energy. One of them corresponds to a P212121 space group and agrees with the structure refined against diffraction data. Moreover, Monte Carlo simulations show a spontaneous evolution toward the refined model when parameters that define the packing, such as chain axis shift and setting orientation angles, are relaxed. On the other hand, the proposed packing shows asymmetric interactions that may lead to a molecular distortion.

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Section: Methodsmentioning

confidence: 99%

Crystal Structure of the α-Form of Poly(l-lactide)

2001

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“…Simulations were performed using an advanced MC sampling technique, configurational bias Monte Carlo (CBMC). , The CBMC method consists of the following three steps: (i) a chain is selected at random; (ii) the chain is cut at a random position; (iii) the chain is sequentially regrown bond-by-bond by examining a number of possible torsions ( N s ), which are randomly chosen. This algorithm was specifically adapted for studying comblike polymers and subsequently implemented into a computed program denoted MCDP (Monte Carlo Simulations of Dense Polymers) . In addition to CBMC moves, a small fraction of Metropolis moves was also considered for the alkyl side chains.…”

Section: Model and Computational Methodsmentioning

confidence: 99%

Comblike Poly(α-alkyl γ-glutamate)s: Computer Simulation Studies of an Intermediate Thermal Phase

et al. 2002

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Monte Carlo (MC) simulations have been used to study the structure of an intermediate thermal phase of poly (R-octadecyl γ,D-glutamate). This is a comblike poly(γ-peptide) able to adopt a biphasic structure that has been described as a layered arrangement of backbone helical rods immersed in a paraffinic pool of polymethylene side chains. Simulations were performed at two different temperatures (348 and 363 K), both of them above the melting point of the paraffinic phase, using the configurational bias MC algorithm. Results indicate that layers are constituted by a side-by-side packing of 17/5 helices. The organization of the interlayer paraffinic region is described in atomistic terms by examining the torsional angles and the end-to-end distances for the octadecyl side chains. Comparison with previously reported comblike poly( -peptide)s revealed significant differences in the organization of the alkyl side chains.

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“…The atomistic structure of PAALA-6 was reinvestigated using an advanced Monte Carlo (MC) sampling technique (Continuum Configurational Bias, CCB-MC). , This method has been recently adapted to the study of dense polymers with either partially or completely ordered structures. The method has been implemented into a computer program denoted MCDP (Monte Carlo simulations of Dense Polymers), which has been optimized and parallelized to obtain a maximum computational efficiency. This strategy has been successfully used in the structural study of PAALA- n with n = 8, 12, 14, 16, and 18. ,, In addition to CCB moves, a small fraction of Metropolis moves (20%) were also used in all the simulations.…”

Section: Methodsmentioning

confidence: 99%

“…The method has been implemented into a computer program denoted MCDP (Monte Carlo simulations of Dense Polymers), which has been optimized and parallelized to obtain a maximum computational efficiency. This strategy has been successfully used in the structural study of PAALA- n with n = 8, 12, 14, 16, and 18. ,, In addition to CCB moves, a small fraction of Metropolis moves (20%) were also used in all the simulations.…”

Section: Methodsmentioning

confidence: 99%

Permeation Properties of the Stereoregular Nylon-3 Analogue, Poly(α-hexyl β-l-aspartate)

et al. 2002

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The permeabilities of thin films of the R-helix-like poly(β-peptide), poly(R-hexyl β-Laspartate), to O2, N2, and CO2 penetrants were measured by diffusion experiments at temperatures ranging between 20 and 80 °C. P and D coefficients were found to be higher for CO2 than for the other two gases, and both parameters increased with temperatures for the three gases. Solubilities of N2 and O2 appeared to be independent of temperature whereas that of CO2 decreased significantly upon heating. Solubilities of the three penetrants in the polypeptide were calculated by using advanced Monte Carlo methods specifically developed for the simulation of dense polymers. The structure of the polymer was modeled and optimized in a quasi-hexagonal lateral array of 13/4 helices with an average fixed interchain distance of 14.6 Å. Values predicted at low temperature were in satisfactory agreement with experimental data. At high temperatures significant discrepancies between the measured and calculated data were found for N 2 and O2, which revealed the limitation of the Monte Carlo method to simulate the influence of temperature on the distribution of the unoccupied space.

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MCDP: an advanced tool to simulate comb-like polymers

Cited by 14 publications

References 37 publications

Crystal Structure of the α-Form of Poly(l-lactide)

Crystal Structure of the α-Form of Poly(l-lactide)

Comblike Poly(α-alkyl γ-glutamate)s: Computer Simulation Studies of an Intermediate Thermal Phase

Permeation Properties of the Stereoregular Nylon-3 Analogue, Poly(α-hexyl β-l-aspartate)

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