COMPASS II: extended coverage for polymer and drug-like molecule databases

Sun, Huai; Jin, Zhao; Yang, Changying; Akkermans, Reinier L. C.; Robertson, Struan H.; Spenley, N. A.; Miller, Simon; Todd, Stephen

doi:10.1007/s00894-016-2909-0

Cited by 723 publications

(345 citation statements)

References 26 publications

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“…Forcite Plus module of Materials Studio software (2016, BIOVIA, San Diego, CA, USA) was utilized to import and optimize the structure through energy minimization under COMPAS II force field [21,22]. The optimized calcite structures were cleaved to expose either (104) or (110) surfaces.…”

Section: Methodsmentioning

confidence: 99%

Molecular Dynamics Simulation to Understand the Ability of Anionic Polymers to Alter the Morphology of Calcite

Choi

Kim

2017

International Journal of Polymer Science

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Molecular dynamics was utilized to investigate the ability of anionic macromolecules to drastically change the morphology of calcite in the presence of magnesium ions. Anionic poly(acrylic acid) and poly(methacrylic acid) were compared with cationic poly(ethylene imine) in their binding behavior on calcite (104) and (110) surfaces. Poly(acrylic acid) and poly(methacrylic acid) showed preferential binding on (110) with strong electrostatic attractions, whereas poly(ethylene imine) was only weakly attracted to (104). The extent of the charge imbalance on the surfaces appeared responsible for the current results, which originated from the deficient number of the coordinating oxygen atoms of carbonate around the surface calcium. The results of the current study were in accordance with the previous experimental observations, where the {hk0} surfaces of calcite were elongated under the coexistence of the anionic polymers and magnesium ions. These results could be generally utilized in the polymer-controlled crystallization with broad implications in the specific interactions with crystal surfaces.

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Section: Methodsmentioning

confidence: 99%

Molecular Dynamics Simulation to Understand the Ability of Anionic Polymers to Alter the Morphology of Calcite

Choi

Kim

2017

International Journal of Polymer Science

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“…χ ij can be obtained by the molecular simulation method which is developed by Fan et al and implemented in the blends module of Materials Studio (MS) 7.0

χ_{i j} = z (\frac{E_{i j} - 1 normal/ 2 false(E_{i i} + E_{j j} false)}{R T})

where z is the coordination number; E ij is the binding energy of a unit of component i and a unit of component j ; R is the molar gas constant. In MS blends module, we used the COMPASS II force field to calculate the Flory–Huggins parameters χ ij . Table 1 shows the repulsive parameters a ij between different beads at 298 K. It should be noted that there are four chemical bases in ssDNA, and we take their repulsive parameter average value.…”

Section: Simulation Methodsmentioning

confidence: 99%

Computer Simulation of DNA Condensation by PAMAM Dendrimer

Quan

et al. 2018

Macro Theory & Simulations

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In this study, dissipative particle dynamics is employed to investigate the complexation of poly(amido amine) dendrimer and single‐stranded DNA (ssDNA). A coarse‐grained model for ssDNA is constructed, which reproduces correctly the conformational behavior of the ssDNA molecules. The effects of pH, dendrimer generation, ionic strength, and dendrimer/ssDNA charge ratio on DNA–dendrimer complexes are explored. Simulation results show that ssDNA molecules can be significantly condensed by dendrimers and stable complexes are obtained by regulating the pH value. The ssDNA chain penetration would complicate its release from dendrimer, while this can be tuned by different generations of dendrimer. Salt concentration affects the size and stability of the complexes through ion screening effect. Dendrimer/ssDNA charge ratio can be used to control the size and morphology of the complex. This work can help design dendrimer‐based gene vectors.

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“…All the repeat units (mer) of polyisoprene, EN50, hybrids (EN50Chem and NRChem), and POS (aminopropylisobutyl‐POS) were geometrically optimized prior to any further steps using the COMPASSII forcefield with atom‐based charges (electrostatic and Van der Waals) using a smart algorithm (a cascade algorithm of steepest descent, adjusted basis set, Newton–Raphson [ABNR] and quasi‐Newton [Broyden–Fletcher–Goldfarb–Shanno]) until convergence was achieved for thresholds of 0.00002 kcal mol −1 , 0.001 kcal mol −1 Å −1 , 0.001 GPa, and 0.00001 Å that are reasonable for energy, force, stress, and displacement.…”

Section: Methodsmentioning

confidence: 99%

Natural Rubber with Polyhedral Oligomeric Silsesquioxane, Nanocomposites, and Hybrids Compared by Molecular Modeling

Martinez‐Pardo

Shanks

Adhikari

et al. 2018

Macro Theory & Simulations

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Physical and chemical blends, that is nanocomposites and hybrids, respectively, of natural rubber (NR) and epoxidized natural rubber (ENR) with polyhedral oligomeric silsesquioxane (POS) at different concentrations are modeled and compared using amorphous cell molecular dynamics (ACMD) and a topology method similar to group additivity contribution methods. Pre‐calculations using topology methods are proven useful to determine the optimum number of atoms in ACMD that will predict equivalent reported experimental thermo‐mechanical properties. Densities at infinite relaxation time are used to estimate various thermo‐mechanical transitions using asymptotic and quadratic polynomial functions. Incorporation of POS increases the density and glass transition temperature (T g). The results demonstrate that NR hybrids are preferred to nanocomposites for mechanical properties, though with ENR, T g increase may be problematic and must be considered before choosing between composites or hybrids.

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COMPASS II: extended coverage for polymer and drug-like molecule databases

Cited by 723 publications

References 26 publications

Molecular Dynamics Simulation to Understand the Ability of Anionic Polymers to Alter the Morphology of Calcite

Molecular Dynamics Simulation to Understand the Ability of Anionic Polymers to Alter the Morphology of Calcite

Computer Simulation of DNA Condensation by PAMAM Dendrimer

Natural Rubber with Polyhedral Oligomeric Silsesquioxane, Nanocomposites, and Hybrids Compared by Molecular Modeling

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