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Effect of pH and Generation on Structural Properties of Poly(amidoamine) Dendrons Studied by Molecular Dynamics Simulations

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Molecular dynamics (MD) simulations on G3 poly(amidoamine) (PAMAM) dendrons bearing an alkyne focal point were carried out at three different pH levels and with explicit water and counterions to obtain appropriate simulation conditions and validity for waterless simulations. We find that charged dendron simulation results with distance-dependent dielectric constant without nonbonded cutoff distance are most similar to the ones in explicit water and counterions. Structural changes of PAMAM dendrons and focal point accessibility are understood as functions of pH and dendron generation using MD simulations with the long-range interaction parameters. The simulation results indicate that the radii of gyration of the G3 and G5 dendrons at low pH (≤4) increase ∼67% as compared with those at high pH (≥10) and neutral pH (∼7). The dendron structures exhibit an increasingly hollow interior as pH level decreases. The dendron focal point remained accessible for all generations and pH values studied.


Document Type: Research Article

DOI: http://dx.doi.org/10.1166/jctn.2012.2007

Publication date: January 1, 2012

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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