Molecular Dynamics Studies of the Size, Shape, and Internal Structure of 0% and 90% Acetylated Fifth-Generation Polyamidoamine Dendrimers in Water and Methanol

Lee, Hwankyu; Baker, James R.; Larson, Ronald G.

doi:10.1021/jp056148s

Cited by 85 publications

(113 citation statements)

References 29 publications

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“…Thus, these simulations are routinely used to investigate conformational changes of a single dendrimer in explicit solvent with respect to dendrimer generation (size) and process conditions, such as temperature and solvent pH [52][53][54][55]62,63]. All-atom simulations may also be used to investigate the dynamics of binding between of a single dendrimer and one or more ligands in explicit solvent [24,38,39,64].…”

Section: All-atom Molecular Dynamics Simulationsmentioning

confidence: 99%

“…As with all applications of molecular simulation, selecting an appropriate force field for modeling dendrimers and dendrimer-ligand complexes is critical to obtaining the correct fundamental behavior. In the case of PAMAM dendrimers, it has been frequently shown that predictions from molecular simulation for the swelling behavior of dendrimers as a function of solvent pH and salt concentration are very sensitive to the force field used in those simulations [52][53][54]. The hydrogen bonding parameters in the Dreiding III force field were recently optimized to prevent the swelling of PAMAM dendrimers at low pH and to predict radii of gyration that are consistent with small-angle neutron scattering experiments [63].…”

Section: All-atom Force Fields For Modeling Dendrimersmentioning

confidence: 99%

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Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim

Lamm

2012

Polymers

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Dendrimers have been widely used as nanostructured carriers for guest species in a variety of applications in medicine, catalysis, and environmental remediation. Theory and simulation methods are an important complement to experimental approaches that are designed to develop a fundamental understanding about how dendrimers interact with guest molecules. This review focuses on computational studies aimed at providing a better understanding of the relevant physicochemical parameters at play in the binding and release mechanisms between polyamidoamine (PAMAM) dendrimers and guest species. We highlight recent contributions that model supramolecular dendrimer-guest complexes over the temporal and spatial scales spanned by simulation methods ranging from all-atom molecular dynamics to statistical field theory. The role of solvent effects on dendrimer-guest interactions and the importance of relating model parameters across multiple scales is discussed.

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Section: All-atom Molecular Dynamics Simulationsmentioning

confidence: 99%

Section: All-atom Force Fields For Modeling Dendrimersmentioning

confidence: 99%

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Kim

Lamm

2012

Polymers

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“…Molecular dynamics studies of PAMAM dendrimers have already helped to elucidate the structural features and behavior of these molecules. A study varying the percentage acylation of a generation 5 PAMAM dendrimer showed that their overall shape was not dependent upon the percentage of acyl groups on their surface because intramolecular hydrogen bonds form and break during the simulation [10].…”

Section: Introductionmentioning

confidence: 99%

Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers

et al. 2010

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The partial modification of carboxylic acid terminated polyamidoamine (PAMAM) dendrimers with glucosamine has been reported to give dendrimer glucosamine conjugates novel immuno-modulatory and anti-angiogenic properties. Experimental analysis of these glycosylated dendrimers showed that, on average, eight glucosamine molecules were covalently bound to each dendrimer. In order to better understand the surface loading and distribution of these glucosamine molecules, molecular reactivity was determined by evaluation of electronic properties using frontier molecular orbital theory (FMOT) and molecular dynamics simulations. It was shown that the surface loading and distribution of the zero length amide bond conjugated glucosamine molecules was determined by both electronic effects and by the different dynamic conformations adopted by the modified dendrimer during the incremental addition of glucosamine. Importantly, the structural features and the dynamic behavior of the partially glycosylated generation 3.5 PAMAM dendrimer showed that its flexibility and its polarity changed with the incremental addition of glucosamine. These 2 peripheral glucosamine molecules remained available on the dendrimer"s surface for interaction with the biological target.

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“…The images were rendered using VMD [25]. consistent with previous experimental [23,24,26] and theoretical [20,[27][28][29][30] characterization of PAMAM in solution.…”

Section: Resultsmentioning

confidence: 99%

Single-Molecule Dendrimer-Hydrocarbon Interaction

Pasupathy¹,

Suek²,

Lyons³

et al. 2009

TONANOJ

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Abstract:We report our single-molecule fluorescence microscopy and molecular dynamics simulation studies on the interaction of poly(amidoamine) dendrimer and squalane hydrocarbon in aqueous solution. Our spectrophotometry measurements indicate that this interaction increases with the pH of the solvent. Our simulations show that squalane resides primarily on the perimeter of the dendrimer at low to neutral pH, but becomes encapsulated by the dendrimer at high pH. Using single-molecule fluorescence microscopy, we have identified that the binding between PAMAM and squalane is reversible. At a pH value of 8, the approaching, binding, and characteristic times of a single fluorescently-labeled dendrimer to squalane are 0.5 s, 7.5 s, and 0.5 s, respectively. Both our spectrophotometry measurements and simulations show that the interaction between PAMAM and squalane is stronger for lower generation dendrimers. This study facilitates our understanding of using dendritic and hyperbranched polymers for gas hydrate prevention in the petroleum industry.

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Molecular Dynamics Studies of the Size, Shape, and Internal Structure of 0% and 90% Acetylated Fifth-Generation Polyamidoamine Dendrimers in Water and Methanol

Cited by 85 publications

References 29 publications

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Multiscale Modeling for Host-Guest Chemistry of Dendrimers in Solution

Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers

Single-Molecule Dendrimer-Hydrocarbon Interaction

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