The Dotted Cap Notation: A concise notation for describing variegated dendrimers

Roberts, Benjamin P.; Scanlon, M.J.; Krippner, Guy Y.; Chalmers, David K.

doi:10.1039/b800724a

Cited by 4 publications

(8 citation statements)

References 55 publications

(42 reference statements)

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“…Though this nomenclature can be applied to dendrimer-like molecules, it becomes less clear with the increase of dendrimers’ size and does not capture all the necessary structural features (e.g., distribution of residues). Nodal nomenclature based on graph theory is also able to describe dendrimers but has not been widely used [62,63].…”

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

“…However, as the dendrimers increase in size, the notation becomes complex and difficult to interpret. Further simplification on dendrimer nomenclature, taking advantage of their repetitive topology and symmetry has been proposed with a dotted cap notation [63]. This notation represents dendrimers as building blocks, with a core unit, monomers and capping groups.…”

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

“…This notation represents dendrimers as building blocks, with a core unit, monomers and capping groups. The core is bound to the monomers which forms the dendrimer framework where the caps are attached [63]. The dotted cap notation then represents the surface of the dendrimer by means of sequential caps (Figure 4).…”

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

“…In this case the final notation would be WZ●●WZ●●●WZ●●WZ●●●WZ●●WZ●●●WZ●●WZ or (WZ) 8 in condensed notation [63]. Here the ● represents the topology distance between the capping groups from the primary atom represented in the core.…”

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

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Molecular Modeling to Study Dendrimers for Biomedical Applications

et al. 2014

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Molecular modeling techniques provide a powerful tool to study the properties of molecules and their interactions at the molecular level. The use of computational techniques to predict interaction patterns and molecular properties can inform the design of drug delivery systems and therapeutic agents. Dendrimers are hyperbranched macromolecular structures that comprise repetitive building blocks and have defined architecture and functionality. Their unique structural features can be exploited to design novel carriers for both therapeutic and diagnostic agents. Many studies have been performed to iteratively optimise the properties of dendrimers in solution as well as their interaction with drugs, nucleic acids, proteins and lipid membranes. Key features including dendrimer size and surface have been revealed that can be modified to increase their performance as drug carriers. Computational studies have supported experimental work by providing valuable insights about dendrimer structure and possible molecular interactions at the molecular level. The progress in computational simulation techniques and models provides a basis to improve our ability to better predict and understand the biological activities and interactions of dendrimers. This review will focus on the use of molecular modeling tools for the study and design of dendrimers, with particular emphasis on the

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Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

Section: Molecular Modeling Of Dendrimersmentioning

confidence: 99%

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Molecular Modeling to Study Dendrimers for Biomedical Applications

et al. 2014

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“…In the early 1990s, the development of the convergent synthesis by Fréchet et al − provided a relatively straightforward route to dendrimers with different branches attached to the same core. This introduced a new class of dendrimers, which we call variegated dendrimers . The defining characteristic of a variegated dendrimer is that at least one generation of monomers, or the layer of caps, is heterogeneous.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics of Variegated Polyamide Dendrimers

Roberts¹,

Krippner²,

Scanlon³

et al. 2009

Macromolecules

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We have used molecular dynamics simulations to study the structures of a range of heterogeneously functionalized ("variegated") dendrimers and the distributions in space of their caps. By a virtual capping approach, we compare an asymmetric dendrimer (dendritic poly(L-lysine), PLL) and a symmetric polyamide (SPAM) dendrimer. SPAM is larger and more spherical than PLL, and its caps are more evenly distributed throughout the molecule. Protonation of an amine-capped dendrimer causes substantial swelling. The distribution of caps relative to each other is strongly affected by conformational change. Simulation of a SPAM framework with chemically distinct caps shows that whole-dendrimer properties are largely unaffected by the topological arrangement of the caps. Using both modeling approaches, we found that differentiation at the dendrimer's core produces strongly dipolar dendrimers, while differentiation between branches in the outermost generation produces largely nonpolar dendrimers, with a gradual transition between these extremes. The effect of variegation topology on spatial distribution of caps is modified by the interactions between the caps (particularly electrostatic interactions) and with other species in the environment.

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