Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

Maingi, Vishal ; Jain, Vaibhav ; Bharatam, Prasad V. ; Maiti, Prabal K. (2012) Dendrimer building toolkit: Model building and characterization of various dendrimer architectures Journal of Computational Chemistry, 33 (25). pp. 1997-2011. ISSN 0192-8651

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Official URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/jc...

Related URL: http://dx.doi.org/10.1002/jcc.23031

Abstract

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X‐ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra‐molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications.

Item Type:Article
Source:Copyright of this article belongs to John Wiley & Sons, Inc.
Keywords:Molecular Dynamics; PAMAM; PPI; PETIM; Dendrimer Building
ID Code:113266
Deposited On:24 May 2018 08:10
Last Modified:24 May 2018 08:10

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