Nature of the effective interaction between dendrimers

Mandal, Taraknath; Dasgupta, Chandan; Maiti, Prabal K.

doi:10.1063/1.4897160

Cited by 17 publications

(45 citation statements)

References 52 publications

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“…Moreover, our CG models for the study of binary potentials only consider repulsive interactions between beads. This is in contrast with other simulations that directly calculate the potential energy for a pair of dendrimers using forcefields with both attractive and repulsive interactions between beads or atoms . In these calculations, the potential mean field is obtained by restraining the two molecules to maintain a fixed distance between the centre of masses, sampling the dendrimers over a certain number of MD windows.…”

Section: Resultsmentioning

confidence: 99%

“…This potential is consistent with scattering data obtained for some types of dendrimers of intermediate generation number in solution for different concentrations . Furthermore, MD simulations were also performed in order to obtain the interaction between two dendrimers using CG or detailed atomistic models. The dendrimer centers of masses were fixed during each of the successive simulation windows.…”

Section: Introductionmentioning

confidence: 99%

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Coarse‐Grained and Atomistic Simulations for the G = 4 PAMAM‐EDA Dendrimer

Freire

Rubio

McBride

2015

Macro Theory & Simulations

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Extensive fully-atomistic molecular dynamics simulations have been performed for the G ¼ 4 generation of the dendrimer PAMAM-EDA in water, with fully protonated and non-protonated amine groups. Some parameters from these results have been incorporated into a coarsegrained model suitable for Monte Carlo simulations. Satisfactory agreement is found between the dendrimer density profiles obtained from the Monte Carlo and the molecular dynamics simulations, both for the protonated and neutral molecules. The Monte Carlo and molecular dynamics trajectories have also been employed to calculate binary interactions between pairs of dendrimers. The interactions between G ¼ 4 PAMAM-EDA dendrimers can be satisfactorily described by a theoretically proposed Gaussian potential.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Coarse‐Grained and Atomistic Simulations for the G = 4 PAMAM‐EDA Dendrimer

Freire

Rubio

McBride

2015

Macro Theory & Simulations

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“…To our knowledge this is the first such PMF studies for dendrimer-nanotube systems. Dendrimer also offers a distinct advantage over ssDNA because of its pH responsive wrapping mechanism and resulting inter-dendrimer repulsive interaction 48 . The rest of the paper is organized as follows: in section 2 we give the details of the system preparation along with the various computational methods used in this work.…”

Section: Introductionmentioning

confidence: 99%

Dendrimer assisted dispersion of carbon nanotubes: a molecular dynamics study

Pramanik

Maiti

2016

Soft Matter

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Various unique physical, chemical, mechanical and electronic properties of carbon nanotube (CNT) make it very useful materials for diverse potential application in many fields. Experimentally synthesized CNTs are generally found in bundle geometry with a mixture of different chirality and present a unique challenge to separate them. In this paper we have proposed the PAMAM dendrimer to be an ideal candidate for this separation. To estimate efficiency of the dendrimer in dispersion of CNTs from the bundle geometry, we have calculated potential of mean forces (PMF). Our PMF study of two dendrimer wrapped CNTs shows lesser binding affinity compared to the two bare CNTs. PMF study shows that the binding affinity decreases for non-protonated dendrimer and for the protonated case, the interaction is fully repulsive in nature. For both the non-protonated as well as protonated cases, the PMF increases with increasing dendrimer generations from 2 to 4 gradually compare to the bare PMF. We have performed PMF calculations with (6,5) and (6,6) chirality to study the chirality dependence of PMF. Our study shows that the PMFs between two (6,5) and two (6,6) CNT's respectively are ~ -29 kcal/mol and ~ -27 kcal/mol. Calculated PMF for protonated dendrimer wrapped chiral CNT's is more compared to the protonated dendrimer wrapped armchair CNTs for all the generations studied. However, for non-protonated dendrimer wrapped CNTs such chirality dependence is not very prominent. Our study suggests that the dispersion efficiency of protonated dendrimer is more compared to the non-protonated dendrimer and can be used as an effective dispersing agent in dispersion of CNT from the bundle geometry.

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“…All bonds involving the hydrogen atom are constrained using the SHAKE 45 algorithm allowing for a longer time step of 2 fs during the MD simulations. Our previous studies 28,29,[46][47][48][49][50][51] showed that the above mentioned MD protocol produces a very stable MD trajectory for various complex systems.…”

Section: Methodsmentioning

confidence: 98%

pH controlled gating of toxic protein pores by dendrimers

et al. 2016

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Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl(-) counter ions to the P dendrimer creates a zone of high Cl(-) concentration in the vicinity of the internalized dendrimer and a high concentration of K(+) ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections.

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Nature of the effective interaction between dendrimers

Cited by 17 publications

References 52 publications

Coarse‐Grained and Atomistic Simulations for the G = 4 PAMAM‐EDA Dendrimer

Coarse‐Grained and Atomistic Simulations for the G = 4 PAMAM‐EDA Dendrimer

Dendrimer assisted dispersion of carbon nanotubes: a molecular dynamics study

pH controlled gating of toxic protein pores by dendrimers

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