Structure of Carbon Nanotube-dendrimer composite

Using all atomistic molecular dynamics (MD) simulations we report the microscopic picture of the nanotube-dendrimer complex for PAMAM dendrimer of generation 2 to 4 and carbon nanotube of chirality (6,5). We find compact wrapping conformations of dendrimer onto the nanotube surface for all the three generations of PAMAM dendrimer. The degree of wrapping is more for non-protonated dendrimer compared to the protonated dendrimer. For comparison we also study the interaction of another dendrimer, poly(propyl ether imine) (PETIM), with nanotube and show that PAMAM dendrimer interacts strongly as compared to PETIM dendrimer as is evident from the distance of closest approach as well as the number of close contacts between the nanotube and dendrimer. We also calculate the binding energy between the nanotube and the dendrimer using MM/PBSA methods and attribute the strong binding to the charge transfer between them. Dendrimer wrapping on CNT will make it soluble and can act as an efficient dispersing agent for nanotube

Structure of DNA-Functionalized Dendrimer Nanoparticles

Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long simulation period. From the RMSD values of ssDNAs, we find relative stability in the case of purine rich ssDNA strands than pyrimidine rich ssDNA strands. The degree of wrapping of ssDNA strands on the dendrimer molecule was found to be influenced by the charge ratio of DNA and the dendrimer. As G4 dendrimer contains relatively more positive charge than G3 dendrimer, we observe extensive wrapping of ssDNAs on the G4 dendrimer. The ssDNA strands along with the linkers are seen to penetrate the surface of the dendrimer molecule and approach closer to the center of the dendrimer indicating the soft sphere nature of the dendrimer molecule. The effective radius of DNA-functionalized dendrimer nanoparticle was found to be independent of base composition of ssDNAs and was observed to be around 19.5 {\AA} and 22.4 {\AA} when we used G3 and G4 PAMAM dendrimer as the core of the nanoparticle respectively. The observed effective radius of DNA-functionalized dendrimer molecule apparently indicates the significant shrinkage in the structure that has taken place in dendrimer, linker and DNA strands. As a whole our results describe the characteristic features of DNA-functionalized dendrimer nanoparticle and can be used as strong inputs to design effectively the DNA-dendrimer nanoparticle self-assembly for their active biological applications.Comment: 13 pages, 10 figures, 3 Table

Superelastic and pH-Responsive Degradable Dendrimer Cryogels Prepared by Cryo-aza-Michael Addition Reaction

Dendrimers exhibit super atomistic features by virtue of their well-defined discrete quantized nanoscale structures. Here, we show that hyperbranched amine-terminated polyamidoamine (PAMAM) dendrimer G4.0 reacts with linear polyethylene glycol (PEG) diacrylate (575 g/mol) via the aza-Michael addition reaction at a subzero temperature (−20 °C), namely cryo-aza-Michael addition, to form a macroporous superelastic network, i.e., dendrimer cryogel. Dendrimer cryogels exhibit biologically relevant Young’s modulus, high compression elasticity and super resilience at ambient temperature. Furthermore, the dendrimer cryogels exhibit excellent rebound performance and do not show significant stress relaxation under cyclic deformation over a wide temperature range (−80 to 100 °C). The obtained dendrimer cryogels are stable at acidic pH but degrade quickly at physiological pH through self-triggered degradation. Taken together, dendrimer cryogels represent a new class of scaffolds with properties suitable for biomedical applications

Structure of poly(propyl ether imine) (PETIM) dendrimer from fully atomistic molecular Dynamics Simulation and by Small Angle X-ray scattering

We study the structure of carboxylic acid terminated neutral poly (propyl ether imine) (PETIM) dendrimer from generation 1 through 6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation such structural properties as: radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by Small Angle X-Ray Scattering (SAXS) experiment on dendrimer of generation 2 to 4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ~ N^x with the number of monomers. We find two distinct exponents depending on the generations: x = 0.47 for G1-G3 and x = 0.28 for G3-G6 which reveals their non-space filling nature. In comparison with the amine terminated PAMAM dendrimer, we find Rg of G-th generation PETIM dendrimer is nearly equal to that of (G+1)-th generation of PAMAM dendrimer as observed by Maiti et. al. [Macromolecules,38, 979 2005]. We find substantial back folding of the outer sub generations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules suggesting using PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.Comment: 33 page

Trapping time statistics and efficiency of transport of optical excitations in dendrimers

We theoretically study the trapping time distribution and the efficiency of the excitation energy transport in dendritic systems. Trapping of excitations, created at the periphery of the dendrimer, on a trap located at its core, is used as a probe of the efficiency of the energy transport across the dendrimer. The transport process is treated as incoherent hopping of excitations between nearest-neighbor dendrimer units and is described using a rate equation. We account for radiative and non-radiative decay of the excitations while diffusing across the dendrimer. We derive exact expressions for the Laplace transform of the trapping time distribution and the efficiency of trapping and analyze those for various realizations of the energy bias, number of dendrimer generations, and relative rates for decay and hopping. We show that the essential parameter that governs the trapping efficiency, is the product of the on-site excitation decay rate and the trapping time (mean first passage time) in the absence of decay.Comment: 26 pages, 6 figure

Partitioning of Poly(amidoamine) Dendrimers between n-Octanol and Water

Dendritic nanomaterials are emerging as key building blocks for a variety of nanoscale materials and technologies. Poly(amidoamine) (PAMAM) dendrimers were the first class of dendritic nanomaterials to be commercialized. Despite numerous investigations, the environmental fate, transport, and toxicity of PAMAM dendrimers is still not well understood. As a first step toward the characterization of the environmental behavior of dendrimers in aquatic systems, we measured the octanol−water partition coefficients (logK_(ow)) of a homologous series of PAMAM dendrimers as a function of dendrimer generation (size), terminal group and core chemistry. We find that the logKow of PAMAM dendrimers depend primarily on their size and terminal group chemistry. For G1-G5 PAMAM dendrimers with terminal NH_2 groups, the negative values of their logK_(ow) indicate that they prefer to remain in the water phase. Conversely, the formation of stable emulsions at the octanol−water (O/W) interface in the presence of G6-NH_2 and G8-NH_2 PAMAM dendrimers suggest they prefer to partition at the O/W interface. In all cases, published studies of the cytotoxicity of Gx-NH_2 PAMAM dendrimers show they strongly interact with the lipid bilayers of cells. These results suggest that the logKow of a PAMAM dendrimer may not be a good predictor of its affinity with natural organic media such as the lipid bilayers of cell membranes

Interactions of Poly(amidoamine) Dendrimers with Human Serum Albumin: Binding Constants and Mechanisms

The interactions of nanomaterials with plasma proteins have a significant impact on their in vivo transport and fate in biological fluids. This article discusses the binding of human serum albumin (HSA) to poly(amidoamine) [PAMAM] dendrimers. We use protein-coated silica particles to measure the HSA binding constants (K_b) of a homologous series of 19 PAMAM dendrimers in aqueous solutions at physiological pH (7.4) as a function of dendrimer generation, terminal group, and core chemistry. To gain insight into the mechanisms of HSA binding to PAMAM dendrimers, we combined ^1H NMR, saturation transfer difference (STD) NMR, and NMR diffusion ordered spectroscopy (DOSY) of dendrimer−HSA complexes with atomistic molecular dynamics (MD) simulations of dendrimer conformation in aqueous solutions. The binding measurements show that the HSA binding constants (K_b) of PAMAM dendrimers depend on dendrimer size and terminal group chemistry. The NMR ^1H and DOSY experiments indicate that the interactions between HSA and PAMAM dendrimers are relatively weak. The ^1H NMR STD experiments and MD simulations suggest that the inner shell protons of the dendrimers groups interact more strongly with HSA proteins. These interactions, which are consistently observed for different dendrimer generations (G0-NH_2vs G4-NH_2) and terminal groups (G4-NH_2vs G4-OH with amidoethanol groups), suggest that PAMAM dendrimers adopt backfolded configurations as they form weak complexes with HSA proteins in aqueous solutions at physiological pH (7.4)

Molecular modeling to study dendrimers for biomedical applications

© 2014 by the authors; licensee MDPI; Basel; Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). Date of Acceptance: 17/11/2014Molecular 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 efforts that have been made to improve the efficacy of this class of molecules in biomedical applications.Peer reviewedFinal Published versio

Charge-induced conformational changes of dendrimers

We study the effect of chargeable monomers on the conformation of dendrimers of low generation by computer simulations, employing bare Coulomb interactions. The presence of the latter leads to an increase in size of the dendrimer due to a combined effect of electrostatic repulsion and the presence of counterions within the dendrimer, and also enhances a shell-like structure for the monomers of different generations. In the resulting structures the bond-length between monomers, especially near the center, will increase to facilitate a more effective usage of space in the outer-regions of the dendrimer.Comment: 7 pages, 12 figure