Structure of poly(propyl ether imine) 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 generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such 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 experiment on dendrimer of generations 2-4 (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 approximately Nx 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 reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth 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 subgenerations 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 the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.     

Molecular dynamics study of charged dendrimers in salt-free solution: effect of counterions

Polyamidoamine dendrimers, being protonated under physiological conditions, represent a promising class of nonviral, nanosized vectors for drug and gene delivery. We performed extensive molecular dynamics simulations of a generic model dendrimer in a salt-free solution with dendrimer's terminal beads positively charged. Solvent molecules as well as counterions were explicitly included as interacting beads. We find that the size of the charged dendrimer depends nonmonotonically on the strength of electrostatic interactions demonstrating a maximum when the Bjerrum length equals the diameter of a bead. Many other structural and dynamic characteristics of charged dendrimers are also found to follow this pattern. We address such a behavior to the interplay between repulsive interactions of the charged terminal beads and their attractive interactions with oppositely charged counterions. The former favors swelling at small Bjerrum lengths and the latter promotes counterion condensation. Thus, counterions can have a dramatic effect on the structure and dynamics of charged dendrimers and, under certain conditions, cannot be treated implicitly.     

Implicit solvent coarse‐grained model of polyamidoamine dendrimers: Role of generation and pH

Highly branched polymers such as polyamidoamine (PAMAM) dendrimers are promising macromolecules in the realm of nanobiotechnology due to their high surface coverage of tunable functional groups. Modeling efforts of PAMAM can provide structural and morphological properties, but the inclusion of solvents and the exponential growth of atoms with generations make atomistic simulations computationally expensive. We apply an implicit solvent coarse‐grained model, called the Dry Martini force field, to PAMAM dendrimers. The reduced number of particles and the absence of a solvent allow the capture of longer spatiotemporal scales. This study characterizes PAMAM dendrimers of generations one through seven in acidic, neutral, and basic pH environments. Comparison with existing literature, both experimental and theoretical, is done using measurements of the radius of gyration, moment of inertia, radial distributions, and scaling exponents. Additionally, ion coordination distributions are studied to provide insight into the effects of interior and exterior protonation on counter ions. This model serves as a starting point for future designs of larger functionalized dendrimers. © 2015 Wiley Periodicals, Inc.     

Poly(amidoamine) dendrimers on lipid bilayers II: Effects of bilayer phase and dendrimer termination

The molecular structures and enthalpy release of poly(amidoamine) (PAMAM) dendrimers binding to 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayers were explored through atomistic molecular dynamics. Three PAMAM dendrimer terminations were examined: protonated primary amine, neutral acetamide, and deprotonated carboxylic acid. Fluid and gel lipid phases were examined to extract the effects of lipid tail mobility on the binding of generation-3 dendrimers, which are directly relevant to the nanoparticle interactions involving lipid rafts, endocytosis, lipid removal, and/or membrane pores. Upon binding to gel phase lipids, dendrimers remained spherical, had a constant radius of gyration, and approximately one-quarter of the terminal groups were in close proximity to the lipids. In contrast, upon binding to fluid phase bilayers, dendrimers flattened out with a large increase in their asphericity and radii of gyration. Although over twice as many dendrimer-lipid contacts were formed on fluid versus gel phase lipids, the dendrimer-lipid interaction energy was only 20% stronger. The greatest enthalpy release upon binding was between the charged dendrimers and the lipid bilayer. However, the stronger binding to fluid versus gel phase lipids was driven by the hydrophobic interactions between the inner dendrimer and lipid tails.     

Solvent quality changes the structure of G8 PAMAM dendrimer, a disagreement with some experimental interpretations

We have performed approximately 20-40 ns of molecular dynamics (MD) simulations for the generation 8 PAMAM dendrimer in explicit water under varying pH conditions to study the structure of the dendrimer (approximately 156,738 atoms at low pH). This is the first report of such a long MD simulation of a larger generation PAMAM dendrimer including the effect of salt and counterions with explicit water molecules. We find that changing the pH from a high value (approximately 12) to a low value (approximately 3) changes the radius of gyration from Rg = 37.8 to 43.1 A (increasing by 13%). We also find significant back-folding of the primary amines and a large amount of water penetration inside the polymer. The increase in size with decrease in pH is consistent with our earlier studies on G3-G6 and agrees with the Monte Carlo theory by Welch and Muthukumar of G8 (Macromolecules, 1998, 31, 5892) and the experiments on G5 and G8 PAMAM dendrimer by Topp et al. (Macromolecules, 1999, 32, 7232). However, these results disagree dramatically with the interpretations of SANS experiments of G8 PAMAM dendrimers by Nisato et al. (Macromolecules, 2000, 33, 4172) who observe no change in the size of the dendrimer with variations of solution pH and ionic strength. We assume that the disagreement might arise from neglecting nonspherical shape, penetration of water and ions into the core, and aggregation, all of which might depend on pH.     

PAMAM树状大分子对酮基布洛芬溶解度的影响

以酮洛芬为模型药物,研究聚酰胺-胺(PAMAM)树状大分子对酮洛芬的增溶作用,并探讨其作用机理.采用紫外光谱法测定了G1.0、G1.5、G2.0、G2.5、G3.0、G3.5PAMAM在不同浓度和不同pH时对酮洛芬的增溶量.并运用计算机模拟方法对PAMAM与酮洛芬相互作用的机理进行了探讨.实验结果表明,酮洛芬的溶解度随溶液pH值变化而变化,在pH4.0～6.0范围内,PAMAM树状大分子对酮洛芬的增溶量随着PAMAM的代数、浓度和溶液pH的增加而增大.整代和半代都具有增溶作用.然而,在同一pH条件下,对于具有相同官能团数目的整代和半代,整代增溶效果要高于半代.计算机模拟结果表明PAMAM与酮洛芬主要靠静电作用力结合.增溶机理可能是酮洛芬的羧基与PAMAM的伯胺和叔胺发生静电作用.     

Preparation and characterization of dense films of poly(amidoamine) dendrimers on indium tin oxide

Indium tin oxide (ITO) substrates were modified with a layer of poly(amidoamine) (PAMAM) dendrimers to change their surface properties and, in particular, the substrates' work function. The functionalization procedure involved the electrostatic adsorption of positively charged PAMAM dendrimers of generation five onto negatively polarized ITO surfaces. Three different PAMAM dendrimers were used: PAMAM-NH2 and PAMAM-OH with terminal amine and hydroxyl groups, respectively, as well as Q-PAMAM-NH2, which had been prepared from PAMAM-NH2 by quaternization of the dendrimer's terminal and internal amine groups with methyl iodide. The resulting organic films were analyzed by contact angle goniometry, X-ray photoelectron spectroscopy, ellipsometry, and Kelvin probe force microscopy to confirm the presence of a dense layer. A Langmuir isotherm was derived from surface densities of fluorescence-labeled PAMAM-NH2 dendrimers from which we deduced an equilibrium binding constant, K(eq), of (1.3 +/- 0.3) x 10(5) M(-1). Kelvin probe measurements of the contact potential difference revealed a high reduction of the work function from 4.9 eV for bare ITO to 4.3 eV for ITO with a dense film of PAMAM-NH2 of generation five. PAMAM-OH and Q-PAMAM-NH2 resulted in slightly smaller work function changes. This study illustrates that the work function of ITO can be tuned by adlayers composed of PAMAM dendrimers.     

Interactions of 3, 3.5, 4, and 4.5 generations of poly(amido amine) dendrimer with cationic surfactants

The conductivity (κ), turbidity (τ), NMR, and Krafft temperature (T _K) studies have been carried out for hexadecylpyridinium bromide (HPyBr), hexadecylpyridinium chloride (HPyCl), and hexadecyltrimethylammonium bromide (HTAB) in the presence of 3G, 3.5G, 4G, and 4.5G generations of poly(amido amine) dendrimers (PAMAM) in aqueous phase. The cmc of all present surfactants were evaluated from κ and τ measurements, both in the presence as well as in the absence of PAMAM. The cmc values decrease in the presence of PAMAM in comparison to that in pure water, especially in the presence of amine terminated PAMAM. Krafft temperature values of pure surfactants also decrease in the presence of various generations of PAMAM. A comparison of all present results from different techniques indicates that HPyBr interacts more strongly with all generations of PAMAM rather than HPyCl and HTAB.     

Effect of dendrimers on pure acetylcholinesterase activity and structure

The effect of polyamidoamine (PAMAM) dendrimers on activity and fluorescence of pure acetylcholinesterase (EC 3.1.1.7.) was studied. It has been shown that all dendrimers studied decreased the enzymatic activity of acetylcholinesterase. This effect depended on the type of dendrimers. The data on the intrinsic fluorescence have shown that the dendrimers changed acetylcholinesterase conformation and the strongest effect was induced by PAMAM G3.5 dendrimer.     

溶液中柔性树枝状高分子的分子动力学模拟

采用分子动力学模拟方法研究了柔性树枝状高分子在无热溶剂中的静态和动态行为. 模拟结果表明: 在分子尺寸和回转半径Rg满足标度律Rg~N1/5(G+1)2/5P2/5(其中N为树枝状分子的聚合度, G为代数, P为链节长度, g为子代代数)时; 随着代数的增加, 树枝状分子和硬球的静态结构因子相似, 表明其内部结构发生了由“类星形”向“近球形”转化. 随着树枝状分子代数和链节长度的增加, 出现了“单元”(Monomer)密度几乎不变的区域. 树枝状分子的回折能力随着链节长度的增加而增强, 随着代数的增加而减弱. 树枝状分子各子代的运动能力不同, 与内层子代相比, 外层子代在短时间内扩散较慢, 但其松弛较快. 相对于Rouse指数, 树枝状分子“单元”运动的标度更接近Zimm指数.     

A structural study of carbosilane dendrimers versus polyamidoamine

Several types of substituted carbosilane-based dendrimers are studied in comparison with polyamidoamine (PAMAM), using molecular mechanics approach, to evaluate the shape and steric interactions when the generation number (G) increases. A scaled van der Waals energy parameter: the scaled steric energy, is defined, and used, to compare the steric repulsion in these dendrimers. Our calculations indicate that the steric repulsions, between the end groups at the surface of dendrimers, do not increase for higher generations of such macromolecules. Density calculations show that this property decreases with the increase of G. The moment of inertia calculations show that the shape of the considered dendrimers is asymmetrical for lower generations and becomes spherical at higher generations. The shape of the carbosilane dendrimers is more spherical than PAMAM. The results show that higher generations can afford the increased number of terminal groups at the surface of the macromolecules, without increase of the density in this region, therefor these factors (steric repulsion between the end groups at the surface, or high density) would not impede the chemistry to build higher generations of completely branched dendrimers.     

CE of poly(amidoamine) succinamic acid dendrimers using a poly(vinyl alcohol)-coated capillary

Various generations (G1-G8) of negatively charged poly(amidoamine) (PAMAM) succinamic acid dendrimers (PAMAM-SAH) were analyzed by CE using a poly(vinyl alcohol)-coated capillary. Due to its excellent stability and osmotic flow-shielding effect, highly reproducible migration times were achieved for all generations of dendrimer (e.g., RSD for the migration times of G5 dendrimer was 0.6%). We also observed a reverse trend in migration times for the PAMAM-SAH dendrimers (i.e., higher generations migrated faster than lower generation dendrimers) compared to amine-terminated PAMAM dendrimers reported in the literature. This reversal in migration times was attributed to the difference in counterion binding around these negatively charged dendrimers. This reverse trend allowed a generational separation for lower generation (G1-G3) dendrimers. However, a sufficient resolution for the migration peaks of higher generations (G4-G5) in a mixture could not be achieved. This could be due to their nearly identical charge/mass ratio and dense molecular conformations. In addition, we show that dye-functionalized PAMAM-SAH dendrimers can also be analyzed with high reproducibility using this method.     

Alpha-cyclodextrin-induced self-assembly of a double-hydrophilic block copolymer in aqueous solution

Double-hydrophilic poly(ethylene oxide)-b-poly(acrylic acid) (PEO-b-PAA) self-assembled into nanostructures in basic solution upon the addition of alpha-cyclodextrin (alpha-CD) as a result of the complexation between alpha-CD and PEO. The nanostructures produced were spherical in shape as observed by transmission electron microscopy (TEM) and possessed radii that were much larger than that of a single stretched polymeric chain. The ratio of Rg/Rh (where Rg is the z-average radius of gyration and Rh is the hydrodynamic radius) obtained from laser light scattering (LLS) was approximately approximately 1.0, and the aggregation number was approximately 4100. The zeta-potential of complex particle was -45 mV, suggesting that the particle possessed a stable negatively charged surface, attributed to ionized PAA segments. The above results suggested that the nanostructures formed in the PEO-b-PAA/alpha-CD solution at high pH were likely to be spherical vesicles.     

Geometrical characteristics of polyelectrolyte nanogel particles and their polyelectrolyte complexes studied by dynamic and static light scattering

The geometric characteristics of nanogel particles in aqueous solutions were studied by determining their ratios of radius of gyration (mean-square radius; Rg) to hydrodynamic radius (Rh), Rg/Rh, derived from static light scattering and dynamic light scattering experiments, respectively. The various nanogel samples studied included ones composed of lightly cross-linked N-isopropylacrylamide (NIPA) polymer, NIPA-based anionic or cationic copolymers, and amphoteric terpolymers. Polyelectrolyte complexes between anionic or cationic nanogels and oppositely charged polyions or nanogels having opposite charges were also studied. Most NIPA and NIPA-based polyelectrolyte nanogels in a swollen state had Rg/Rh values >0.775, which is the theoretically predicted value for a solid sphere. In a collapsed state, one may expect nanogel particles to be spherical in shape; however, this was not the case for a variety of nanogel samples, either with or without charges. These data were consistent with the idea that the surfaces of these nanogel particles were decorated with attached dangling chains. The Rg/Rh data from polyelectrolyte-nanogel complexes, however, indicated different structures from this. It was found that most of the polyelectrolyte-nanogel complex particles had Rg/Rh approximately 0.775. This suggested that the complexed nanogel particles were spherical in shape and that there were no dangling surface chains.     

小肽修饰的PAMAM树枝状化合物的生物活性

合成了甘氨酸 (Gly) 天冬氨酸 (Asp)组成的肽链Gly Asp、Gly Asp Gly Asp、Gly Asp (Gly Asp) 2 .分别将天冬氨酸及上述合成的肽链引入到聚酰胺 胺型树枝状化合物 (PAMAM)的表面 .对所得化合物进行了分子模拟 ,结果表明Gly Asp (Gly Asp) 2 肽链在PAMAM表面可形成接近于 β sheet的构象 .由实验得知 ,经Asp、Gly Asp、Gly Asp Gly Asp、Gly Asp (Gly Asp) 2 修饰的PAMAM树枝状化合物对抗坏血酸还原FeⅢ 细胞色素C(cytc)的反应有干扰作用 ,导致该反应速率下降 .这说明所合成的化合物与cytc有较好的结合能力 .特别是Gly Asp (Gly Asp) 2 修饰的PAMAM ,其与cytc的结合常数为 1 6ⅹ 1 0 5.     

以聚酰胺-胺树形分子为模板制备AgI纳米簇

本文以聚酰胺-胺(PAMAM)树形分子为模板,原位制备AgI纳米簇.系统地研究了AgI纳米簇制备过程中各种反应条件如树形分子端基、反应时间、Ag⁺与PAMAM摩尔比等对AgI纳米簇粒径的影响,分别用紫外-可见光谱、荧光光谱、透射电镜等对所制备的纳米簇进行表征.在相同的条件下,以G4.5-COOH₃为模板较以G5.0-NH₂为模板制备的AgI纳米簇粒径小、分布均匀,这主要取决于G4.5-COOCH₃PAMAM树形分子所起的“内模板”作用.G4.5-COOH₃树形分子浓度为1×10^-5mol/L,Ag⁺与树形分子摩尔比为30:1时所制备的AgI纳米簇的粒径分布均匀、稳定性好,室温避光可稳定存在两个月以上.     

Specific binding structures of dendrimers on lipid bilayer membranes

Dissipative particle dynamics simulations are used to study the specific binding structures of polyamidoamine (PAMAM) dendrimers on amphiphilic membranes and the permeation mechanisms. Mutually consistent coarse-grained (CG) models both for PAMAM dendrimers and for dimyristoylphosphatidylcholine (DMPC) lipid molecules are constructed. The PAMAM CG model describes correctly the conformational behavior of the dendrimers, and the DMPC CG model can properly give the surface tension of the amphiphilic membrane. A series of systematic simulations is performed to investigate the binding structures of the dendrimers on membranes with varied length of the hydrophobic tails of amphiphiles. The permeability of dendrimers across membranes is enhanced upon increasing the dendrimer size (generation). The length of the hydrophobic tails of amphiphiles in turn affects the dendrimer conformation, as well as the binding structure of the dendrimer-membrane complexes. The negative curvature of the membrane formed in the dendrimer-membrane complexes is related to dendrimer concentration. Higher dendrimer concentration together with increased dendrimer generation is observed to enhance the permeability of dendrimers across the amphiphilic membranes.     

Effects of various thiol molecules added on morphology of dendrimer-gold nanocomposites

Interactions between poly(amidoamine) dendrimer (PAMAM)-gold nanocomposites and alkanethiols and between the former nanocomposites and thiol-modified poly(amidoamine) dendrons in ethyl acetate were investigated by adding alkanethiols, such as 1-propanethiol and 1,3-propanedithiol, and thiol-modified poly(amidoamine) dendrons, generations 0.5 and 2.5 (G0.5-SH and G2.5-SH). The PAMAM dendrimers with surface methyl ester groups used were generations 1.5 and 5.5 (G1.5 and G5.5). The mean particle sizes of PAMAM-gold nanocomposites were about 2.1 for G1.5 and 2.4 nm for G5.5. In both nanocomposite systems where 1-propanethiol and 1,3-propanedithiol were added, the mean particle size was about 4 nm, twice that of the systems where these thiols were not added. Increasing the addition of 1,3-propanedithiol made the average particle size smaller for both nanocomposites systems. To compare with alkanethiol, thiol-modified poly(amidoamine) dendron with a highly branched structure on one side was synthesized. Using G2.5-SH as a protective agent, dendron-gold nanocomposites with mean diameters of 3 to 4 nm were obtained. The difference in particle size was seen only when the combination of PAMAM-gold nanocomposites and thiol-modified dendron was less sterically dense, modified dendron (G0.5-SH). The mechanisms for morphology changes in the dendrimer-gold nanocomposites by the addition of these thiols are discussed.     

Structural and dynamical properties for confined polymers undergoing planar Poiseuille flow

The authors present the results from nonequilibrium molecular dynamics simulations for the structural and dynamical properties of highly confined linear polymer fluids undergoing planar Poiseuille flow. They study systems confined within pores of several atomic diameters in width and investigate the dependence of the density profiles, the mean squared radius of gyration, the mean squared end-to-end distance, streaming velocity, strain rate, shear stress, and streaming angular velocity as functions of average fluid density and chain length. Their simulation results show that, sufficiently far from the walls, the radius of gyration for molecules under shear in the middle of the pore follows the power law Rg=ANbnu, where Nb is the number of bonds and the exponent has a value of 0.5 which resembles the value for a homogeneous equilibrium fluid. Under the conditions simulated, the authors find the onset of flat velocity profiles but with very little wall slippage. These flat profiles are most likely due to the restricted layering of the fluid into just one or two molecular layers for narrow pore widths compared to chain length, rather than typical plug-flow conditions. The angular velocity is shown to be proportional to half the strain rate in the pore interior when the chain length is sufficiently small compared to the pore width, consistent with the behavior for homogeneous fluids in the linear regime.     

Theoretical aspects and computer simulations of flexible charged oligomers in salt-free solutions

The structural and thermodynamic properties of a model solution containing flexible charged oligomers and an equivalent number of counterions were studied by means of the canonical Monte Carlo simulation and integral equation theory. The oligomers were represented as freely jointed chains of charged hard spheres. In accordance with the primitive model of electrolyte solutions, the counterions were modeled as charged hard spheres and the solvent as a dielectric continuum. Simulations were performed for a set of model parameters, independently varying the chain length and concentration of the oligomers. Structural properties in the form of pair distribution functions were calculated as functions of model parameters. In addition, thermodynamic properties such as the excess energy of solution and the excess chemical potential of counterions were obtained. These properties were correlated with the conformational averages of oligomers as reflected in the end-to-end distances and radii of gyration obtained from the simulations. The relation with the experimental data for heats of dilution and for the activity coefficient is discussed. Finally, theories based on Wertheim's integral equation approach (product reactant Ornstein-Zernike approach) [J. Stat. Phys. 42, 477 (1986)] in the so-called polymer mean spherical and polymer hypernetted chain approximations were tested against the new and existing computer simulations. For the values of parameters examined in this study, the integral equation theory yields semiquantitative agreement with computer simulations.