Polymer translocation through a nanopore: a two-dimensional Monte Carlo study

We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau required for the polymer to completely exit the pore on either end. We find numerically that tau scales with the chain length N as tau approximately N(1+2nu), where nu is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R(g). For LR(g), we find tau approximately N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that tau has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R( parallel) approximately L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.     

A Monte Carlo study of amphiphilic dendrimers: spontaneous asymmetry and dendron separation

We study via Monte Carlo simulation the conformation of amphiphilic dendrimers for which terminal monomers (t) and internal monomers (i) interact differently with the solvent (s). Specifically, we have studied g = 3,6 dendrimers as a function of chi(it), chi(is), and chi(ts) (chi is the differential contact energy between the different particles) for parameter values chi(it) = 0, +/-1 and -1 < chi(is), chi(ts) < 1. We have allowed negative chi values in order to model attractive polar interactions (e.g., hydrogen bonding) which are believed to be important in many dendrimer/solvent systems. We find the "phase diagram" of dendrimer conformations to be extremely rich and to be a strong function of g, chi(is), and chi(ts) but only a weak function of chi(it), For chi(is), chi(ts) > 0, we observe dendrimer conformations, such as unimolecular normal micelles and inverted loopy micelles. However, for chi(is) < 0 or chi(ts) < 0, we observe more exotic molecular conformations, for example, the spontaneous development of asymmetry and dendron separation. These properties are analyzed in terms of snapshots as well as more quantitatively in terms of the radii of gyration, radial density profiles, pair-correlation functions, degree of asymmetry, and dendron overlap factor. By exploiting the dramatic conformational changes under different solvent conditions, we suggest the possibility of using amphiphilic dendrimers as stimuli-responsive smart materials.     

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.     

Molecular dynamics simulations of charged dendrimers: low-to-intermediate half-generation PAMAMs

We have performed atomistic molecular dynamics simulations of PAMAM dendrimers of generations 0.5, 1.5, 2.5, 3.5, and 4.5. The simulated systems comprise the charged dendrimer and its counterions embedded in a dielectric continuum (i.e., without explicit solvent). Structural properties of these dendrimers, like the radius of gyration, the principal moments of inertia, and the segment density profiles, were evaluated from the simulations. The average radius of gyration obtained for the intermediate half-generations 2.5, 3.5, and 4.5 follows the same scaling law that was previously inferred from simulations of full-generation PAMAMs, Rg approximately M1/3, and is characteristic of space-filling objects. The low half-generations 0.5 and 1.5 deviate, however, to greater Rg values. The shape of the smaller dendrimers is approximately that of a prolate ellipsoid, which becomes more spherical for higher generations. The segment density profiles show features identical to those obtained in other simulations of flexible-chain dendrimers, like dendron-backfolding. Two slightly different configurations, in terms of size and shape, were identified for generation 2.5. The radial distributions of counterions extracted from the simulations compare well with the solutions of Poisson-Boltzmann cell model, and the dendrimer's effective charge was estimated using the Bjerrum criterion. The influence of electrostatic interactions in the dendrimer's conformation due to repulsion between the charged end-groups and its relation to counterion effects is discussed for the several generations simulated. The form factors calculated from the simulations are compared with the model of a homogeneous ellipsoid of revolution. The overall results are in agreement with the previously established morphological transition of PAMAM dendrimers toward a more spherical and compact conformation above generations 3 or 4.     

Scaling and structural properties of a polymer in a simple solvent: A study based on integral equations

We present a statistical mechanical theory for polymer–solvent systems based on integral equations derived from the polymer Kirkwood hierarchy. Integral equations for pair monomer–monomer, monomer–solvent, and solvent–solvent correlation functions yield polymer–solvent distribution, chain conformation in three dimensions, and scaling properties associated with polymer swell and collapse in athermal, good, and poor solvents. Variation of polymer properties with solvent density and solvent quality is evaluated for chains having up to 100 bonds. In good solvents, the scaling exponent v has a constant value of about 0.61 at different solvent densities computed. For the athermal solvent case, the gyration radius and scaling exponent decrease with solvent density. In a poor solvent, the chain size scales as N^v with the value of the exponent being about 0.3, compared with the mean field value of ⅓. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 3025–3033, 1998     

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength E, length of the chain N, and length of the pore L on forced translocation. As our main result, we find a crossover scaling for the translocation time tau with the chain length from tau approximately N2nu for relatively short polymers to tau approximately N1+nu for longer chains, where nu is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains v approximately N-nu, which crosses over to v approximately N(-1) for long polymers. The reason for this is that with increasing N there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which R parallel, the radius of gyration Rg along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large N, however, the asymptotic scaling tau approximately N1+nu is recovered. In this regime, tau is almost independent of L. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for R parallel approximately L. We show here that this minimum persists for weak fields E such that EL is less than some critical value, but vanishes for large values of EL.     

Unforced translocation of a polymer chain through a nanopore: the solvent effect

The authors have performed the Langevin dynamics simulation to investigate the unforced polymer translocation through a narrow nanopore in an impermeable membrane. The effects of solvent quality controlled by the attraction strength lambda of the Lennard-Jones cosine potential between polymer beads and beads on two sides of the membrane on the translocation processes are extensively examined. For polymer translocation under the same solvent quality on both sides of the membrane, the two-dimensional and three-dimensional simulations confirm the scaling law of tautrans approximately N1+2upsilon for the translocation in the good solvent, where tautrans is the translocation time, N is the chain length, and upsilon is the Flory exponent. For the three-dimensional polymer translocation under different solvent qualities on two sides of the membrane, the translocation efficiency may be notably improved. The scaling law between tautrans and N varies from tautrans approximately N1+2upsilon to tautrans approximately N with the increase of the difference of solvent qualities, and the crossover occurs at the theta temperature point, where a scaling law of tautrans approximately N1.27 is found. The simulation results here also show that the translocation time changes from a wide and asymmetric distribution with a long tail to a narrow and symmetric distribution with the increase of the difference of the solvent qualities.     

Effect of solvent quality on the conformations of a model comb polymer

The effect of solvent quality on the equilibrium structure of a densely branched comb polymer is investigated based on the structure factor analyses by off-lattice Monte Carlo simulations. First, theta temperature (theta(infinity)) must be determined to identify the solvent condition. We locate the characteristic temperature theta(A)(N) at which the second virial coefficient vanishes and the transition temperature theta(R)(N) at which radius of gyration R(g) of the chain varies most rapidly with temperature, i.e., d(2)R(g)/dT(2)|(theta(R)) = 0. N represents the total number of monomers of a comb. As N --> infinity, theta(A) and theta(R) coincide to a point that is identified as the true theta temperature (theta(infinity)). The structure factors of the main chain, the side chain, and the whole polymer are calculated, respectively. It is found that at T = theta(infinity), the structural factors S(qR(g)) for the overall comb polymers match quite well with those of their Gaussian counterparts. When T< theta(infinity), the overall comb polymer assumes collapsed conformations, similar to a homogeneous sphere. However, the structure factor of the side chain indicates that it always remains in an expanded state regardless of the solvent condition. It is attributed to the strong interactions between side chains. The same effect leads to enhanced rigidity of the main chain in comparison to the linear chain, as clearly observed from the rescaled Kratky plot.     

Corrections to scaling and crossover from good- to theta-solvent regimes of interacting polymers

We exploit known properties of universal ratios, involving the radius of gyration R(g), the second and third virial coefficients B(2) and B(3), and the effective pair potential between the centers of mass of self-avoiding polymer chains with nearest-neighbor attraction, as well as Monte Carlo simulations, to investigate the crossover from good- to theta-solvent regimes of polymers of finite length L. The scaling limit and finite-L corrections to scaling are investigated in the good-solvent case and close to the theta temperature. Detailed interpolation formulas are derived from Monte Carlo data and results for the Edwards two-parameter model, providing estimates of universal ratios as functions of the observable ratio A(2)=B(2)/R(g) (3) over the whole temperature range, from the theta point to the good-solvent regime. The convergence with L (L< or =8000) is found to be satisfactory under good-solvent conditions, but longer chains would be required to match theoretical predictions near the theta point, due to logarithmic corrections. A quantitative estimate of the universal ratio A(3)=B(3)/R(g) (6) as a function of temperature shows that the third virial coefficient remains positive throughout, and goes through a pronounced minimum at the theta temperature, which goes to zero as 1/ln L in the scaling limit.     

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.     

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.     

Dynamical scaling of single chains on adsorbing substrates: diffusion processes

We study the dynamics of tethered chains of length N on adsorbing surfaces, considering the dilute case; for this we use the bond fluctuation model and scaling concepts. In particular, we focus on the mean-square displacement of single monomers and of the center of mass of the chains. The characteristic time tau of the fluctuations of a free chain in a good solvent grows as tau approximately N(a), where the coefficient a obeys a=2nu+1. We show that the same coefficient also holds at the critical point of adsorption. At intermediate time scales single monomers show subdiffusive behavior; this concurs with the behavior calculated from scaling arguments based on the dynamical exponent a. In the adsorbed state tau(perpendicular), the time scale for the relaxation in the direction perpendicular to the surface, becomes independent of N; tau(perpendicular) is then the relaxation time of an adsorption blob. In the direction parallel to the surface the motion is similar to that of a two-dimensional chain and is controlled by a time scale given by tau(parallel) approximately N(2nu(2)+1)L(-2Delta(nu/nu)), where nu(2) is the Flory exponent in two dimensions, nu is the Flory exponent in three dimensions, and Deltanu=nu(2)-nu. For the motion parallel to the surface we find dynamical scaling over a range of about four decades in time.     

Direct addition of alcohols to organonitriles activated by ligation to a platinum(IV) center

Treatment of trans-[PtCl(4)(RCN)(2)] (R = Me, Et) with R'OH (R' = Me, Et, n-Pr, i-Pr, n-Bu) at 45 degrees C in all cases allowed the isolation of the trans-[PtCl(4)[(E)-NH=C(R)OR'](2)] imino ester complexes, while the reaction between cis-[PtCl(4)(RCN)(2)] and the least sterically hindered alcohols (methanol and ethanol) results in the formation of cis-[PtCl(4)[(E)-NH=C(R)OR'](2)] (R/R' = Me/Me) or trans-[PtCl(4)[(E)-NH=C(Et)OR'](2)] (R' = Me, Et), the latter being formed via thermal isomerization (ROH, reflux, 3 h) of the initially formed corresponding cis isomers. The reaction between alcohols R'OH and cis-[PtCl(4)(RCN)(2)] (R = Me, R' = Et, n-Pr, i-Pr, n-Bu; R = Et; R' = n-Pr, i-Pr, n-Bu), exhibiting greater R/R' steric congestion, allowed the isolation of cis-[PtCl(4)[(E)-NH=C(R)OR'][(Z)-NH=C(R)OR']] as the major products. The alcoholysis reactions of poorly soluble [PtCl(4)(RCN)(2)] (R = CH(2)Ph, Ph) performed under heterogeneous conditions, directly in the appropriate alcohol and for a prolonged time and, for R = Ph, with heating led to trans-[PtCl(4)[(E)-NH=C(R)OR'](2)] (R = CH(2)Ph, R' = Me, Et, n-Pr, i-Pr; R = Ph, R' = Me) isolated in moderate yields. In all of the cases, in contrast to platinum(II) systems, addition of R'OH to the organonitrile platinum(IV) complexes occurs under mild conditions and does not require a base as a catalyst. The formed isomerically pure (imino ester)Pt(IV) complexes can be reduced selectively, by Ph(3)P=CHCO(2)Me, to the corresponding isomers of (imino ester)Pt(II) species, exhibiting antitumor activity, without change in configuration of the imino ester ligands. Furthemore, the imino esters NH=C(R)OR' can be liberated from both platinum(IV) and platinum(II) complexes [PtCl(n)[H=C(R)OR'](2)] (n = 2, 4) by reaction with 1,2-bis(diphenylphosphino)ethane and pyridine, respectively. All of the prepared compounds were characterized by elemental analyses (C, H, N), FAB mass spectrometry, IR, and (1)H, (13)C[(1)H], and (195)Pt (metal complexes) NMR spectroscopies; the E and Z configurations of the imino ester ligands in solution were determined by observation of the nuclear Overhauser effect. X-ray structure determinations were performed for trans-[PtCl(4)[(E)-NH=C(Me)OEt](2)] (2), trans-[PtCl(4)[(E)-NH=C(Et)OEt](2)] (10), trans-[PtCl(4)[(E)-NH=C(Et)OPr-i](2)] (11), trans-[PtCl(4)[(E)-NH=C(Et)OPr-n](2)] (12), and cis-[PtCl(4)[(E)-NH=C(Et)OMe](2)] (14). Ab initio calculations have shown that the EE isomers are the most stable ones for both platinum(II) and platinum(IV) complexes, whereas the most stable configurations for the ZZ isomers are less stable than the respective EZ isomers, indicating an increase of the stability on moving from the ZZ to the EE configurations which is more pronounced for the Pt(IV) complexes than for the Pt(II) species.     

Structure and conformation of DAB dendrimers in solution via multidimensional NMR techniques.

NOESY-HSQC 3D-NMR and NOESY 2D-NMR techniques have been used on a 750 MHz spectrometer to study the chain conformations of different generation DAB dendrimers (poly[propylene imine] dendrimers) in chloroform and benzene solutions. The high-field multidimensional NMR techniques provided the chemical shift dispersion needed to resolve all of the unique resonances in the dendrimers. By studying the NOE interactions among dendritic chain protons, information about through space interactions between protons on different parts of the dendrimer chain is obtained, which is directly related to the conformation of the dendrimer. These experiments also give further proof of the chemical shift assignments obtained from the HMQC-TOCSY 2D and 3D NMR experiments. The concentration effects on chemical shifts have also been observed, revealing information about the interactions between solvent and different parts of dendrimer molecules. These studies clearly show for DAB dendrimers, that folded chain conformations can occur in nonpolar solvents such as benzene and extended chain conformations are predominant in polar solvents such as chloroform.     

Starlike dendrimers in solutions: structural properties and internal dynamics

We measured the shape and the internal dynamics of starlike dendrimers under good solvent conditions with small-angle neutron scattering and neutron spin-echo (NSE) spectroscopy, respectively. Architectural parameters such as the spacer length and generation were varied in a systematic manner. Structural changes occurring in the dendrimers as a function of these parameters are discussed, i.e., in terms of the fractal dimension and deviations of the radius of gyration from the Gaussian value. A first cumulant evaluation of the NSE spectra for each scattering vector q separately yields the length scale dependent relaxation rates. We observe a local minimum in the normalized relaxation rates Omega(q)q(3) on length scales corresponding to the overall dendrimer dimension. The dynamics is discussed within a Rouse-Zimm approach generalized to the case of starlike dendrimers of arbitrary geometry. The model allows an identification of the modes contributing to the relaxation of the dendrimer in the q and time range of the NSE experiment. The local minimum is due to collective breathing motions of (parts of) the dendrons relative to each other. Shape fluctuations are not observed.     

Molecular dynamics studies of the size, shape, and internal structure of 0% and 90% acetylated fifth-generation polyamidoamine dendrimers in water and methanol

We have performed molecular dynamics simulations of 0% and 90% acetylated fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in water and methanol and obtained radii of gyration of 2.51-2.57 and 2.11-2.33 nm, respectively, similar to those measured experimentally in methanol by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and in water by Choi et al. (Nano Lett. 2004, 4, 391-397). Calculation of the moments of inertia and the relative shape anisotropy show that both 0% and 90% acetylated G5 are modestly ellipsoidal. The distribution of branch points relative to the center of the dendrimer and penetration of solvent show that the core and surface of the dendrimer are more exposed to water than is the region between the core and the surface due to the interactions between monomers, including hydrogen bonds that rapidly break and re-form as solvent molecules compete for hydrogen-bonding sites on the monomers. The water and methanol solvents seem to produce similar numbers of hydrogen bond interactions between monomers.     

Role of solvent and dendritic architecture on the redox core encapsulation

Dendrimers with redox cores can accept, donate, and/or store electrons and are used in nanoscale devices like artificial receptors, magnetic resonance imaging, sensors, light harvesting antennae, and electrical switches. However, the dendrimer molecular architectures can significantly alter the encapsulation of the redox core and charge transfer pathways, thereby changing the electron transfer rates. In this study, we used molecular dynamics simulations to investigate the role of solvent and peripheral groups on molecular structure and core encapsulation of iron-sulfur G2-benzyl ether dendrimers in polar and nonpolar solvent. We found that the dendrimer branches collapse in water and swell in chloroform. The presence of the long hydrophobic alkyl groups at the periphery deters the encapsulation of the core in water which may cause an increase in electron transfer rate. However, in chloroform, the dendrimer branches remain in the extended form, which leads to an increased radius of gyration. Our results suggest that peripheral alkyl chains in dendrimers cause steric hindrance, which prevents branches from back folding in chloroform solvent, but in water it reverses the trend. Overall, the presence of a hydrophobic interior and hydrophilic periphery in a dendrimer improves core encapsulation in water while hindering encapsulation in chloroform.     

The size of RNA as an ideal branched polymer

Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, ?R(g)=√R(g)(2). We consider two sets of sequences--random and viral--with nucleotide sequence lengths (N) ranging from 100 to 10,000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller ?R(g)) than the random RNAs. For the random sequences we find that ?R(g) varies as N(1/3). These results are contrasted with the scaling of ?R(g) for ideal randomly branched polymers (N(1/4)), and with that from recent modeling of (relatively short, N ≤ 161) RNA tertiary structures (N(2/5)).     

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.