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Highly branched polymers such as polyamidoamine (PAMAM) acidic, neutral, and basic pH environments. Comparison with
dendrimers are promising macromolecules in the realm of existing literature, both experimental and theoretical, is done
nanobiotechnology due to their high surface coverage of tun- using measurements of the radius of gyration, moment of
able functional groups. Modeling efforts of PAMAM can pro- inertia, radial distributions, and scaling exponents. Additionally,
vide structural and morphological properties, but the inclusion ion coordination distributions are studied to provide insight
of solvents and the exponential growth of atoms with genera- into the effects of interior and exterior protonation on counter
tions make atomistic simulations computationally expensive. ions. This model serves as a starting point for future designs
We apply an implicit solvent coarse-grained model, called the of larger functionalized dendrimers. V C 2015 Wiley Periodicals,
Methodology
All simulations are conducted using the Large-scale Atomic/
Molecular Massively Parallel Simulator (LAMMPS) package.[26]
Non-bonded interaction parameters originate from the Dry
Martini force field of Arnarez et al.[25] The PAMAM Martini
structure are derived from Lee et al.[22] and includes bond and
angle parameters. A temperature of 298 K is maintained with
a Langevin[27] thermostat in a canonical ensemble, with a
damping parameter set to 4.0 ps along with a time step of 10
fs. The cubic simulation box has a dimension of 13.5 nm.
Upon equilibration of the energy and radius of gyration, each
system is simulated for 10 ns and sampled every 0.1 ns. To
ensure reproducibility of results, the simulations are repeated
for four random seeds.
The Martini CG-scheme involves mapping approximately
four nonhydrogen atoms to 0.47 nm diameter beads of vary-
ing levels of polarity.[24] For PAMAM at a neutral pH, the CG
dendrimer is composed of three groups[22]: internal tertiary
amine junctions (56 g/mol), amide branches (70 g/mol), and
terminal protonated primary amines (31 g/mol). In acidic envi-
ronments (pH < 5), high concentrations of hydronium ions
lead to the protonation of all amines via the nitrogen’s lone
pair of electrons. However, only protonation of terminal
amines is assumed to occur in neutral pH environments due
to water accessibility and stable solvation of primary amines
over tertiary amines. Basic pH conditions (pH > 10) allows for
deprotonation of all amines including the terminal groups. Fig-
ure 1 illustrates this dependency of the CG moieties on pH
and the interaction representations. Internal amines are con-
sidered relatively nonpolar “N0” with respect to the other
groups. The more electronegative acyl group on the branch
amides allows it to be designated as moderately polar “P3.”
Protonated amines (11e) are classified as charged species
“Qd” capable of being hydrogen bond donors. Since neutral
and low pH levels result in net positive PAMAM dendrimers,
CG representations of the hydrated chloride (21e) counter
ions (107.453 g/mol) are added to those systems and are also
considered charged species “Qa” but with the ability to be
hydrogen bond acceptors. Such groupings primarily affect the
van der Waals interactions modeled by the Lennard-Jones (LJ)
potential:
12 6 !
rij rij
ULJ 5 4eij 2 (1)
rij rij
axes rotate along with the dendrimer. The ratios are plotted
against dendrimer generation in Figure 4. With a decrease in
aspect ratio of the minor-major axes for all pH levels, PAMAM’s
ellipsoid shape becomes less eccentric as the number of gen- Figure 7. a) Average fractions of chloride ions that are uncoordinated and
b) average number of CG groups coordinating with each chloride (taking
erations increases. In addition, asphericity and relative shape
into account of only ions that have at least one coordination) as a function
anisotropy are calculated from the gyration tensors.[33] Figure of generation. [Color figure can be viewed in the online issue, which is
5a shows indications that the asphericity increases at genera- available at wileyonlinelibrary.com.]
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