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Fjordforsk A.S. Nanofactory, Centre for Advanced Sciences, Vangsnes, Norway; bWestern Norway Research Institute, Fossahaugane Campus, Sogndal,
Norway; cIncotec, Madrid, Spain; dSacyr S.A, Madrid, Spain
ARTICLE HISTORY
ABSTRACT
New water purification technologies are being developed as the worlds water sources are increasingly
being polluted and experience a dramatic consumption with the increasing world population. In this
context, the emerging era of nanotechnology has introduced a series of innovations and materials with
promising potential as sorptive materials for water decontamination. The application of nanomaterials for
the purification of ground/surface water introduces nevertheless a series of important challenges, such as
health and safety, cost, process-efficiency and chemical sorption properties. In this study, we consider the
latter class and present a study of the sorptive properties of carbon nanotubes (CNTs) as potential water
decontaminating materials. Molecular dynamics simulations are used and three molecular candidates of
the water contaminants, cholesterol, perylene and retene were selected for interaction study with CNTs
at different diameters. The results show that CNTs form densely packed clusters with retene, perylene
and cholesterol, binding each strongly to their tubular surfaces, as well as in their hollow tubular spaces.
Cholesterol and perylene bind more strongly than retene, accounting for the calculated binding energies
in vacuo, however the planar geometries of polycyclics may in general favour binding to CNTs over semipolar molecules and can require further studies. Our studies show furthermore that the CNTs retain the
adsorbed molecules also at 100 degrees Celsius, and require therefore additional steps of separation for
eventual recycling and reusing the nanomaterials for additional decontamination. This study is important
in providing data for initiating studies and developments of water purification approaches based on using
CNTs.
1. Introduction
Filtration and purification technologies are estimated to be the
most important technologies for the global population in the
coming 40years.[1] Worldwide water supplies, also in the countries considered as water rich, are experiencing a global threat
given pollution, climate changes and man-made interference
in natural habitats and environments. Climate changes represent one of the most critical causes to shortage of clean water,
especially in south-east Asia, in the Middle East, North Africa
and South America. The increasing global temperatures and
reduction of glaciers are the most eminent causes to the ongoing shortage of water supplies deriving from rivers and lakes, as
the annual water masses which derive from natural ice-melting
are already experiencing a dramatic decline.[2] In parallel, the
expansion of metropolitan cities are additional causes, especially
in emerging economies such as China, Africa, India and Brazil,
where water supply locations are being artificially altered and
rivers and deltas are re-routed for hydroelectric power plants,
affecting water availability for rural communities and altering
the natural habitats.[24]
sergio.manzetti@fjordforsk.no
S. Manzetti et al.
Modeller (http://www.jcrystal.com/products/wincnt/index.
htm). Topologies were built with the GROMACS package
[16] using the g_x2top script. Molecular models of retene,
perylene and cholesterol were prepared using the ATB automated topology builder.[17] These molecules were chosen
as PAHs and cholesterol are frequently found in wastewater, and are candidate molecules of relevance for purification
technologies.[1820] The GROMOS 5.4a7 forcefield [21] was
selected to build topologies. Molecules were then inserted in
101010-nm boxes, to encompass final states of 8 CNT
molecules and 125 molecules of retene, 8 CNT molecules and
125 molecules of perylene and 8 CNT molecules and 125 cholesterol molecules. The preparation of boxes of CNTs was performed with the genconf script, with -dist 3(nm) for CNT10,
12 and 15, and -dist 3.5 for CNT20. This approach generates
eight CNTs spread uniformly across the box at arbitrary rotations and allows one molecule of retene/cholesterol/perylene
at the centre of the box. This point was crucial to allow full
homogeneity in the simulations and prevent premature aggregation of the CNTs to compact bundles. The final group of
MD sets resulted in a total of 12 sets for molecular simulation
(for each molecule, retene, cholesterol and perylene) which
was batched on a 24 CPU AMD Bulldozer architecture with
MPI multi-parallel execution language.
2.1. Energy minimisation
Every simulation input was prepared with 1000 time-steps
of energy minimisation with the steepest descent method, a
Particle-Mesh-Ewald (PME) electrostatics mode with a Coulomb
distance of 12, a van der Waals cut-off mode with a vdW distance of 12, a tolerance of 100kJ/mol.
2.2. Simulated annealing
The generated systems were allowed to relax with a simulated
annealing run of 50 ps, with temperature ranging from 0 to
300K over two annealing points with a time-step of 2fs. The
simulation was run with the PME electrostatics mode [22] with
a neighbour searching frequency of 10fs (Verlet algorithm), in
a Cartesian system with full periodic boundary conditions, a
Coulomb (PME) and van der Waals distance of 1.2nm (cut-off)
and a Fourier spacing grid of 0.1 nm. Pressure coupling was
included with the ParrinelloRahman isotropic scheme [23] at
1atm. Bond constraints were applied using the LINCS algorithm
[24] on all bonds.
2.3. Full gas phase simulation
The full simulation of the described systems was run for 10ns
with a 2fs time-step, and same electrostatics and bond parameters as above. The simulation was run without pressure coupling
in order to let the molecules gradually assemble in spontaneous
states of clustering. A full simulation was run for all the described
complexes of CNTs+retene/perylene/cholesterol and for each
component individually as well, in order to estimate complexation energies.
Molecular Simulation
Figure 1.(Color online) CNT (20 diameter purple) with retene molecules (green)
bound non-covalently via van der Waals forces.
Notes. Top left: clustering effect of 8 CNT molecules and 125 retene molecules;
Bottom left: Close-up of cluster 1 with visible retene molecules encapsulated inside
and on the surface of CNT; Right: Detailed inspection of the bonding mode of stacking effects between two retene molecules and the CNT surface with distances
of 3.2 (hydrogencarbon atoms) and 4.0 (carboncarbon) and two retene
molecules on the opening of the carbon nanotubes structure (4.1 distance).
2.4. Energies
Lennard-Jones energies describe the non-covalent interaction
between neutral atoms, and are given by the simple relationship
[25] which evolves from the classic Lennard-Jones potential:
12 (r) =
A 12 B 6
r
r
(
)
Ebind = Ecomplex ECNT + Emol
where EMOL defines the total energy of each of the molecules separately,
retene, perylene and cholesterol. ECNT, defines the total energy of the
CNTs of specific diameters. Ecomplex defines the total energy of the all
the complexes of CNTs and the molecules adsorbed. Ebind defines the
conclusive energy required to bind the two together, which must be
negative in order to proceed favourably. The total energies are calculated
using g_energy in the GROMACS package.[16]
2.6. Analysis
Analysis of trajectory was performed with g_dist, g_density and
g_energy in GROMACS package.[16] Graphical analysis performed with Pymol.[26]
2.7. Water phase particle collision simulations
Three 10-ns simulations were run for the retene and CNT results
from the full in vacuo simulations. In other words, all inputs to
S. Manzetti et al.
Figure 4.(Color online) Binding modes of cholesterol to carbon nanotubes of various diameters. Left CNT20, middle CNT10, right CNT15. CNT12 is omitted for graphical
purposes.
Molecular Simulation
3.2. Energies
In order to understand the energetic properties of binding
between the three molecules and the CNTs, a simple consideration of binding energies and methods of estimation is necessary. The interactions between neutral molecules in every system
(CNTX+retene/perylene/cholesterol) can be ideally described
by Lennard-Jones (LJ) mathematical expressions (charge molecules follow Coulomb attraction models which are not discussed here). The expressions describe the interaction between
each pair of bonded and non-bonded atoms in the system. All
energies have to be negative to indicate equilibrated and stable
conformations. The LJ energies describe in other words the sum
of the potential energy for the covalent and for the non-covalent interactions between the neutral atoms of the CNTs and the
retene molecules. The LJ energies are reported in Figure 5 and
show that with narrower CNT diameters, larger negative energies result for (CNT10+RET/PER/CLR) than for CNT12 and
CNT15. This may however be verified by calculating the energy
of binding per atom, as the energy fluctuations between diameters are not solely proportional to the potential energy landscape.
The most favourable potential energies result therefore at wide
tube diameters.
This is known [35] to affect the CNTs resonance -energy,
changing from less aromatic to more aromatic for increasing tube
diameters. This relationship is the same for all systems, cholesterol, perylene and retene all result in complexes with LJ energies
that are more favourable with larger CNT diameters.
In order to define and differentiate the degree of binding
between CNTs and cholesterol, retene and perylene, the calculation of binding energies for the complexes is critical. The binding energies are estimated by calculating the difference between
the total energies of the simulated complexes and the sums of
the individual total energies of each of the molecular ensembles
(Figure 6(A) see a retene droplet) and the CNTs (Figure 6(B) a
nanotube cluster). Binding energies, also known as complexation
energies or complex-formation energies, and given an accurate
estimate on whether the binding between two groups (CNTs and
retene/perylene/cholesterol) is favourable (negative energies) or
unfavorable (positive energies) and most importantly, the degree
of binding: the stronger the binding, the lower the final binding energy, Ebind (see methods). The binding energies are show
in Table 1 and show that binding between retene and perylene
to the CNTs increases linearly in magnitude with larger CNT
diameters and are the strongest binding modes in this analysis,
as expected with the size of the CNT systems. Cholesterol binds
slightly weaker to the CNTs, as it uses hydrophobic packing in
the binding mode and it does not induce a stronger binding only
to large diameters, but also to the most narrow (CNT10 Table
S. Manzetti et al.
Figure 5. (Color online) Lennard-Jones energies for the three systems of molecules with four CNT types. Each label designates the energy plot below. All energies
show favourable interactions within each group of mixtures throughout the 10ns simulation and define a stable trajectory. Top: CNT+Perylene simulations, middle
CNT+Retene, bottom CNT+Cholesterol.
Molecular Simulation
Figure 6.(Color online) Retene molecules and carbon nanotubes aggregated to nanoclusters in a vacuum space (separate simulations. Left: 125 retene molecules packed
in a dense droplet at zero pressure; Right: Eight carbon nanotubes of 10 diameter 26 length converged to a cluster of ~0.34mm3 at zero pressure.
Lennard-Jones energy
(kJ/mol)
Average distance to
the CNT ()*
Average packing
density (ng/mm3)*
3305.7
5032
6194.1
11115.2
6412.3
12064.8
23618.2
25588.6
32289.3
23,390
3
2.1
1.8
2.1
2.25
256
264
285
305
277.5
0.35
0.49
0.45
0.46
0.43
13398.4
5429.9
6975.6
10968.1
9193
23,660
25,991
29,799
33,568
28254.5
3.2
8.1
13.8
7.1
8
798
960
964
928
912.5
0.17
0.16
0.19
0.21
0.18
10,350
10486.8
12032.5
16,025
12223.2
9412.3
21642.9
27472.4
30019.1
22136.7
5.5
5.6
3.1
3.3
4.4
260
235
336
318
287.2
0.35
0.31
0.32
0.57
0.38
Notes. CNT10, 12, 15 and 20 designate, respectively, their diameters in . Energies are calculated using g_energy in the GROMACS package. Average distance estimated
using g_dist in the GROMACS package. The distance is not representative for bonding estimates, and rather illustrates the degree of clustering between CNTs and each
of the molecular ensembles during the 10ns simulations. Packing density is estimated use g_density.
*Values are approximate and derived with the program Xmgrace (Paul Turner) running averages, and extracting the density at the final point of the simulation. Average
particle volume is estimated using Pymol.[26]
however cholesterol shows potential artefacts in the average distances between cholesterol molecules and the nanotubes with
extensive long distances in the CNT15 simulations (Table 1
large average distances from molecule to CNT). This is explained
by the clustering pattern of the CNTs in this very simulation
were cholesterol and the CNTs aggregated not uniformly around
each other, but in two separate regions. The particle density for
cholesterol and CNTs were 23X higher than for retene, which
attributes to the better packing ability of cholesterol with its more
flexible non-aromatic rings. Cholesterol is in other words a molecule type which easily can potentially generate fouling in any
CNT-related sorption approach/technology. Perylene bound, as
mentioned above, most strongly to the CNTs and formed dense
clusters (Figures 1 and 2). These figures show common thread
of planar polycyclics binding to the CNTs, where the CNTs pack
PAHs rather densily on the surface, and can be, as sorptive materials, ideal for extraction of PAHs of hydrophobic types, such as
benzo[a]pyrene, pyrene, phenanthrene, antracene and chrysene
to mention a few, as these retain the same chemistry as perylene
and retene at large.[20] A critical feature of this study is however
how the molecules react not as single entities, as calculated in
the vacuum simulations above, but as agglomerated clusters, as
these types of molecules exist primarily as dissolved nanoparticles in water phases.[36] This property of PAHs rests on the
chemical features of aromatics, which do not blend with water
and agglomerate to clusters when immersed in water. In order
to reveal the behaviour of CNTs as sorptive materials in water
phases, for intended use in water purification technologies [37]
the study proceeds on analysing the collision between a CNT
cluster and a retene cluster in water phase. This part is critical
S. Manzetti et al.
Figure 7.(Color online) The particle collision study in water (redwhite) between carbon nanotubes (blue) and retene (green). From top left to bottom right, trajectory
snapshots taken at 10, 100, 500, 1500, 2500, 3500, 4500, 6500 and 8500ps. Note the -packing at 6500ps around the axial nanotube, where green molecules pack in a
circumference around the carbon nanotube. Each snapshot shows movement of the carbon nanotubes from left to right.
distribution of pull effect on the clusters and a continuous fluctuation mode of the particle before and after collision with the
retene cluster and is therefore analysed further (see Figure 7).
In the given simulation at 1000kJ/mol nm, the 125 molecules of retene remained isolated as a droplet in the presence
of the 30,682 water molecules in the 1000nm virtual box. The
simulation show that the CNT moved across the box before and
after collision, and glued the retene molecules on its surface at
the first moment of contact between the two bodies. The simulation showed furthermore that the formed CNT10+RET particle moved about the box coherently, without detachment of the
retene molecule, even at the high temperature of 373K (Figure 5),
indicating ultra-stable cluster above the boiling point of water.
The interaction with water was also assessed for physical properties using the GROMACS energy analysis tools, where stable
Molecular Simulation
Figure 8.Analysis of the physical properties of the waterCNT system. Top left: Coulomb energy of the water phase during the simulation. Top right: Lennard-Jones energy
of the CNT immersed in the water phase. Bottom left: potential energy of the system. Bottom right: temperature of the water simulation.
4. Conclusions
CNTs are potential candidates as novel sorptive materials for
water decontamination. The molecular dynamics simulation
study shows that the CNTs with the largest diameter bind
aromatic compounds more strongly than hydrophobic, and
CNTs with smallest diameter have a higher potential to bind
less aromatic compounds, such as cholesterol. Tailoring the
dimensions of nanotubes for water treatment approaches is
critical, and shows here that the diameters of 1.4nm are most
suitable to remove both the aromatic as well as hydrophobic
components from contaminated water. The study shows furthermore with a picosecond precision on how the CNTs bind
retene in water even at 373 K, in an endothermic reaction.
The water phase particle collision analysis shows also that the
retene cluster retains its shape upon collision with the CNTs,
and form together a pi-packed cluster of molecules and nanotubes. This study shows the potential of molecular dynamics
simulations in preliminary developing technologies of societal
importance using high-performance computational systems,
in order to understand the effects of using carbon nanomaterials as purification materials on molecular models of water
contaminants.
Disclosure statement
No potential conflict of interest was reported by the authors.
10
S. Manzetti et al.
ORCID
Otto Andersen
http://orcid.org/0000-0003-2111-0279
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