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Molecular Simulation

ISSN: 0892-7022 (Print) 1029-0435 (Online) Journal homepage: http://www.tandfonline.com/loi/gmos20

Molecular simulation of carbon nanotubes as


sorptive materials: sorption effects towards
retene, perylene and cholesterol to 100 degrees
Celsius and above
Sergio Manzetti, Otto Andersen, Cristian Garcia & Elena Campos
To cite this article: Sergio Manzetti, Otto Andersen, Cristian Garcia & Elena Campos (2016):
Molecular simulation of carbon nanotubes as sorptive materials: sorption effects towards
retene, perylene and cholesterol to 100 degrees Celsius and above, Molecular Simulation, DOI:
10.1080/08927022.2016.1155212
To link to this article: http://dx.doi.org/10.1080/08927022.2016.1155212

Published online: 26 Apr 2016.

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Date: 26 April 2016, At: 23:57

Molecular Simulation, 2016


http://dx.doi.org/10.1080/08927022.2016.1155212

Molecular simulation of carbon nanotubes as sorptive materials: sorption effects


towards retene, perylene and cholesterol to 100 degrees Celsius and above
Sergio Manzettia, Otto Andersenb , Cristian Garciac and Elena Camposd
a

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

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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]

CONTACT Sergio Manzetti

sergio.manzetti@fjordforsk.no

2016 Informa UK Limited, trading as Taylor & Francis Group

Received 18 August 2015


Accepted 14 February 2016
KEYWORDS

Carbon nanotube; water;


sorption; molecular;
simulation

Urbanisation introduces also one of the major causes to


shortage of clean water pollution which is represented by
endocrine disruptors, heavy metals, nitrosoamines, phthalates
and several other pollutants regarded as part of the toxic sevens.[5] Man-made pollution encompasses also the problem of
emerging pollutants, pharmaceuticals, antibiotics and other
compounds which are toxic even at trace concentrations.[1,6]
These issues are pivotal for the importance of clean water supply
in an age of global environmental and resource difficulties and
increasingly expanding population. Water purification technologies are therefore on the advance, particularly for the cause of
supplying energy-efficient, environmentally sustainable, low-cost
and chemically green methods of water purification, where the
majority of these emerging pollutants, organic contaminants and
other pollutants are removed safely, without extensive maintenance of the purification technology.
Purification technologies have also to be simple, inversely to
many modern decontamination approaches, which require rigorous technical experience, expensive equipment and large-scale
systems of multi-million dollar budgets. For this reason, even in
Europe, recent movements have been towards the reduction of

S. Manzetti et al.

chemical treatment via the use of engineered natural systems for


drinking water production in order to reduce residual chemicals
in the distribution systems.[7] The rationale of purification of
water without release of the purified contaminants has emerged
recently [1] in concert with WHO priorities.[7] This development has led to a new state of the art focus which encompasses
the strategic removal of critical contaminants with the maximum
use of natural resources and components.

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1.1. Molecular species in organic matter fractions of


drinking water and wastewater
The organic matter fraction found in drinking water originates
mainly from natural chemical processes from decay and transformation of organic matter in the soil. For wastewaters, the
origin of contamination is purely artificial and derives from
anthropogenic pollution. The majority of the components in
the former case can be classified as naturally occurring organic
compounds (NOM or natural organic matter), which derive
from lakes, marsh lands, rivers, deltas and ground water.[8] In
wastewater however, the majority of organic compounds can
be classified into hydrocarbons, polycyclic aromatics, polymers,
persistent organic compounds, endocrine disruptors and pharmaceuticals, all deriving from industrial and societal activities.
[9] Nevertheless, recent studies show that these two phases in
the continental water-cycle are becoming increasingly blended
through the diffusion of persistent compounds through the soil,
water and air phases.[6] This results in the contamination of
surface- and ground-water supplies by antibiotics, endocrine disruptors, plastics and hormone analogues.[10,11] The presence
of these toxic compounds in drinking water sources makes the
development of advanced technologies for the decontamination
of drinking water, in addition to wastewater, a critical path of
technology development, as the contaminants induce a series
of toxicological hazards when supplied at small and continuous
concentrations to the local populations.[12,13]
In this study, we have therefore constructed a molecular model
of a potential sorptive material based on eight carbon nanotubes
(CNTs), to be simulated for sorptive effects against three representative molecules from wastewater and contaminated drinking water:
cholesterol, retene and perylene. This selection of molecular candidates is supported also by the study by Gbursky et al. [14] which
sheds light on the behaviour of CNTs towards cholesterol in context
with protein simulations and an initial introduction of the potential of using CNTs to purify organic compounds from wastewater.
[15] In order to further advance on this state of the art, and supply
novel information on the state of sorptive nanomaterials, the authors
attribute the strength of molecular dynamics on the given systems,
and evaluate their mode of interaction using also pull force simulations and above-boiling point analysis. The study shows the potential
of MD simulations to prepare and reveal crucial properties applied
to study and develop new materials for water purification systems.

2. Materials and methods


CNT of diameter of 10 (CNT10), 12 (CNT12), 15 (CNT15)
and 20 (CNT20) were prepared using the software Nanotube

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

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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

where r is the distance between two neutral atoms, A=412


and B = 46. Here, is the well depth energy, is the value
of r at which 12(r) = 0. The minimum value of 12(r) at
r=rmin, which is pivotal to find the energy minimum is given
by rmin/=21/61.12246.
Lennard-Jones energies are calculated using g_energy in the
GROMACS package.[16]
2.5. Binding energies of complexes
The binding energy is estimated between the CNTs of various
diameters and the three molecules in pairwise calculations. The
simple relationship for complex-formation energy is therefore:

(
)
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

the water phase particle collisions are based on input starting


structures from the relaxed and converged in vacuo simulations
The clusters were extracted in their GROMACS format and
immersed in a box of water using genbox in the GROMACS
package.[16] This resulted in three boxes each containing 30,682
water molecules, solvating the extracted CNT clusters (10-nm
diameter) and 125 retene molecules. The systems were minimised using 1000 time-steps of the steepest descent method,
and a preliminary short simulation for a short period of 50ps,
at 1fs time-step with simulated annealing from 0 to 300K. After
this equilibration, the systems were simulated with applied pull
forces on the CNT cluster, in order to generate a particle collision,
between the CNTs and the retene cluster. The simulation was
run for 10ns at 1-fs time-step, with the Verlet cut-off scheme,
nstlist of 10fs, with a grid type ns_type. Rlist and rvdw was set
to 1.2nm. Temperature was set at 373K to observe the behaviour of the particles at boiling temperature of water, for recycling
purposes. An isotropic temperature scheme was used with the
Berendsen temperature coupling bath.[27]
Each of the three described simulations were subjected to a
unique pull force magnitude exerted on the CNT cluster. The
cluster was imposed to move across the box at a pull rate of 1nm/
ns, resulting in an overall displacement of the CNT cluster of
10nm after 10-ns simulation. This pull force was exerted on all
three simulations, however the first simulation had an imposed
force constant on the nanotubes of 500kJ/molnm, the second
1000kJ/mol nm and the third 2000kJ/mol nm. This momentum was applied using the force constant in a direction-periodic
geometry using a translation vector [1, 0, 0].

3. Results and discussion


3.1. Structures
The molecular systems of 8 CNTs with 125 retene, cholesterol and
perylene molecules (each in separate boxes) were equilibrated
and run for 10-ns simulations with each CNT diameter (10, 12,
15 and 20) using the molecular dynamics integrator. Binding
between CNTs and each of the molecular types was observed
within the 10-ns interval for all CNT diameters, with variation in
the packing modes of the three molecules, depending on the molecule bound to CNTs. The binding mode of retene and perylene
to the CNTs resulted in observed -stacking effects inside the
tubular structures, this was observed for the simulations of retene
and perylene mixed with CNTs of 15 and 20 diameters in
particular (Figures 1 and 2).
-stacking effects [28,29] are central modes of binding of
planar aromatic molecules in solutions and crystals, and indicate that the simulation produced accurate and equilibrated noncovalent bonding states between molecules. The distances
between retene molecules and CNTs vary between 3.8 and 4.2
accounting for non-covalent CC interactions, and 2.83.3 for
non-covalent CH interactions (Figure 1). Cholesterol bound
more loosely to the CNTs, given its lack of aromaticity in the
molecular architecture, and gave mean distances of 4.85.0
between its carbon atoms and the CNT surface (Figure 3).
Similar distances have been calculated in a separate study
by Britz and colleagues.[30] The CNT with diameter of 20
formed stable clusters with each of the three types of molecules at 300K, with dimensions of ~8090 in diameter and

S. Manzetti et al.

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Figure 2.(Color online) PeryleneCNT(15).


Notes. The distances to the left are given: 4.2 surface carbon to perylene carbon
atoms, 5.8 from inner wall carbon of CNT and encapsulated perylene molecule.
3.8 pi-stacking distance inside the nanotube between two sandwiched perylene
molecules.

Figure 3.(Color online) Cholesterol molecules packed around CNT15 structures.


Notes. Slightly right to the centre, a CNT of 15 diameter is displayed with
encapsulated cholesterol molecules as well as layer of cholesterol molecules on
the surface. Mean distance between the surface and the cholesterol molecules is
5, while internal distances between cholesterol and the CNT wall as 4.85.0.

volumes of 0.250.3m3, while more narrow CNTs generated


slightly smaller clusters. The simulations of cholesterol and the
four CNT types (CNT+CLR) differed from CNT+retene and
CNT+perylene simulations in that cholesterol generated a set
of particularly dense clusters with CNTs. This is explained by
that the cholesterol molecules, being more flexible and having
more improper torsions across their structures, packed around
the nanotubes at a higher density and with a larger number of
molecules per nanotube (Figure 2).
The most dense packing around a CNT reported in this analysis is shown in Figure 4, where cholesterol stacked around the
CNT surface with approximately 20 molecules per tube (tubes of
25 length), a feature which was observed in another study by
Calvaresi and colleagues [31]. This molecular relationship shows
that CNTs are able to bind approximately 10 cholesterol per nm
of CNT at the given diameters (a rough estimate of 10 cholesterol molecules per 320 total nanotube surface estimated by
visual inspection). This binding mode is sustained completely by
the final effect of hydrophobic packing catalysed by cholesterols
molecular flexibility. Cholesterol packed also inside the tubular
structures from 12 and up to 20 in diameter and aggregated in spherical clusters around the tubes (Figure 3). Similar
effects have been observed also for other molecules in a separate
study by Kondratyuk and Yates [32]. The simulations of CNTs
of diameter of 10 with each of the three molecules resulted in
no encapsulation of retene, perylene or cholesterol inside their
hollow spaces. The CNTs of 12 in diameter gave the first effects
of encapsulation of molecules inside the tubular structures, for
all molecules except for perylene which is considerably wider
than cholesterol and retene. Upon encapsulation in the CNTs, the
binding distances of CH groups between encapsulated retene
molecules and the inner CNT walls packed to 2.8, while the
bonding distances on the surface between retene and nanotube
atoms are similar to the other CNT diameter types (diameter
20 and 10, 3.84.2 Figure 1). The narrow diameters of the
CNTs at 10 and 12 lead however to bending of the benzene
moieties of CNTs which affects to a significant extent the packing
of aromatic molecules around the surfaces (retene and perylene).

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

These molecules bound to the surfaces of CNTs with the narrow


diameters (10, 12) at more dense arrangements than the larger
diameters (15, 20), considering visual inspection. The simulation of the CNT with 15 and 20, gave contrary to 10 and 12
diameters simulations with several molecules in full -stacking
on the outside as well as on the inside the tubular structures
for both retene (Figure 1) and perylene (Figure 2), with two or
more molecules in sandwich conformations (Figure 1), which
is frequently found in PAH crystals.[33,34]

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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

1). The potential energy calculations show that there is little


discrepancy between CNT20, CNT15, CNT12 and CNT10 in
terms of binding to the three molecules, and these seem as quite
similar. (Table 1). CNT20 has, worth noting, a higher planarity
of the surface given the larger diameter than the other CNTs, as
also noted by Niyogi and colleagues [35] who found a proportionality ratio between increasing aromaticity and expanding
diameter. This ratio is close to 1:1, and derives that when the
diameter is doubled, the electronic rearrangements which sustain
aromaticity are doubled [35]. Very wide CNTs will therefore be
purely aromatic and display attraction to aromatic substances
on their surface and bind retene/perylene more strongly. In
overall, perylene binds strongest to the nanotube, followed by
cholesterol and retene which utterly display higher binding energies (Table 1 Average for all CNT diameters). As mentioned,
cholesterol molecules do not follow this rationale of binding
as categorically as retene and perylene, given that cholesterol
has no conjugated aromatic electrons, and results as a largely
hydrophobically bound to the CNT surfaces, which is weaker
in overall binding energy. This gave also a larger non-linearity
in the relationship between binding energy and CNT diameters (Table 1), where the peak of binding energy is at the largest
and smallest tubular diameters. The cholesterol molecules, not
responding as in -stacking mode, and having a higher flexibility
about their molecular centres were able to conform to the tubular
structures with narrow diameters and bent -geometries, and
thus yielded more favourable binding energies. This feature is
also observed for the large diameter CNT20 simulations. Visual
inspection (Figure 4) does not suggest different packing modes
of cholesterol and CNTs at different diameters, thus the energetic
preference of large and small diameters can potentially be best
explained by the structural flexibility of cholesterol adapting to
the two different surfaces.
3.3. Cluster properties
Table 1 displays also the features of packing of CNTs and retene,
perylene and cholesterol molecules. The clusters formed between
CNT of narrow diameters and retene molecules generate less
dense clusters, with lowest density for the CNT10 type of 245ng/
mm3 and also lowest average distance of interaction between
the molecules in the blends (Table 1). The relationship between
diameter for the retene + CNT simulation reflect a ratio of
~20ng/mm3 increase in particle density for every the diameter
of CNTs is expanded by. All numerical values are approximate,
and rely CNT10, 12, 15 and 20. The relationship between the estimated binding energies (Table 1) and the increment in diameter
for CNT10, 12, 15 and 20, respectively, results to an average
increase in binding efficiency of retene by 867kJ/mol per
increment in diameter. In other words, an increase in the CNTs
diameter by 1 (0.1nm) gives a more optimal binding energy
with ~1MJ/mol for retene. This figure is a factual result of the
calculations and is in good agreement with the reported pattern
of increase in aromaticity reported for larger CNT surfaces.[35]
The exact figures are however difficult to measure empirically, as
the experimental selection and combination of such small clusters and mixtures is virtually impossible. The simulations serve
therefore as an estimate for an empirical outcome. For perylene
and cholesterol the features of particle formation are similar,

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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

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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.

Table 1.Table of energies, and physical quantities of the formed nanoclusters.


System (name)
Retene and CNT:
CNT10+RET
CNT12+RET
CNT15+RET
CNT20+RET
Average for all CNT
diameters
Cholesterol and CNT:
CNT10+CLR
CNT12+CLR
CNT15+CLR
CNT20+CLR
Average for all CNT
diameters
Perylene and CNT:
CNT10+PER
CNT12+PER
CNT15+PER
CNT20+PER
Average for all CNT
diameters

Binding energy (kJ/


mol)

Lennard-Jones energy
(kJ/mol)

Average distance to
the CNT ()*

Average packing
density (ng/mm3)*

Average particle volume (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.

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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.

to move the in vacuo patterns concluded in the first part of the


study to a simulated water phase, to observe how the PAH clusters interact with nanotubes in a fully solvated state.
3.4. Water phase analysis
Solvation simulations are critical to model the interactions of
the molecules under the presence of water. The water solvation
simulations give answers to the effect of the high dielectric constant of water and its effect on the clustering of non-polar compounds, such as retene and the CNTs. As nanotubes are known to
aggregate intensively in a water phase,[35] it is expected that the
cluster derived from the gas phase simulations retains its agglomerated conformation. The three simulations carried out showed
that the pull force of 1000kJ/mol nm gave the most harmonic

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

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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.

Lennard-Jones energy of the nanotubes and retene and Coulomb


energy of water indicate an equilibrated water simulation (Figure
8). This simulation assists in other words in understanding the prerequisites of how to test, prepare and fabricate filtration technology
based on using CNTs as sorption materials, and which pitfalls to
expect. In order to gain more data on the interaction between
nanotubes and water phase, a set of water simulation studies on
the systems described can be carried out in future studies, also to
study the levels of encapsulated states of water inside the nanotubes and to determine their coordination, energy and interactions
with the nanotubes, as nanotubes have shown to induce unusual
effects on crystals in their hollow structures.[38] In this context,
it is worth noting to include studies such as the surface binding
energies of CNTs [39] and similar studies on binding patterns of
CNTs towards additional types of molecules.[40] Furthermore,
studies on the properties of molecules absorbed inside and outside
the nanotubes can be of important auxiliary literature particularly
for method-related approaches, considering the work by Tian and
colleagues [41], and properties of aggregates.[42] (see Figure 8).

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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