Developing novel water purification technologies with

Molecular Dynamics Simulations

A study of adsorbing organic matter with carbon nanotubes.
Speaker:
Dr. Otto Andersen
Western Norway Research Institute

Sergio Manzetti1, Cristian Garcia2, Elena Campos3, and Otto Andersen4*

1. Fjordforsk A.S. Institute for Science and Technology. Midtun, 6894 Vangsnes. Norway.
2. Incotec. C/ Princesa 25. Planta 2. Oficina 1. 28008 Madrid, Spain.
3.
4. Western Norway Research Institute. Fosshaugane Campus. Sogndal, Norway.

Molecular Dynamics Simulations (1)

- Apply the Newtonian equation of motion, F = ma, on molecules and
particles to simulate their behavior in the microscopic world of
molecules.
- Atoms are presented in Cartesian coordinates.
- Bonds are simulated with harmonic potentials of bond stretching and
contraction.
- Coulomb-integrals are used to determine the electrostatic
interactions between charged atoms.
- Van der Waal forces between neutral atoms are estimated using
various mathematical models, such as the Lennard-Jones potential.

Molecular Dynamics Simulations (2)

- Molecular dynamics simulations can be used to simulate biological
systems (proteins, enzymes, membranes), nanomaterials (carbon
nanotubes, graphene, fullerenes etc), gases and liquids, ions,
solvents and nanoparticles.
- The advantage of MDS lies in the predictive potential of the
simulations in anticipating effects of physical and nature, material
properties, interactions and effects at the molecular level.
- MDS is a powerful tool to design, predict and calculate the
properties of nanomaterials, the functions of membranes and the
effects of specific materials in water purification systems.
- Currently, MDS is being used to develop a new rationale for a
technology for removing organic matter from water by the use of
carbon nanotubes (CNTs).

Potential filtering materials: Carbon nanotubes

(1)
- Carbon nanotubes (CNTs) are composed of hexagonal carbon moieties (benzene
groups) arranged in contiguous tubular structures and can be arranged in one or several
tubular structures on top of each other (single-walled or multi-walled).
- CNTs have extraordinary physical strength, tensile strength and high resilience and
comprise normally diameters ranging from 1.5nm 2.5nm.
- CNTs can be synthesized at industrial or medical grade purity using various methods
such as arc-discharge, aerosol methods, or other methods.

Potential filtering materials: Carbon nanotubes

(2)
- Carbon nanotubes have aromatic surfaces, defined by their conjugated chemistry, and have properties that are normally associated with organic
solvents such as naphthalene, and anthracene.
- The chemical properties of CNTs are unique, because of their special angle of
curvature across their tubular ensembles.
- The carbon atoms are in a chemical configuration which lies between the
purely aromatic (e.g. benzene) and the aliphatic class (such as alkanes), given
the physical strain that is exerted on the -orbitals of the carbon atoms by the
curved shape of the surface.
- Increasing diameters, giving a lower curvature give therefore also more
aromatic properties of the surfaces compared to narrow tubular structures.

Molecular dynamics analysis of CNTs as

sorptive materials for organic matter.

Three molecules representing organic

matter where selected: Retene (A),
perylene (B) and cholesterol (C).
125 copies of each were inserted in
virtual boxes of 1000nm along with 8
CNTs of different diameters (1nm->2nm).
The mixtures of thousands of atoms and hundreds of
molecules were simulated for 10ns at 300K.
Interactions between CNT and each of the three molecular
types were studied at nanometer resolution.
Energies of binding and energies of the formed complexes
were calculated.

Methods - simulation

The GROMACS package was used for all calculations.

All systems were equilibrated from 0 Kelvin and 1 atm. to
300K with PME method of electrostatics and Cut-off for
van der Waal forces for 100 picoseconds.
LINCS algorithms used for simulating all bonds. ParrinelloRahman scheme for pressure coupling in the equilibration
run.
Full simulation of 10 nanoseconds run in vacuum, at 0 atm,
300K to observe particle and molecular behavior without
influence from other factors (eg. solvent, high
temperatures, pressure etc).

Methods - energies
Total energies were calculated with g_energy in the
GROMACS package.
Lennard-Jones potentials calculated to quantify the overall
energy of the formed complexes between CNTs and the
three molecules individually.
Binding energies were calculated using the formality:
Ebind = Ecomplex (ECNT + EMOL)

(where EMOL is the total energy of the retene, perylene or cholesterol molecules and ECNT the total energy of the
nanotubes.

Graph: The energy of the

formed complex must be
lower than the sum of its
components in order for the
complex to form
spontaneously.

Results
All molecules bound strongly to the CNTs.
The CNTs with large diameters bound the aromatic
molecules perylene and retene more tightly, based on the
effects of -electrons.
Figure: Retene bound and encapsulated by CNT of 2nm diameter.

Results

The effects from -electrons dominated all bonding to CNTs

from retene and perylene, particularly from 1.5nm and up to
2nm in diameter of the CNTs.
CNTs with diameter larger than 1.2 nm were able to encapsulate
retene molecules inside their hollow structures. These bound
also through -stacking.
Cholesterol bound through pure hydrophobic forces (non-planar
and flexibly) and formed the most dense clusters with all CNT
types (Figure), based on its more flexible geometry.

Left: CNT20+Cholesterol, Middle CNT10+Cholesterol, Right: CNT12+Cholesterol

Results
CNTs and each of the molecules were also analyzed
individually and show to form dense clusters with high very
stable hydrophobic and aromatic packing effects.

Left: 125 mols. Retene, Right: Eigth CNTs, 1nm diam.

Energies
All hydrophobic energies were in favorable configurations and
the larger the diameter the more relaxed and equilibrated are
the interactions.

Lennard-Jones potentials for CNTs and Perylene mixtures. All

energies are negative and in favorable states. Larger diameters
give more favorable states.

Lennard-Jones potentials for CNTs and Retene mixtures.

All energies are negative and in favorable states.

Lennard-Jones potentials for CNTs and Cholesterol mixtures. All

energies are negative and in favorable states. Larger diameters
give more favorable states. Larger diameters give more
favorable states.

Physical and chemical properties quantities of the formed nanoclusters.

CNT10, 12, 15 and 20 designate respectively their diameters in .

Interpretation

Perylene, which is large and planar aromatic binds with

strongest energy to the CNTs.
Cholesterol which is flexible and hydrophobic clusters in more
dense arrangements, with highest packing density. This
generates also the smallest particles of all molecules.
CNTs with large diameters generally bind all molecules better,
because of encapsulation inside and good packing on the
surface, independently of molecule.
CNTs can be used as sorptive materials to purify water,
however the binding to the test compounds is so strong that
eventual reuse of CNTs may require rigorous treatment.
CNTs bind up to 10 molecules of cholesterol pr cylindrical unit
of 2 . This means that for CNTs of length of 2.6nm (as studied)
can bind up to 130 molecules. For CNTs of such dimensions,
this implies a sorption ratio of 1 : 130 molar ratio.

Further studies

Particle collisions in water phase.

Simulations of CNT and molecules in water at
various temperatures.
Estimation of interaction profiles in water.
Simulations with other molecules, such as
pharmaceuticals.
Estimation of best CNT propertiers for general
purification approaches.