MolecularSimula-onstudiesofOrganicsaltsinsidecarbon nanopores - - PowerPoint PPT Presentation

Molecular
Simula-on
studies
of
Organic
salts
inside
carbon
 nanopores


Harsha
Dissanayake

 Dr.
Francisco
R.
Hung
 Dr.
Joshua
D.
Monk
 Ramesh
Singh


Cain
Department
of
Chemical
Engineering,
Louisiana
State
University,
 Baton
Rouge,
LA,
USA


What
are
Ionic
liquids?


• An
ionic
liquid
is
a
salt
in
liquid
phase
at
room


temperature.



• Made
up
of
ions
and
have
ionic
bonds.


• Posses
low
vapor
pressure
and
are
moderate
or
low


electric
conductors.


• Highly
tunable
properIes;
109
‐
1018
ILs
could
be


formed
by
varying
caIons,
anions.


• Vast
number
of
applicaIons
due
to
disInct
properIes


in
many
fields
such
as
Organic
chemistry,
Engineering,
 Electro
chemistry,
Catalysis
and
Physical
chemistry.
 (Solvents,
electrolytes,
etc)


1,3‐dimethylimidazolium
chloride
 [DMIM+][Cl‐]











Importance
of
Ionic
Liquids(IL’s)


IL’s
can
be
synthesized
to
possess
fluorescent,
magneIc
and
many
other
 qualiIes
according
to
necessity.



Ionic
liquids
can
be
synthesized
from
safe,
FDA‐
approved
 compounds;
therefore
could
be
used
in
Bio‐medical
 applicaIons.


Image
courtesy
of
the
Warner
group


1‐butyl‐2,3‐methylimidazolium
 hexafluorophosphate,
 
[bm2im+][PF6ˉ
]



[PF6ˉ
]


• Nanomaterials
with
fluorescent
proper-es
can
be
used


to
label
Issues
and
cells
for
biomedical
imaging


• Nanomaterials
with
magne-c
proper-es
can
be
used
in


cancer
treatment
(magneIc
hyperthermia).
Aber
 acaching
them
to
cancer
cells,
the
paIent
can
be
 exposed
to
a
safe
magne-c
field
and
the
heat
generated
 by
the
magneIc
nanoparIcles
will
destroy
the
respecIve
 cancer
cells
that
they
are
acached
to.



• The
properIes
of
ionic
liquids
confined
inside


nanopores
can
be
very
different
from
what
we
 see
in
day
to
day
usage
(bulk
systems).



• It
is
extremely
difficult
to
extract
experimental


data
regarding
such
systems


• Molecular
dynamics
(MD)
simulaIon
is
a
very


useful
technique
in
such
cases
to
give
insights
to
 experimental
scienIsts
and
to
complement
their


• bservaIons
regarding
properIes
and


characterisIcs
of
molecules
at
nanolevel.




Why
molecular
simulaIon?


5


10-15 10-12 10-9 10-6 10-3 100 10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (µm) (fs) (ps) (ns) (µs) (ms)

LENGTH/meters TIME /s

Mesoscale methods Semi-empirical methods Ab initio methods

Monte Carlo Molecular dynamics tight-binding MNDO, INDO/S

Continuum

Lattice Monte Carlo Brownian dynamics

Methods

Overview
of
simula-on
methods 


Atomistic simulation methods

Dissipative particle dynamics

Molecular
dynamics:
a
quick
introduc-on


• In
molecular
dynamics
(MD),
we
follow
the
posiIons
and
velociIes
of
each
molecule


in
Ime
by
solving
Newton’s
equaIons
of
moIon:
 i=1,2,3,…N
 U
=
inter/intra‐molecular
potenIal
(i.e.,
interacIons
between
atoms)
 ri
=

posiIon
vector
of
atom
i
 Fi
=
force
acIng
over
atom
i
 mi
=
mass
of
atom
i


6


• In MD these equations are integrated numerically to obtain the time evolution
• f the system

Pair
Poten-als:
Large,
Flexible
Mols.


• Total
pair
energy
breaks
into
a
sum
of
terms:


DNA


• Ustr
‐
stretch

• Ubend
‐
bend

• Utors
‐
torsion

• Udisp
‐
dispersion
(van
der
Waals)

• Uelec
‐
electrostaIc

• Upol
‐
polarizaIon


7


System
to
be
studied


1,3‐dimethylimidazolium
chloride
[DMIM+][Cl‐]


Molar
mass
‐

132.5
mols/gram


Maolin
Sha,
Guozhong
Wu,
Haiping
Fang,
Guanglai
Zhu,
and
Yusheng
Liu
 J.
Phys.
Chem.
C,
2008,
112
(47),
18584‐18587•
DOI:
10.1021/jp8079183
•
Publica?on
Date
(Web):
30
October
2008


• In
my
summer
project
I
will
be
invesIgaIon
various
properIes
of
the


ionic
liquid
[DMIM+][Cl‐]
when
it
is
confined
in
a
mulI‐walled
carbon
 nanotube.


• I
will
be
using
Gromacs
MD
sobware
to
perform
MD
simulaIons
of


[DMIM+][Cl‐]



MulI‐walled
carbon
nanotube


hcp://www.photon.t.u‐tokyo.ac.jp/~maruyama/agallery/ nanotubes/mwnt.gif


[DMIM+][Cl‐]
molecules
inserted
into
 carbon
nanotube


System
 without
 [Cl‐]
atoms


IniIal
 configuraIon
 Minimized
Energy
 state
 Melted
state


The
[Cl‐]
ion
has
not
been
depicted
for
visualizaIon
purposes.


0
 200
 400
 600
 800


Density


Density
 10
per.
Mov.
Avg.(Density)
 0
 0.2
 0.4
 0.6
 0.8
 1
 1.2
 0
 700
 1400
 2100
 2800
 3500
 4200
 4900
 5600
 6300
 7000
 7700


rmsd


rmsd
 10
per.
Mov.
Avg. (rmsd)
 0
 0.5
 1
 1.5
 2
 2.5
 3
 3.5
 4
 0
 0.078
 0.156
 0.234
 0.312
 0.39
 0.468
 0.546
 0.624
 0.702
 0.78
 0.858
 0.936
 1.014
 1.092
 1.17
 1.248
 1.326
 1.404
 1.482


rdf


rdf
 10
per.
Mov.
Avg.(rdf)


Aber
running
the
system
under
bath
condiIons
for
approximately
10ns

we
can
 extract
the
data
and
analyze
it
to
understand
the
molecular‐level
properIes
and
 characterisIcs
of
the
system.
This
informaIon
can
be
useful
to
experimentalists.


End


13


Molecular
dynamics:
Introduc-on


• MD
simula5ons
are
similar
to
real
experiments

• In
a
basic
MD
simulaIon
program:

• ‘Prepare
the
sample’:


• IniIal
energy
(or
temperature)

• Number
of
parIcles
N

• Box
size
(N/L3
=
density)

• Force
field
equaIons,
parameters

• Time
step
dt
for
integraIng
equaIons
of
moIon

• IniIalize
posiIons
and
velociIes
of
all
parIcles

• ‘Do
the
experimental
measurement’:

• Compute
forces
on
all
parIcles

• Integrate
Newton’s
equaIons
(F
=
ma)

• Update
parIcle
posiIons
and
velociIes

• Calculate
instantaneous
properIes

• Stop
aber
iteraIng
tmax
steps


Repeat
unIl
we
reach
an
 appropriate
‘simulated
Ime’