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Intercalation of Organic Molecules into
Layered Double Hydroxide (LDH):
Comparison of Simulation with Experiment
H. Zhanga,b, Z. P. Xub, G. Q. Lub and S. C. Smitha,b
a) Centre for Computational Molecular Science,
Australian Institute for Bioengineering and Nanotechnology
The University of Queensland, Qld 4072, Brisbane, Australia.
b) ARC Centre for Functional Nanomaterials,
Australian Institute for Bioengineering and Nanotechnology,
The University of Queensland, Qld 4072, Brisbane, Australia.
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Outline
• Introduction
– Hybrid system: layered double hydroxides (LDHs) +
sulfonate; LDH + siRNA; LDH + Heparin.
• Method
– MD simulations with COMPASS for hybrid organicinorganic system.
– DFT for smaller model systems.
• Selected results
LDH + sulfonate: Zhang, Xu, Lu, and Smith, J
Phys Chem C, 2008, 113, 559.
Current focus: siRNA / heparin + LDH
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Layered double hydroxides (LDH)
- Importance: heterogeneous catalysis, heat stabilizers,
molecular sieves or ion exchangers, biosensors and halogen
scavengers, drug delivery, and gene therapy.
M12x M x3 (OH)2 ( Axn n )  mH2O
Mg6Al2(OH)16CO34H2O
Space group: r3-m
Rhombohedral lattice
parameters a = 3.0460 Å, c
= 22.772 Å,  = 90,  = 90
and γ = 120
anion exchangeable: C8H17SO3-; siRNA;
heparin
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Part I LDH + siRNA System
•
Inorganic Nanoparticles as Carriers of Nucleic
Acids (DNA/RNA) into Cells
1.
The transfer of DNA / RNA into living cells, that is, transfection,
is a major technique in current biochemistry and molecular
biology. This process permits the selective introduction of
genetic material for protein synthesis as well as the selective
inhibition of protein synthesis (antisense or gene silencing).
2.
In particular, the introduction of small interfering RNA (siRNA)
into mammalian cells has become an essential tool for
analyses of gene structure, function and regulation; It is also
the conceptual basis for a medical technique called “gene
therapy” that potentially allows the treatment of a wide variety
of diseases of both genetic and acquired origin.
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LDH + siRNA (Cont.)
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1.
No matter how good and 'smart' these therapeutic siRNAs
are, efficient carriers are needed as nucleic acids alone are
not able to penetrate the cell wall. Furthermore, they need to
be protected from enzyme destruction while they are on their
way to the target cells.
2.
Besides viral, polymeric, and liposomal agents, inorganic
nanoparticles like LDH are especially suitable for this purpose
because they can be prepared and surface-functionalized in
many different ways. As a result of their small size,
nanoparticles can penetrate the cell wall as well as the blood
–brain barrier and deliver siRNA into living systems.
The transfer mechanism of
nanoparticles into a cell and into its
nucleus. I Adsorption on the cell
membrane. II Uptake by endocytosis. III–
IV Escape from endosomes and
intracellular release. V Nuclear targeting.
VI Nuclear entry and gene expression.
(Angew. Chem. Int. Ed. 2008, 47, 1382)
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Simulation Method
1. For smaller models, a general ab initio force field
(Condensed-phase Optimized Molecular Potentials for
Atomistic Simulation Studies: COMPASS) and quantum
mechanical density functional theory are used to
perform geometry optimization, to compute IR spectrum
and to calculate atomic charges.
2. For the hybrid LDH systems, the general ab initio force
field (COMPASS) is used for all the molecular dynamics
simulations (Discover in Material Studio MS 4.4).
3. For powder x-ray diffraction pattern calculations, we
have employed the REFLEX module in MS 4.4.
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Current Focus I (siRNA-LDH)
(b)
(a)
Fig. 1 Minimized structures using Discover and COMPASS forcefield.
(a) A-RNA and (b) A’-RNA. Sequence of the 21 base pair siRNA are:
Sense
5'- GCAACAGUUACUGCGACGUUU-3'
Antisense
3'- UUCGUUGUCAAUGACGCUGCA -5’
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Current Focus I (LDH-siRNA)
(a)
(b)
(b) LDH+A’-RNA
(a) LDH+A-RNA
Fig. 2 Structures for LDH/siRNA hybrid systems.
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(b)
(a)
(b) LDH+A’-RNA
(a) LDH+A-RNA
Fig. 3 Minimized structures from fix LDH layer simulations.
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(a)
(b)
(b) LDH+A’-RNA
(a) LDH+A-RNA
Fig. 4 Minimized structures for fully relaxed LDH-siRNA systems.
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Current Focus I (LDH + siRNA)
Movie 1: fixed LDH layer simulations for LDH+A-RNA
system from 500 ps MD simulations.
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(a)
(c)
Intensity
Intensity
100
100
90
90
80
Intensity
(b)
80
Intensity
100
70
100
70
90
60
90
60
(d)
Fig. 5 Calculated PXRD for the hybrid system from minimized structures.
(a) fixed LDH +80
80
50A-RNA; (b) relaxed LDH + A-RNA;
50 (c) fixed LDH + A’-RNA;
(d) relaxed LDH + A’-RNA.
70
40
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Atomic density
20
18
16
14
12
10
8
6
4
2
0
Al --- red;
O --- blue;
Cl --- cyan;
P --- green.
0
10
20
30
40
50
z-distance (angstrom)
Fig. 6 Atomic density profiles from 500 ps of fully relaxed MD simulations
for the LDH + A-RNA system at 300 K. The red line represents Al atoms in
the LDH layer, the blue line represents oxygen atoms of water, and the
cyan line represents Cl anions, and the green line represents P atoms in
siRNA.
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Part II: LDH-Heparin System
1. Motivation ------ pharmaceutical applications for drug delivery
using LDH as carriers.
------ their low toxicity compared to other nanoparticles;
------ high anion-exchange properties;
------ protective delivery carriers for drugs;
------ stability through tight binding with LDH layers;
------ enhanced drug effects;
------ enhanced cellular uptake (optimum size 100 to 200 nm);
------ improved solubility and biocompatibility of drugs;
------ controlled drug release through partial dissolution of
nano-layers in slightly acidic cellular organisms.
2. AIBN experimental work:
1) Gu, Thomas, Xu, Campbell and Lu, Chem. Mater., 2008, 20, 3715.
2) Xu, Niebert, Porazik, Walker, Cooper, Middelberg, Gray, Bartlett, Lu, J.
Control. Release., 2008 (doi:10.1016/j.jconrel.2008.05.021).
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Fig. 1 Optimized geometry for the model of heparin uronic acids
and glucosamine residues using quantum Dmol3. Population
analysis was performed after the geometry optimization (see
Table 1)
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Element
n
Hirshfeld
Mulliken
ESP
O
1
-0.3854
-0.442
-0.512
S
2
0.4014
0.650
0.811
O
3
-0.3306
-0.510
-0.552
O
4
-0.3764
-0.450
-0.535
O
5
-0.1660
-0.400
-0.301
C
6
0.0188
-0.081
-0.093
H
7
0.0211
0.235
0.167
C
8
0.0068
0.026
0.088
H
9
0.0031
0.195
0.087
O
10
-0.2789
-0.685
-0.737
H
11
0.0766
0.438
0.445
Table 1 Charge partitioning by Hirshfeld method; Mulliken atomic
charges; and ESP-fitted charges (selected atoms only for
illustration purpose).
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Fig. 2 Optimized structure for heparin molecule in the gas phase
using Smart Minimizer in Discover and COMPASS forcefield. The
convergence level is set to medium and maximum iteration
number is set to 5,000.
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(a)
(b)
Fig. 3 Optimized structures for fixed LDH layer + heparin (a) and
fully relaxed LDH + heparin (b). Amorphous Cell is employed to
construct the intercalate layer of heparin and water molecules.
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(a)
(b)
Fig. 4 Snapshots from 2 ns MD simulations for the hybrid LDHheparin system using Discover with COMPASS forcefield. (a) for
fixed LDH layer simulation; and (b) for fully relaxed simulation.
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Intensity (a.u.)
400
300
200
100
0
10
20
30
40
50
2
Fig. 5 PXRD patterns for LDH-heparin system. Solid line is the
simulated XRD pattern from fully relaxed LDH system, while
dotted line is the simulated pattern from partially relaxed LDH
system. The dashed line is the experimental result for LMWH100LDH.
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Current Focus II (LDH-Heparin)
Movie 1: fixed LDH layer simulation for LDH + heparin
system from 2 ns MD simulations.
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Part III
LDH + Sulfonate System
(a)
(b)
Fig. 1 Optimized structures for C8H17SO3- using COMPASS force field (a)
and quantum mechanical DFT (b). One angle between hydrocarbon chain
and SO3- group is highlighted, which has the most noticeable change
after intercalation into LDH.
(Zhang, Xu, Lu, and Smith, J Phys Chem C, 2008, 113, 559)
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(a)
(b)
Fig. 2 The minimized structure (a) and the final structure (b) after
500 ps MD simulations for fully relaxed LDH/sulfonate system.
During the simulations the full hybrid system is allowed to relax.
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8
8
(a)
(b)
MSD(angstrom2)
MSD(angstrom2)
7
6
5
4
3
6
4
2
2
1
0
0
50
100
150
200
250
t(ps)
0
50
100
150
200
250
t(ps)
Fig. 3 Calculated MSDs for sulfonate (a) and for water (b) from 500 ps of
fully relaxed MD simulations at 300 K. From MSD the self diffusion
coefficients of the interlayer sulfonate and water are estimated to be 2.05
 10-7 cm2/s and 3.07  10-7 cm2/s, respectively.
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Relative intensity (a.u.)
Relative intensity (a.u.)
(a)
8000
6000
4000
2000
(b)
8000
6000
4000
2000
0
0
0
10
20
30
0
40
10
20
30
40
2(degree)
2degree)
Fig. 4 Comparison of PXRD pattern for the LDH-sulfonate system. The red
line represents the calculated XRD pattern, whereas the blue line
represents the experimental XRD pattern. In (a) the calculated XRD
pattern is based on the structure from fixed LDH layer simulations, and in
(b) the calculated XRD pattern is based on the structure from the fully
relaxed simulations.
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Relative Absorbance (a.u.)
800
(a)
600
400
200
0
500
1000 1500 2000 2500 3000 3500 4000
Wavenumber (cm-1)
Relative Absorbance (a.u.)
4.4
(c)
4.2
4.0
3.8
3.6
3.4
3.2
3.0
1000
2000
3000
4000
Wavenumber (cm-1)
Fig. 5 Comparison of FTIR spectra for LDH-sulfonate hybrid. In (a)
calculated IR spectra based on the minimized structure for fixed LDH
layer simulation; In (c) the experimental FTIR spectra of Xu et al.
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Future Work
Simulations will be extended to other LDH-siRNA systems:
I siRNA-Htt#1 (21 bps double stranded siRNA):
sense 5’- GCGCCGCGAGUCGGCCCGAGG -3’
antisense 3’- GCCGCGGCGCUCAGCCGGGCU -5’
II siRNA-DCC#1 (21 bps):
sense strand 5’-GCAAUUUGCUCAUCUCUAAtt-3’
antisense strand 3’-ttCGUUAAACGAGUAGAGAUU-5’
III siRNA-DCC#2 (21 bps):
sense strand 5’-CGAUGUAUUACUUUCGAAUtt-3’
antisense strand 3’-gtGCUACAUAAUGAAAGCUUA-5’
IV siRNA-MAPK1 (21 bps):
sense 5’-GGGCUAAAGUAUAUCCAUUtt -3’
antisense 3’-ctCCCGAUUUCAUAUAGGUAA -5’
These simulations are closely related to the nano-neuro initiative
“Novel hybrid inorganic nano-particles for effective siRNA delivery to
neurons” between QBI and AIBN .
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Acknowledgement
Prof. Sean C. Smith,
CCMS/AIBN, Uni. of Queensland.
Dr. Zhipng Xu,
ARCCFN, Uni. Of Queensland.
Prof. Max Lu,
ARCCFN, Uni of Queensland.
CCMS
ARCCFN
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