md simulation of the effect of side-chain length on dynamics in the peo system andi hektor 1, alvo...
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MD simulation of the effect of side-chain MD simulation of the effect of side-chain
length on dynamics in the PEO systemlength on dynamics in the PEO system
Andi HektorAndi Hektor11, Alvo Aabloo, Alvo Aabloo22, Mattias Klintenberg, Mattias Klintenberg33 & &
Josh ThomasJosh Thomas44
1. Institute of Materials Science, Tartu University, Tähe 4, 51010 TARTU, Estonia.2. Institute of Physics, University of Tartu, Tähe 4, 51010 TARTU, Estonia.3. Condensed Matter Theory Group, Department of Physics, Uppsala University, Box 530, SE-751 21 Uppsala, Sweden.4. Materials Chemistry, Ångström Laboratory, Uppsala University, Box 538, SE-751 21 Uppsala, Sweden.
E-mail: [email protected]
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IntroductionIntroduction
Poly(ethylene oxide) (PEO): -(CHPoly(ethylene oxide) (PEO): -(CH22-CH-CH22-O)-O)nn--
Fig. 1. PEO unit – ethylene oxide (EO). Fig. 2. PEO chain (80 EO units).
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IntroductionIntroduction
Electrolyte, side-chainElectrolyte, side-chain
Fig. 3. Electrolyte (PEO+LiCl) including a single side-chain.
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IntroductionIntroduction
PEO topologyPEO topology
A long PEO backbonewith shorter side-chains
A long PEO connected by short cross-links
A 3-D polymer network
Fig. 4. Different PEO topologies.
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IntroductionIntroduction
Fig. 5. PEO backbone with a side-chain (1) and the zoomed-in linkage region (2).
12
PEO chain with a side-chain and linkage-pointPEO chain with a side-chain and linkage-point
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IntroductionIntroduction
Effects of side-chainEffects of side-chain
• Side-chains affect the dynamics of PEO
• From experiment: the biggest effect is around the 6-8 EO monomers
• Can we use MD to understand these effects?
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IntroductionIntroduction
Molecular Dynamical (MD) simulationsMolecular Dynamical (MD) simulations
• Classical Newtonian mechanics
• Potentials
2
1 2U( ,..., )
i
iN im t
r
rr r
1 internal external
internal bond angle torsion
external electrostatic long-range
U( ,..., ) ,
,N U U
U U U U
U U U
r r
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IntroductionIntroduction
MD simulation analyseMD simulation analyse
• Radial distribution function (RDF):
1 1,
1RDF( ) ( )
N N
iji j
j i
r r rN
• Mean Squared Displacement (MSD) and 3D diffusion coefficient (D):
• Average Velocity (AV):
2MSD( ) ( ) (0) ,r t r r
1D lim MSD( )
6tt
t
0
1AV
T
nnT
v
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MethodMethod
PotentialsPotentials
• The majority of the potentials we use for PEO originate from earlier work
• The torsional potential for the C-C-C-O dihedral angle in the side-chain linkage region is calculated by Quantum Mechanics (QM)
Fig. 6. The region of the calculated torsional potential.
C
C
C
O
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• QM method and basis-sets: HF/6-31G**, HF/6-31++G**
• Technical information: A total of 784 CPU hours was used on our in-house Linux PC-cluster using NWChem software
• Analytical torsion potential function:
MethodMethod
Calculation of torsion potential C-C-C-OCalculation of torsion potential C-C-C-O
3
0 2 1 21
[ cos( ) sin( )],k kk
u u k u k
ui are constants and is the torsion angle.
-3
-2
-1
0
1
2
3
0 100 200 300
Angle
Energ
y /
kcal/
mol/
Fig. 7. Fitting of the calculated data (the red squares) to a 7th order trigonometric polynom.
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MethodMethod
Fig. 8. The “unpacked” configuration with a single side-chain for MD simulation.
• 9 side-chain systems (marked as s5-s9, s11, s15, s19 and s23): a cubic periodic box (24.5 x 24.5 x 24.5 Å) containing a 186 EO-monomer PEO chain with a 5-9, 11, 15, 19, and 23 EO-monomer PEO side-chains.
• Reference system (marked as r): a cubic periodic box (24.5 x 24.5 x 24.5 Å) containing a single PEO chain involving 193 EO-monomers with no side-chain.
Simulation boxes generated by controlled pivotal Monte Carlo growth. The density maintained around 1.0 g/cm3.
MD configurationsMD configurations
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MD simulationsMD simulations
• Intramolecular force fields: rigid bonds; angle and torsional potentials
• Long-range force fields: electrostatic and Buckingham’s potentials
• Calculation: Ewald summation of long-range forces used
• Configuration: a cubic MD box (24.5 x 24.5 x 24.5 Å) with periodic boundary conditions; density maintained at ~1 g/cm3
• Simulation process: time-step 0.5 fs, temperature 290 K, starting with NVT and followed by NpT for the 1000 ps
• Technical information: a total of 3900 CPU hours used on our in-house Linux PC cluster using DLPOLY software
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ResultsResults
Animation 1. ”Unpacked” chain
Animation 2. Zoomed-in version
Animations of the MD simulationsAnimations of the MD simulations
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ResultsResults
Radial distribution function (RDF)Radial distribution function (RDF)
0.0
0.4
0.8
1.2
1.6
2.0
2 3 4 5 6 7 8 9 10
r (Å)
RD
F in
arb
itra
ry u
nit
s
Fig. 9. RDF (C-C and C-O) identical for all the systems.
C-C
C-O
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ResultsResults
Mean Square Displacement (MSD) (e.g., for r and Mean Square Displacement (MSD) (e.g., for r and s7)s7)
0
2
4
6
8
10
0 50 100 150 200 250 300 350 400 450 500
Time (ps)
MS
D (
Å2 )
Fig. 10. MSD for the carbon atoms: Cr – the reference system, Cs7 – the side-chain system s7.
Cr
Cs7
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ResultsResults
3D diffusion coefficients3D diffusion coefficients
Fig. 11. 3D diffusion coefficents for the C and O atoms. Note: the strong “immobilising” effect around 6-8 EO monomers.
0.005
0.007
0.009
0.011
0.013
0.015
0.017
0.019
0 2 4 6 8 10 12 14 16 18 20 22 24
Number of EO monomers in a side-chain
Dif
fusio
n c
oeff
icen
t (1
0-9 m
2 /s)
C
O
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ResultsResults
Diffusion coefficents for the side-chain C-atomDiffusion coefficents for the side-chain C-atom
Fig. 13. Diffusion coefficents for the side-chain C-atoms.
C
O
5
6
7
8
9
1115
19
23
0.001
0.002
0.003
0.004
0.005
0.006
0.007
0.008
4 6 8 10 12 14 16 18 20 22 24
Number of EO monomers in a side-chain
Diff
. coeffic
ent (1
0-9
m2/s
)
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0.7
0.8
0.9
1.0
1.1
0 1 2 3 4 5 6 7 8
Side-chain atom
Avera
ge v
elo
cit
y (
Å/p
s)
ResultsResults
Average velocity (AV) for O-atoms along the side-Average velocity (AV) for O-atoms along the side-chain (e.g., s7)chain (e.g., s7)
Fig. 14. AV for O-atoms along the side-chain (e.g. s7); “1” means the first from the linkage-point; “7” means the free end.
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ResultsResults
AV for O-atoms along the side-chain for different side-chains AV for O-atoms along the side-chain for different side-chains lengthslengths
Fig. 15. AV for O-atoms along the side-chain for different lengths.“1”: 1st atom“max”: end of side-chain
1.2
1.4
1.6
1.8
2.0
2.2
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Side-chain atom
Aver
age v
elocit
y (Å/
ps)
s23
s11
s8
s6
s5
s7
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ResultsResults
Averaged AV for O-atoms at different side-chain Averaged AV for O-atoms at different side-chain lengthslengths
5 6
7
8
9
11
15
1923
1.30
1.35
1.40
1.45
1.50
1.55
1.60
1.65
0 2 4 6 8 10 12 14 16 18 20 22 24 26
Number of EO monomers in the side-chain
Av
era
ge
ve
loc
ity
(Å
/ps
)
Fig. 16. Averaged AV for O-atoms at different side-chain lengths (s5-s9, s11, s15, s19 and s23).
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SummarySummary
• RDF for the reference system (r) and all the side-chain systems (s5-s9, s11, s15, s19, s23) are identical
• The addition of side-chains decreases chain mobility
• A minimum occurs in the diffusion coefficents between 6 and 9 EO side-chain units – in excellent agreement with experiment!
• A maximum occurs in the side-chain diffusion coefficents between 5 and 11 EO side-chain units
• A maximum occurs in the side-chain atoms AVs between 6 and 8 EO side-chain units
• The average AV depends the side-chain length: two maxima a appear - at 8 and 15 EO side-chain units
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ReferencesReferences
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2. A. Nishimoto, K. Agehara, N. Furuya, T. Watanabe and M. Watanabe, Macromolecules, 1999, 32, 1541.
3. W. Krawiec, L. G. Scanlon, Jr., J. P. Fellner, R. A. Vaia, S. Vasudevan and E. P. Giannelis, J. Power Sources,
1995, 54, 310.
4. S. Neyertz, D. Brown and J. O. Thomas, J. Chem. Phys., 1994, 101, 10064.
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6. A. Aabloo and J. O. Thomas, Comp. and Theor. Poly. Sci., 1997, 7, 47.
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8. A. Aabloo, M. Klintenberg and J. O. Thomas, Electrochimica Acta, 2000, 45, 1425.
9. R. J. Harrison et al, ”NWChem, A Computational Chemistry Package for Parallel Computers Version 4.0.1"
(2001), Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA
10. The DL_POLY Project, W. Smith and T. Forester, TCS Division, Daresbury Laboratory, Daresbury, Warrington
WA4 4AD, England.
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AcknowledgementsAcknowledgements
• The Nordic Energy Research Programme (NERP)
• The Swedish Natural Science Research Council (NFR, now VR)
• The Estonian Science Foundation (ETF), grant no 4513