Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymer

INTERDISCIPLINARY TRANSPORT PHENOMENA

Molecular Dynamics of Ions in Two Formsof an Electroactive PolymerD. A. Morton-Blake and Darren LeithSchool of Chemistry, Trinity College, Dublin, Ireland

Molecular dynamics (MD) are performed in all-atom simulations of two polymer speciesbased on polythiophene. In one case the amphiphilic polymer forms a monolayer inter-face between a vacuum and an aqueous layer containing ions. The electroactive natureof the polymer is invoked by conferring a negative charge on it to compensate for chargeimbalance in the Na+ and Cl− concentrations of the aqueous layer. The effects of hydro-static pressure and charge imbalance on the stability of the monolayer are investigated.In another simulation a polythiophene oligomer is wound into a helix where it servesas an ion channel between two aqueous regions on both sides of a phospholipid bilayermembrane.

Key words: molecular dynamics; electroactive polymer; charged monolayer; helical ionchannel

Introduction

Polythiophene chains can minimize theirsteric repulsion in one of two ways. The mostcommon one is the anti conformation1 in whichsuccessive sulfur atoms along the chain point“up” and “down,” as shown in Figure 1.

The same polymer in a helical conformationis shown in Figure 2. It is generated by twistingthe entire chain to the right of each inter-ringbond in turn, by the same torsional angle.

The backbones of these polymers are π con-jugated, and because this property confers onthem a reduced band gap compared with all-σsystems, they can undergo redox changes thatpermit them to acquire overall positive or neg-ative charge, which is located principally in thethiophene rings.

The properties of this kind of polymer arealso influenced by substituting the H atomson the “3” position of the thiophene rings byvarious groups; alkyl substitution renders thepolymer soluble in largely nonpolar solvents,

Address for correspondence: D. A. Morton-Blake, School of Chemistry,Trinity College, Dublin 2, Ireland. Voice: 353 1 8961943; fax: 353 1671826. [email protected]

whereas oxygen-containing substituents wouldfavor a protic environment. These propertieswill be exploited in the molecular dynamics(MD) investigations described here.

Part 1: Amphiphilic PolymerMonolayer

Consider the substitution of the “3” posi-tions of successive thiophene rings alternatelywith an alkyl side chain, which is here the hy-drophobic group octyl (C8H17), and with thehydrophilic chain -(CH2-O-CH2)4-CH2-OH.Because these “3” positions alternate along thebackbone, the side groups that they bear also al-ternate “up” and “down,” as shown in Figure 3.The result2 is an amphiphilic polymer with theability to form monolayers on a water surface;the hydrophilic oxanoyl chains enter the aque-ous layer, whereas the hydrophobic alkyl chainsare directed almost normal to the water sur-face into the vacuum. We previously3 appliedMD to simulate a stable, ordered film of a self-assembled stable monolayer interface of thesepolymers at a water surface.

In a quest for materials for novel nanoscaledevices, we wish to characterize the stability of

Interdisciplinary Transport Phenomena: Ann. N.Y. Acad. Sci. 1161: 105–116 (2009).doi: 10.1111/j.1749-6632.2009.04095.x C⃝ 2009 New York Academy of Sciences.

105

106 Annals of the New York Academy of Sciences

Figure 1. An anti sequence of a polythiophene chain backbone.

Figure 2. Polythiophene in a syn conformation,resulting in a helical chain. (In color in Annals online.)

the monolayer film to the application of hy-drostatic pressure and when the electroactivecharacter of the polythiophene backbone is ex-ploited by allowing it to assume an overall elec-tric charge. (The charge will be compensatedby unbalancing concentrations of the Na+ andCl− solutes in the water layer.)

Computation

The code used for the MD was DL_POLY,4

which was run with periodic boundary condi-tions (forming Ewald coulombic sums along themembrane surface) usually for 105 time steps (1time step = 0.001 ps) in a Hoover thermostatat 300 K at a series of constant pressures. Us-

Figure 3. The amphiphilic polymer poly(3-octyl3′-oxanoyl bithiophene). The red and yellow atomsare, respectively, oxygen and sulfur. (In color inAnnals online.)

ing code written for parallel processors, suchan MD run took 90 h of CPU time on a com-puter cluster of two nodes, both consisting oftwo processors. The atomistic potentials usedwere intramolecular (bond and bond angle) andnonbonding (intermolecular), which were as-signed according to the DREIDING genericformulation5—except for those involving thewater molecule, for which the SPC potentialsof Berendsen et al. were used,6 and those forthe Na+ and Cl− ions, which were described

Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 107

by the potentials of Rasaiah et al.7 The potentialparameters for the interactions between waterand the other atoms, and between the ions andother atoms, were obtained by the commonlyused geometric-mean rule. Torsional potentialsin the polythiophene main chain were assignedas described in our previous work.8

The partial atomic charges on the thiophenerings were taken from DFT calculations on neu-tral and charged oligothiophenes,9 and thoseof the oxidized polymer main chain were as-signed by distributing the additional chargeevenly over the five atoms of each thiophenering in the polymer chains. The atoms of thehydrophobic octyl side chains were assumedto have no net charges, and those on thehydrophilic oxanoyl chains were taken fromthe work of Udier-Blagovic et al.10 on modelcompounds.

Monolayer Molecular Model

The unit cell constituting the MD simulationbox contained chains of poly(3-octyl 3′-oxanoylbithiophene), whose primary structure was de-scribed in the introduction and a fragment ofwhich is illustrated in Figure 3. The structuralrepeat unit of the cell’s polymer componentconsisted of two such chains with a mutualdisplacement of half a bithiophene unit alongthe polymer backbone. In this way steric en-ergy was minimized because the side groupsof each chain corresponded with the gaps be-tween those of the adjacent one when viewedin the sense of Figure 3. The MD simulationbox was a two-dimensional unit cell in the abplane, consisting of six pairs of chains. The boxtherefore contained a total of 12 chains alongthe b axis, and 6 substituted bithiophenes alonga, making a total of 72 bithiophene units. Thepolymer constituted the interface between thevacuum and an aqueous layer, which was po-sitioned to overlay the oxanoyl side chains. Itconsisted usually of 2222 water molecules anda total of about 290 ions from the NaCl elec-trolyte, resulting in a 11% NaCl solution.

Results of Monolayer Investigation

Pressure

We have shown that application of lateralpressure, which is equivalent to compressingthe monolayer by a piston in the interfacialplane, as in a Langmuir trough, first disor-ders and then ruptures the monolayer with in-creasing pressure.3 Hydrostatic pressure, on theother hand, which we describe here, is appliedisotropically to the complete system.

Electrolyte Solutions

An optimum statistical analysis of the be-havior of the ions in the NaCl solution wouldrequire many ions to be present in the aqueouslayer. We therefore worked with a mole fractionof 11% NaCl in water, which is the maximumconcentration achievable under normal con-ditions. Using the electroactive facility of thepolymer to acquire an overall electric charge(although the electrochemical species that pro-mote this charge were not explicitly included inthe simulation), we compensated the polymercharge by removing the equality of the concen-trations of the Na+ and Cl− ions in the aque-ous layer. We must also decide on the range ofcharges to confer on the polymer and the com-pensating electrolyte solutions. An upper limitof such a range would normally be the max-imum charge that oxidized electroactive poly-mer can acquire by the transfer of electroniccharge by a redox mechanism. For heteroaro-matic ring polymers this value is that of a chainin which approximately half the rings acquirea unit electron charge.11 Because there are 144thiophene rings in our MD box and only about145 ions in all, compensating such a large poly-mer charge by unbalancing the concentrationsof the Na+ and Cl− ions would be unrealistic.Because in any case such a charge would de-stroy the monolayer, we must use much lowerdegrees of polymer oxidation or reduction. Toexamine the effect on the monolayer, we there-fore performed a series of calculations in which


Figure 4. View of the polymer monolayer on the aqueous layer along a direction parallel to the interface,which is also the direction of the polythiophene chains. The sulfur atoms (yellow) of the thiophene rings tracethe polymer backbone. (In color in Annals online.)

the Na+ and Cl− ion concentrations were un-balanced up to a maximum of 30%.

Results

Hydrostatic Pressure

Figure 4 shows the monolayer system onan 11% aqueous NaCl solution after dynam-ics periods of 100 ps at hydrostatic pressuresof from atmospheric to 1000 bar. In theseatomic plots the system is viewed along theinterface parallel to the directions of the poly-mer chains. The thiophene rings in the polymerbackbone can be identified by the yellow sulfuratoms. During the 100-ps period at 1-bar pres-sure, order is retained in the main chains ofthe polymer (though not in the side chains).The packing of the polymers had been de-fined in the initial (input) structure with ad-jacent chains displaced by half a bithiopheneunit in accordance with the structures of bulklattice poly(alkylthiophene)s12; in this way thio-phene rings in adjacent chains formed a stag-gered stacked relationship. A detailed exami-nation of the postdynamics equilibrium struc-tures at 1-bar pressure, however, showed thatthe chains had been displaced into positions inwhich the thiophene rings now showed near-eclipsed stacking. Energy was reduced by a slightup–down slipping of alternate chains along thec axis (normal to the interface).

Water molecules and Na+ and Cl− ions ap-pear in the space of the oxanoyl side chains butdo not venture into the region occupied by thepolymer backbone. At a pressure of 10 bars sev-eral polymer chains are displaced significantly“upward” (into the vacuum layer) or “down-ward” (into the aqueous layer) from their for-mer surface positions. Because the monolayer“seal” is broken, water molecules and the ionscan seep into the region that was formerly as-sociated with the interface.

Because the pressures were imposed instan-taneously at the outset of the dynamics ratherthan successively, the higher pressures of 100and 1000 bars preclude the “slipping” of thepolymer chains out of the interface region inthe manner that occurs at 10 bars. As a result,although individual thiophene rings twist out oftheir former planes normal to the interface, thehigh pressures immobilize the chains in the in-terface, sealing the region of the polymer back-bone from invasion by water molecules andions, which can reach only the region of theoxanoyl chains.

The radial distribution function (RDF) plotsin Figure 5 indicate the probabilities of findinga specified pair of atom types at various sepa-rations. Because one sulfur atom is present ineach thiophene ring in the polymer main chain,the function gSS(r) in part A of the figure candemonstrate the degree to which adjacent thio-phene rings twist around their interconnecting


Figure 5. RDFs for the atom pairs (A) S . . . S and (B) S . . . O (where O is an oxygen atom in water) atfour values of hydrostatic pressure. (In color in Annals online.)

bonds. In a polythiophene chain in which thethiophene rings are coplanar and adjacent ringsare in an anti conformation (i.e., trans in theS−C−C−S link) the smallest S . . . S separa-tion is that between S atoms in adjoining rings,which is 4.31 A. At a pressure of 1 bar Figure 5Ashows that the sharpest peak is a narrow oneat r = 4.18 A, indicating a twist from transof about 45◦ around inter-ring bonds, whichwould bring the S atoms closer. The peak heightincreases with the application of greater pres-sure, the maximum shifting to r = 4.3 A, imply-ing that the pressure induces greater uniformityon the main-chain torsions. An examination ofindividual chains showed that the torsional an-gles of successive thiophene rings alternated ina rather regular manner. From the foregoing wecan infer a result that was not obvious from theatomic plots in Figure 2, namely, that althoughhydrostatic pressure reduces the positional orderof the polymer chains their conformational orderis increased by the pressure.

In a regular planar polythiophene chain theseparation of S atoms in next-nearest-neighborrings is 7.76 A. The second narrow g(r) peak inFigure 5A is at r = 7.7 A, a distance that doesnot change significantly with pressure. How-ever, 7.7 A is also the separation of S atoms inthe near-eclipsed stacked columns of thiophenerings, and the broader RDF peaks in this regionarise from the buckling of the main-chain di-rections, which widens the range of separationof the S atoms in pairs of adjacent chains.

Figure 6. The distribution of torsional anglesS−C−C−S around the inter–thiophene ring C−Cbonds in the amphiphilic polymer at the hydrostaticpressures shown (anti, 180◦; syn, 0◦). The links arein largely gauche conformations, but there is a sub-stantial trans population (±180◦) particularly at highpressures.

The principal g(r) peak for the atom pair S . . .O in Figure 5B, where O is the oxygen atom inthe water molecules, decreases markedly withincreasing applied pressure, showing that be-cause of the denser packing of the alkanoyl sidechains at high pressures, water molecules aredenied access to the polymer backbone of thesolvent.

Figure 6 shows the distribution of torsionalangles ϕ in the polythiophene backbone. Thetraces confirm our preceding conclusionsfrom the atom plots and the RDF curves,that although the anti conformation of thebithiophene unit (trans S−C−C−S, ϕ = 180◦)is common, most of them are in equally


Figure 7. The surface of an 11% NaCl aqueous solution in which the monolayer bears a series ofnegative charges compensated by appropriate values of excess Na+ in the electrolyte. (In color in Annalsonline.)

weighted gauche conformations g+ and g− withϕ ≈ ±120◦.

Charged Polymer

We have already described that redox pro-cesses can confer overall charges on such poly-mers as polythiophene to the extent of imposinga unit charge (on average) on every two thio-phene rings along the chain. However, that con-dition would be for a bulk electrolytic mediumin which the coulombic energy is lowered by theclose approach of counterions to the chargedchain sites. We have yet to see whether theNa+ or Cl− ions could penetrate the regionof densely packed oxanoyl chains of the mono-layer sufficiently readily to access the oppositelycharged thiophene rings.

A series of monolayers were simulated inwhich the charge balance of the 290-ionNa+/Cl− ion system in the aqueous layer (con-stituting an 11% NaCl solution) was graduallydecoupled by converting the requisite num-ber of Cl− ions into Na+ ions. Distributionof the compensating negative charge evenly onthe thiophene rings produced charged polymermonolayers on NaCl solutions that had excessnegative charge varying from 1% to 30% of thetotal ion concentration.

Figure 7 shows the structure at the water–polymer interface after 50,000 time steps (50 ps)for a series of systems with the charge excesspercentage in the aqueous layer indicated. Thefigures show that the monolayer structure iswell preserved up to 14% excess but that it de-teriorates markedly at higher polymer charge.An examination of the interface region shows


Figure 8. RDF traces for atom pairs (A) S, O (where O is a water oxygen atom) and (B) S, Na+ in systemsof different excess charges. (In color in Annals online.)

that at 6% excess charge Na+ ions are attractedinto the interface region and begin to occupysites between the polymer’s stacked (negativelycharged) thiophene rings. The fact that nouncharged water molecules make it into this re-gion for the neutral polymer (at least in the timescale of the MD) and that it is observed to occuronly when there is an Na+/Cl− charge imbal-ance in the aqueous layer demonstrates the ef-fectiveness of the electric field arising from thecoulombic charge on the polymer main chainin attracting the Na+ ions and water moleculesof hydration.

Because of the short intervals characterizingMD runs, it is difficult to specify the criticalcharge excess that ruptures the monolayer. In-terfaces that have achieved stability after 105

time steps (0.1 ns) might be found to destabi-lize in laboratory intervals that are inaccessibleto MD. But it is apparent from the results pre-sented here that a polymer monolayer with nooverall charge is more stable than a chargedmonolayer. Investigations have been cited ofelectroactive polymer films that have been sub-jected to a maximum oxidation that confers aunit charge on every three rings.13 A mono-layer instability setting in (as suggested by ourresults, say) 10% charge excess implies an ex-cess of 30 Na+ in 290 ions. This requires thatthe compensating charge of −30e is distributedover the 144 thiophene rings of the polymer.On average, then, one unit negative chargewould be distributed over about five thiophenerings. This might well be possible in a polymer

film or poly(3-alkylthiophene) solution, wherewe have shown9 that counterions can accessthe charged rings and lower the electrostaticenergy by forming ion pairs with the oppo-sitely charged site on the polymer. However,in a system such as the one considered herethe acquisition of one charge per three ringswould correspond to 48 charges spread over144 thiophene rings and a charge imbalance of16.5% between the polymer and the 290 ions insolution.

Because the monolayer starts to break downat 11% charge excess, such an imbalance wouldbe fatal to the structure of the monolayer. Wehave mentioned the entry of Na+ ions and afew H2O molecules of hydration into the inter-face region for monomer/aqueous-electrolytesystems shown in Figure 7 with the Na+ con-centration exceeding that of the Cl− ions. Moredetails of this event are presented in Figure 8,which shows the RDF functions between theS atoms of the thiophene ring and the Na+

ions in part A of the figure and between Sand the water oxygen atoms in part B. Al-though the penetration of both species intothe interface region occurs, a comparison ofthe amplitude of the g(r) scale between partsA and B of the figure confirms the resultsfrom the atom plots, that the electric field ofthe charged polymer attracts the Na+ ionsmore strongly than the water atoms, the lat-ter probably arriving in the interface throughparticipation in the solvent sheaths of theNa+ ions.


Figure 9. Phospholipid dipalmitoyl-phosphatidylcholine (DPPC).

Part 2: Amphiphilic Polymer IonChannel

Molecular Model

The transport of ions across a cellular mem-brane is central to the functioning of a liv-ing cell. Recognizing the advances being madein nanoscience, we consider the possibility ofa synthetic channel that conducts ions acrossa conventional bilayer membrane consistingof the amphiphilic phospholipid zwitterion di-palmitoyl phosphatidyl choline (DPPC), whosemolecular structure is shown in Figure 9. Thepolar head group consists of a trimethylammo-nium cation, a negatively charged phosphateanion, and two hydrophobic C14 alkyl chaintails. The artificial transporter is a short lengthof a polythiophene derivative that is twisted intoa helical conformation. The resulting ratherrigid channel possesses the electroactive prop-erty of being capable of maintaining a charge ofeither sign. The DPPC phospholipid moleculeswere assembled with their alkyl chains perpen-dicular to a two-dimensional ab plane, defininga structural cell with periodic boundary con-ditions in the plane of the membrane. A “ba-sic” cell contained two DPPC molecules, whoserelative orientations were varied to minimizepacking forces, which occurred when the car-bon planes of the (four) alkyl chains were almostparallel. The structural cell was then assembledinto a 4 × 6 supercell, which contained a to-tal of 96 phospholipid molecules placed end toend to form a bilayer, leaving a gap of 0.75A between the closest hydrogen atoms in the

terminal methyl groups in the two monolay-ers. The two aqueous layers, each of depth32.3 A, consisting of 4000 water molecules di-vided equally between the layers, were sepa-rated by two lengths of phospholipid chain,each 17.93 A. If we include the tip-to-tip gapbetween the alkyl chains, the aqueous regionswere thus separated by distance of 36.5 A. Na+

and Cl− ions were then created in the aque-ous layers by replacing water molecules withions at regular separations that were consistentwith the required NaCl concentrations, whichwere around 0.015 M. Ionic imbalances couldbe created by varying the relative sodium andchloride concentrations in such a way that then(Na+):n(Cl−) ratio in one layer was preciselymatched by its inverse n(Cl−):n(Na+) ratio inthe other to preserve overall charge neutrality.

Ion Transporter Channel

We simulated a substitutional derivative ofan oligothiophene chain, which in Figure 10is shown in the planar all-anti conformation.When the entire chain to the right of the inter-ring bond labeled a is twisted by 175◦ about a,and the process repeated in turn around eachinter-ring bond to the right along the chain, atight helical conformation is generated. The ex-ternal and internal diameters of the helix are,respectively, 21.0 and 11.5 A, and the screwaxes have close to 11 thiophene rings per turn.Such helices of polythiophene and polypyrrolehave been observed in the solid phase and insolution and have been structurally character-ized.14 For the helical chain to function as anion channel it must span the 35.9-A thicknessof the membrane between the two aqueous lay-ers. For this purpose an oligothiophene chainconsisting of 94 thiophene rings was simulated.Also, the chain must be capable of hydrophilicassociation with the aqueous layers above andbelow the phospholipid membrane as well aslipophilic association with the membrane bi-layer itself. For this reason hydrogen atoms inthe thiophene “3” positions on the 11 rings ateach end of the chain are substituted by polar


Figure 10. The terminal portion of the substituted oligothiophene chain showing the polar(left) and nonpolar (right) rings.

Figure 11. The 94-ring oligothiophene helix ion channel, lateral and axial views (A) and (B). The black,white, yellow, and red atoms are, respectively, those of carbon, hydrogen, oxygen, and sulfur. (In color inAnnals online.)

hydroxyl groups, and each terminal ring in ad-dition is “capped” with a carboxylic acid group,COOH. In this way the “first” and “last” com-plete turn in the helix, both of which contactedthe aqueous electrolyte layers, were renderedhydrophilic. The remaining 72 rings of the he-lix, which were embedded in the membrane’snonpolar phospholipid tails, were made hy-drophobic by substituting in the “3” positions

with methyl groups. The resulting chain is illus-trated in Figure 11, where the atoms are iden-tified by the colors in the figure caption andFigure 12 shows the predynamics extent of thehelix channel bridging the aqueous layers onboth sides of the DPPC membrane. The singleturn of the coil in each layer has been renderedhydrophilic by the substitution of hydroxyl andcarboxylic groups, whereas the remaining coils,


Figure 12. The polythiophene helix of Figure 11embedded in a DPPC bilayer and two layers of aque-ous NaCl solution prior to the MD; (A) side and (B)axial view. (In color in Annals online.)

which are embedded in the bilayer membrane,are made hydrophobic by methyl groups.

The bridged membrane structure, relaxedby the MD, is shown in Figure 13. In part B,the phospholipid molecules have been removedto show the helix, which is still anchored tothe aqueous layers and to the membrane byits hydrophilic and hydrophobic moieties. Al-though the chain exhibits distortions comparedto Figure 11, their dynamic nature retains achannel whose diameter averages 6–7 A.

Because the aim is to study the migration ofions along the transporter channel, we placed

the ions in the two aqueous layers near eachend of the helix channel bridging the layersto avoid prohibitively long MD run times. Al-though charge neutrality was preserved by cre-ating equal numbers of Na+ and Cl− ions over-all, a charge imbalance between the aqueouslayers was sometimes created by allowing thecomposition of the ion mixture to vary at eachend of the channel.

DPPC molecules have been removed to ex-pose the oligothiophene helix bridging the twolayers. The helix channel is revealed by the yel-low sulfur atoms in the thiophene rings. Blueand green atoms show Na+ and Cl− ions, re-spectively, in the aqueous layers.

The migration of the ions was monitoredby RDF functions for which the atom pairsselected were (Na+, S) and (Cl−, S) for, as isclear from Figure 11, sulfur is a unique atomspecies to the interior of the channel. By 105

time steps (100 ps) the ions in the channel havereached a steady-state concentration and therather scattered (because of the paucity of Na+

and Cl− ions) RDF traces in Figure 14 show theprogress of the three migrating species—Na+,Cl−, and the water molecules—along the chan-nel. Not surprisingly, because the thiopheneS atom bears partial charges of +0.26e, thestrongest peaks are those for the Cl− ions, whichshow temporary halting sites (or slowdown re-gions) at roughly evenly spaced intervals of 3.6,5.2, 7.2, 8.4, and 10.2 A, whereas those for theNa+ ion are less well defined with a principalNa+–S distance of 6 A. The water molecules,although polar, do not show well-defined asso-ciations with the channel atoms.

Conclusions

The two structural modifications of polythio-phene described in this work demonstrate thewide properties of this electroactive polymer.We have shown that the amphiphilic propertiesof both 3-octyl 3′-oxanoyl and the derivatizedhelical 3-methyl polythiophene species canbe deployed to perform nanoscale activities,


Figure 13. (A) The phospholipid bilayer membrane separates the two aqueous layers(red O atoms). In (B) DPPC molecules have been removed to expose the oligothiophenehelix bridging the two layers. The helix channel is revealed by the yellow sulfur atoms in thethiophene rings. Blue and green atoms show Na+ and Cl− ions, respectively, in the aqueouslayers. (In color in Annals online.)

provided that the excess charge is less thanabout 12%. However, the stabilizing effect ofhydrostatic pressure provides hope that evena charged monolayer film may be preserved.The charged monolayer formed by the alkyl–oxanoyl polymer opens up the possibility thatthe material might be used in multilayers asa molecular membrane separating protic andnonprotic liquid layers such as water and chlo-roform, which we are currently investigating.The polymer’s ability to occlude ions from thelayers could confer novel properties on the re-sulting mono- and multilayer systems.

To our knowledge, the use of the helical poly-mer to form an ion transporter between twonanoscale aqueous electrolyte regions as de-scribed in the second part of the work has nothitherto been proposed, but a simple channel

Figure 14. RDF traces expressing the associa-tions of the three migrating species along the poly-thiophene helix channel. (In color in Annals online.)

of this kind might be a valuable for practical in-vestigations into the migration of ions, solventmolecules, and other dissolved species bridgingelectrolyte systems.


Acknowledgment

We acknowledge support from Institud umTheicneolaıcht Eolais agus Riomhfhorbairt(IITAC).

Conflicts of Interest

The authors declare no conflicts of interest.

References

1. McCullough, R.D. & P. Ewbank. 1998. Regioregular,head-to-tail coupled poly(3-alkylthiophene) and itsderivatives. In Handbook of Conducting Polymers, 2nd ed.T.A. Skotheim, R.L. Elsenbaumer & J.R. Reynolds,Eds.: 225. Marcel Dekker. New York; van Hutten,P. & G. Hadziioannou. 1998. The crystallography ofconductive polymers. In Handbook of Organic ConductiveMolecules and Polymers, Vol. 3. H.S. Nalwa, Ed.: 2. JohnWiley & Sons. Chichester.

2. Bjørnholm, T., D.R. Greve, N. Reitzel, et al. 1998.Self-assembly of regioregular, amphiphilic polythio-phenes into highly ordered π-stacked conjugatedpolymer thin films and nanocircuits. J. Amer. Chem.Soc. 120: 7643–7644; Reitzel, N., D.R. Greve, K.Kjaer, et al. 2000. Self-assembly of conjugated poly-mers at the air-water interface, structure and proper-ties of Langmuir and Langmuir-Blodgett films of am-phiphilic regioregular polythiophenes. J. Am. Chem.Soc. 122: 5788–5800.

3. Leith, D. & D.A. Morton-Blake. 2005. A moleculardynamics simulation of the structure and propertiesof a self assembled monolayer formed from an am-phiphilic polymer on a water surface. Mol. Simul. 31:987–997.

4. Smith, W. & T.R. Forester. 1996. DL_POLY_2.0: ageneral-purpose parallel molecular dynamics simu-lation package. J. Mol. Graph. 14: 136–141.

5. Mayo, S.L., B.D. Olafson & W.A. Goddard. 1990. Ageneric force field for molecular simulation. J. Chem.Phys. 94: 8897–8909.

6. Berendsen, H.J.C., J.R. Grigera & T.P. Straatsma.1987. The missing term in effective pair potentials.J. Chem. Phys. 91: 6269–6271.

7. Rasaiah, J.C., J.P. Noworyta & S. Koneshan. 2000.Structure of aqueous solutions of ions and neutral so-

lutes at infinite dilution. J. Am. Chem. Soc. 122: 11182–11193.

8. Corish, J. & D.A. Morton-Blake. 2005. The migra-tion of anions through poly(3-octylthiophene) matri-ces. Phys. Stat. Sol. (C) 2: 681–684; Corish, J. & D.A.Morton-Blake. 2005. The migration of ions throughpoly(3-octylthiophene). Synth. Met. 151: 43–48.

9. Morton-Blake, D.A. & E. Yurtsever. 2006. The entryof molecular species into the lattice of an electroactivepolymer during its dissolution. J. Mol. Liquids 124:106–113.

10. Udier-Blagovic, M., P.M. de Tirado, S.A. Pearlman& W.L. Jorgensen. 2004. Accuracy of free energies ofhydration using CM1 and CM3 atomic charges. J.Comp. Chem. 25: 1322–1332.

11. Doblhofer, K. & K. Rajeshwar. 1997. The electro-chemistry of conducting polymers. In Handbook of Con-ducting Polymers, 2nd ed. T.A. Skotheim, R.L. Elsen-baumer & T.R. Reynolds, Eds.: 531–588. MarcelDekker. New York.

12. Kawai, T., M. Nakazono, R. Sugimoto & K. Yoshino.1992. The crystal structure of poly(3-alkylthiophene)and its doping effect. Jpn. J. Appl. Phys. 61: 3400–3406.

13. Chung, T.C., J.H. Kaufman, A.J. Heeger & P. Wudl.1984. Charge storage in doped poly(thiophene): op-tical and electrochemical studies. Phys. Rev. B 30:702–710.

14. Garnier, F., G. Tourillon, J.Y. Barroud & H. Dex-pert. 1985. First evidence of crystalline structure inconducting polythiophene. J. Mat. Sci. 20: 2687–2694; Tourillon, G. & F. Garnier. 1985. Morphol-ogy and crystallographic structure of polythiopheneand derivatives. Mol. Cryst. Liq. Cryst. 118: 221–226; Yang, R., D.F. Evans, L. Christensen & W.A.Hendrickson. 1990. Scanning tunneling microscopyevidence of semicrystalline and helical conductingpolymer structures. J. Phys. Chem. 94: 6117–6122;Kiryi, N., E. Jahne, H.J. Adler, et al. 2003. One-dimensional aggregation of regioregular polyalkylth-iophenes. Nano Lett. 3: 707–712; Nilsson, K.P.R.,M.R. Andersson & O. Inganas. 2002. Conforma-tional transitions of a free amino-acid-functionalizedpolythiophene induced by different buffer systems.J. Phys. Condens. Matter 14: 10011–10020; Nilsson,K.P.R., M.R. Andersson & O. Inganas. 2003. Con-formational transitions in a free amino acid func-tionalized polythiophene. Synth. Met. 135–136: 291–292.

Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymer

Technology

Transcript of Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymer