Solution-Phase Conformation and Dynamics of Conjugated Isoindigo

Subscriber access provided by UNIVERSITY OF ADELAIDE LIBRARIES

Letter

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains Franklin L. Lee, Amir Barati Farimani, Kevin L. Gu, Hongping Yan, Michael F. Toney, Zhenan Bao, and Vijay S. Pande J. Phys. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/acs.jpclett.7b02360 • Publication Date (Web): 25 Oct 2017 Downloaded from http://pubs.acs.org on October 25, 2017

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry Letters is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry Letters

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains Franklin L. Lee,♣† Amir Barati Farimani,♠† Kevin L. Gu,♣ Hongping Yan,♦ Michael F. Toney,♦ Zhenan Bao,♣♠ Vijay S. Pande♠* ♣ Department of Chemical Engineering, Stanford University, Stanford, California 94305 ♠ Department of Chemistry, Stanford University, Stanford, California 94305 ♦ Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025 Corresponding Author *E-mail: [email protected].

1 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 2 of 28

Conjugated polymers are the key material in thin film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular scale understanding of conjugated polymers is important to the optimization of the thin film morphology. In this work, we examine the solution-phase behavior of conjugated isoindigobased donor-acceptor polymer single chains of various chain lengths using atomistic molecular dynamics (MD) simulations. Our simulations elucidate the transition from a rod-like to a coillike conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent with a globule-like conformation in a poor solvent. Overall, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parameterize

higher

level

models.


Page 3 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Conjugated polymers combine the unique flexibility and versatility of organic materials with electronic properties, making them amenable to semiconductor applications in field-effect transistors (FETs)1-2 and solar cells.3-5 One of the most attractive features of conjugated polymer is their ability to be processed from solution, enabling inexpensive, high-throughput scalable production. The polymers first coexist in a dilute solution and then aggregate upon solvent evaporation, resulting in a dense thin film. There exist inherent structure-property-processing relations where the processing conditions affect the thin film morphology, and that in turn affects the performance of the device. For FETs, the important structural features include polymer chain alignment and crystallization.6-7 Meanwhile, for solar cells, the degree of phase separation between donor and acceptor molecules is the key.8-10 The morphology of a polymer film is a function of many interconnected parameters such as polymer conformation and dynamics,11-12 interchain and solvent interactions,13 and concentration in solution.14-16 Many efforts have been performed to understand the morphology of organic semiconductor films from lattice model Monte Carlo simulations for general amorphous films,1718

and continuum models for polymer blends used for bulk heterojunction solar cells.19-21 These

models need to assume physical properties of the polymers in the simulated environment. Once the representative behavior of the polymer dissolved in a solution is known, these simulations can significantly shed light on the aggregation, entanglement, and self-assembly during drying.2021

To gain a deep and accurate understanding of single chain conformation and dynamics,

atomistic scale simulation and analysis of varying chain lengths is necessary. Polymers of different lengths coexist in the film due to polydispersity; single chain polymers with different lengths may adopt completely different conformation and dynamics, which in turn largely affects



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 28

the morphology.22-24 Therefore, it is important to know how the length of a polymer affects its dynamics and conformation. In this work, we systematically studied the conformational changes of single polymer chains in solution from a monomer up to a polymer of 15 units using atomistic molecular dynamics (MD) simulations. The upper chain length limit corresponds to the average molecular weight determined by gel permeation chromatography for the batch of polymer synthesized for experimental device fabrication.25 Atomistic MD simulations aid in the understanding of molecular level details that are difficult to access by experimental characterization. The polymer that we studied is poly(isoindigo-thienothiophene) with 2-octyldodecyl side chains,26 abbreviated as IITT (Figure 1). IITT is an example of a donor-acceptor copolymer used as the semiconductor in organic FETs26 or as the electron donor material in organic solar cells25,

27

that have been

found to be a promising class of polymers to replace the conventional poly(3-hexylthiophene) (P3HT). It has been shown that these polymers exhibit conformational behavior that differs from P3HT at comparable chain lengths.28-29 In addition, there were investigations on the effect of backbone fluorination of polythiophenes30 and the effect of different side chains on poly(para phenylene ethynylenes),31 which demonstrate that minor changes in the chemistry can propagate to significant changes in the chain conformation. This framework can be applied widely to donor-acceptor copolymers, especially those that are not yet well-characterized by experiment. For example, using the force field parameters derived for this polymer chain, the effect of varying the length and branching point of side chains can be systematically studied to provide a qualitative ranking for solubility in different environments. In addition, this polymer backbone contains fragments that are widely used in organic FETs and solar cells, so many parameters will not need to be recalculated for wide application. This would be more difficult for a coarse-


Page 5 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


grained simulation, where each monomer is modeled as a single bead, and atomic scale information would be lost and cannot be transferred from multiple atoms to a single bead. Knowledge of the structure and dynamics over a distribution of chain lengths provides insight into the tendency of these polymers to interact within a polymer chain and to interact with other polymer chains to form aggregates that serve as nuclei growing into crystalline or amorphous aggregates during film formation. Such chain-length dependence tests have been used to characterize critical behavior of a variety of macromolecules.32 We elucidate this chain-length dependence of the chain conformation in dilute conditions; by understanding the behavior of single chains in solution, one can then obtain optimized computational model parameters and further infer the mechanism of chain aggregation. Furthermore, we investigate the effect of the solvent environment on chain conformation.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

a

Page 6 of 28

b

C1

C61

c

d

e


Page 7 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 1. Isoindigo-thienothiophene (IITT) repeat unit represented by its chemical structure (a) and its 3D molecular conformation (b), highlighting the atoms (in black) used to patch together monomers and involved in calculation of end-to-end distances. Visualizations of the 15-unit polymer in a box of CHB molecules (c), at its full contour length prior to equilibration (d), and after equilibration in CHB solvent (e). 1. Single chain dynamics in chlorobenzene First, we investigated the conformational structure and dynamics of the IITT polymer with varying chain lengths, from the monomer to the 15-unit polymer, in chlorobenzene (CHB) solvent. To find the collective motions and the energetically stable conformers of the polymer, we used normal mode analysis (NMA) to find the lowest frequency modes. NMA empowers us to find the energetically favorable global conformations of polymers by projecting them into modes with different frequencies, assuming a simple harmonic potential. Lower frequency modes correspond to lower energy displacements and are thus more accessible in the energy landscape.33 To perform this analysis, we first removed the solvent from trajectories to create polymer trajectories. We used the ProDy package34 to find and analyze the normal modes. For each chain (N=1 to N=15), we computed the first 10 slowest modes and plotted the projected 2D conformations of each chain’s first mode (Figure 2). The first mode is interesting because it has been shown using statistical mechanics that the slowest modes are the dominant conformers in the polymer chains and are thus useful in determining the most probable global fluctuations of the polymer.33,

35

For polymers with N=6-15, a wave-like extended coil conformation is

observed, which corresponds to significant motions at monomers near the ends and centers of the chains. This shape is observed for long polymers with significant backbone rigidity, such as these conjugated polymers, where the worm-like chain model applies.36-38 As the number of units



increases from 6 to 15, the amplitude of the wave increases, demonstrating a more coil-like behavior. In contrast, for polymers with N=1-5, there are only very small motions along the chain, suggesting a rod-like behavior. Additional comparisons between these fluctuations are available in the Supporting Information (Figures S1-S3).

15 14 13 12 11 10 9 8 7 6 5 4 3

0.05

0.04

Mobility (Å2)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 28

0.03

0.02

0.01

0.00 0

1

2

3

4

5

6

7

8

9 10 11 12 13 14 15

Position along polymer chain

Figure 2. RMS fluctuations of the first normal mode (mobility) as a function of the position along the polymer chain (defined in terms of the monomer identity) for various chain lengths. The squared end-to-end distances Re2 of the polymers were measured between the end atoms of the backbone (Figure 3a), labeled as C1 of the first monomer and C61 of the last monomer (Figure 1b). Periodic boundary conditions were addressed by using unwrapped coordinates for these Rg2 =

calculations. 1 N

N

∑

The

radii

of

gyration

of

the

polymers

were

calculated

as

( ri − rmean ) 2 ,39 where rmean is the polymer’s center of mass and N is the number of

i =1


Page 9 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


atoms in the polymer (Figure 3b). These metrics are reported as Re and Rg , the root-mean-square (RMS) values outside of these figures. Calculation of these data is done using the MDTraj analysis package.40 The end-to-end distances and radii of gyration follow predictable trends, where the values increase with increasing chain length. The persistence length Lp of the polymers were calculated from their squared radii of gyration Rg2 and contour lengths Lc from the relation Rg

2

Lp3 L L 1 2 = L p Lc − L p + 2 (1 − p (1 − exp( − c ))) , and also the squared end-to-end 3 Lc Lc Lp

distance Re2 from the relation Re2 = 2 L2p (

Lc L − 1 + exp(− c )) which are applicable to the wormLp Lp

like chain model.41 The contour lengths were estimated as the number of units multiplied by 1.57 nm, the end-to-end distance of the monomer from the QM-optimized geometry. The equation fits for the coil-like polymers (N > 5) with the calculated persistence lengths of 6.7 and 5.4 nm are shown in Figures 3a and 3b respectively. The fit for all N gives the same value of Lp in both cases. The discrepancy between the two values is attributed to finite chain length effects that are not accounted for in the worm-like chain model.42-43 This persistence length falls near the experimentally

characterized

values

for

polyfluorenes44-45

and

poly(p-phenylene-cis-

benzobisoxazole),46 which have persistence lengths above 7.0 nm due to the presence of only small backbone deflections. For P3HT47-49 and other poly(3-alkylthiophenes),47-48,

50-51

the

persistence lengths fall below 3.0 nm due to greater rotational freedom and backbone deflections from the 5-membered rings. IITT’s backbone repeating unit has small deflection connections between the isoindigo and thienothiophene motifs and the slight deflection from the connections between oxindoles within the isoindigo motif (Figure 1a), so the result is consistent with this understanding. Because chains shorter than the persistence length act as rigid rods, this study



Squared end to end distance (nm2)

a

250

200

150

100

50

0 0

2

4

6

8

10

12

14

16

Chain length (monomers)

30

b Squared radius of gyration (nm2)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 28

25

20

15

10

5

0 0

2

4

6

8

10

12

14

16


Figure 3. Squared end-to-end distance (a) and squared radius of gyration (b) as a function of the chain length of the single chain in CHB solution. The points represent MD simulation data, while the solid lines represent the best fits to the worm-like chain equations.


Page 11 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


also demonstrates a clear transition from a rod-like to a coil-like conformation between the pentamer (N=5) and the hexamer (N=6). This is consistent with the observation from the first normal mode, where the collective motions along the chain are small until a similar chain length.

2. Effect of different environments To further understand the effect of solvents on the conformational behavior of conjugated polymer chains with various chain lengths, we examined the effect of different environments in addition to the good solvent CHB environment: a) the gas phase where there is no solvent present; and b) in an aqueous environment as an extreme example of poor solvent. a. Gas phase We simulate each of the polymers (from N=1 to N=15) without solvent, in a gas phase system. The radius of gyration trends as if the polymer were in a poor solvent, with a scaling exponent of 0.31 (Figure 4), close to the ideal value of 1/3.13,

52-53

Additionally, the gyration tensor is

significantly more isotropic in gas phase case than in CHB solution; an example comparison is shown in Table 1. The measured size metrics are also consistently lower in the gas phase; for example, the radius of gyration of the 15-unit polymer is 1.69 nm in the gas phase compared to 4.65 nm in CHB solution. Additionally, the rod-like behavior is not observed in the gas phase. This is because the polymer has stronger interaction with itself compared to the case where it is in a good solvent, causing it to fold into a globular structure at a sufficient chain length (Figure 5a). This agrees with prior studies that demonstrate a significant difference in twist angles for conjugated polymers between the solution phase and the gas phase,54 which would allow for the rigid conjugated polymer to form a collapsed globule.



In addition, we calculate the energy difference between the polymer in CHB solution and in the gas phase as ∆ = − − , where is the total energy of the single chain in CHB solution, is the total energy of the CHB molecules alone, and is the total energy of the single chain in the gas phase (Figure 6). For all chain lengths, the energy is favorable for the mixture (between -140 and -162 kcal/mol), which corroborates the observation of polymer extension in the CHB solution versus collapse in the gas phase.

2

Radius of gyration (nm)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 12 of 28

1

1

2

3

4

5

6

7 8 9 10


Figure 4. Radius of gyration as a function of the chain length of the single chain in the gas phase. The points represent MD simulation data, while the solid lines represent the power law fit with a scaling exponent of 0.31.


Page 13 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table 1. Components of the gyration tensor of the 15-unit polymer in various solvent environments. Environment

[nm2]

, [nm2]

, [nm2]

, [nm2]

CHB

21.60

10.83

9.82

0.89

Gas Phase

2.86

1.00

1.08

0.64

Water

12.15

5.53

5.52

0.85

a

b

Figure 5. Equilibrated 15-unit polymer chain conformation (a) in gas phase conditions. (b) in aqueous solution.



-140

Solvation energy (kcal/mol)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 14 of 28

-145

-150

-155

-160

-165 0

2

4

6

8

10

12

14

16


Figure 6. Solvation energy as a function of the chain length of the single chain in CHB solution.

b. Aqueous solution We also simulate a 15-unit polymer in aqueous conditions (Figure 5b). The polymer prefers to interact with itself rather than the surrounding water molecules, again creating a globular structure, which is expected behavior for a polymer in poor solvent,13, 52-53, 55 and was previously demonstrated using coarse-grained simulations.56-57 The collapse in poor solvents has been shown to affect the aggregation behavior of conjugated polymers, even in dilute solution.58-61 In the gas phase, the polymer has no choice but to interact with itself due to the flexibility of the alkyl side chains; thus, the two scenarios are comparable. However, despite similar qualitative behavior, the polymer in the aqueous solution shows quantitatively less collapse than in the gas phase case; its end-to-end distance (9.90 nm in water compared to 1.66 nm in the gas phase) and RMS radius of gyration (3.49 nm in water compared to 1.69 nm in the gas phase) are 14 ACS Paragon Plus Environment

Page 15 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


significantly higher. The isotropy of the gyration tensor is also significantly lower in water than in the gas phase (Table 1). Performing this comparison of the gyration tensors provides quick insight into how suitable certain solvents would be for solution processing of a polymer of interest to infer the morphology during film casting and drying. Furthermore, these simulations allow exploration of alternative solvent systems, e.g. non-chlorinated solvents, to find optimal conformations for organic electronic devices. For example, previous experimental studies demonstrate that lattice disorder is strongly correlated to FET mobility. The optimized morphology for high mobility contains interconnected aggregates to allow for efficient intramolecular and intermolecular charge transport.62 The longer extended coils in CHB and other good solvents are conducive toward forming these kinds of networks during solution processing, while the shorter rigid rods would form small aggregates but would not connect well to each other. Additionally, the collapsed globules in water and other poor solvents would be unlikely to create this type of aggregate network, instead aggregating into a larger globule. Therefore, investigation of single chain polymers conformation at molecular level will help to design FETs with higher mobility.

We have performed a chain-length dependence test to study conjugated isoindigo-based donoracceptor polymers in solution using atomistic detail MD simulation. Using analysis of the persistence length and normal mode fluctuations, we find a transition from rod-like to coil-like conformation from a pentamer to a hexamer for this IITT polymer in CHB, which is a good solvent. This result allows us to determine at which chain lengths the worm-like chain breaks down to accurately model polydisperse polymer solutions and blends using higher level models, e.g. Monte Carlo. In addition, we have quantified the effect of the chemical environment in



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 16 of 28

which the polymer exists by performing simulations in the gas phase and in aqueous conditions by calculating interaction energies and comparing the polymer size metrics across the three scenarios. In these situations, the polymer tends to interact strongly with itself, leading to a globular conformation, the degree of collapse being greater for the gas phase case than in the aqueous case and quantified by the gyration tensor and its degree of anisotropy. This study demonstrates a quick, quantitative way to determine what solvents should be used for solution processing of certain polymers. We focus on the specific example of IITT, but this framework can be applied widely to donor-acceptor copolymers to understand the chain-length and solvent environment dependences of solution-phase conformational behavior.

Computational Methods 1. Parameterization of polymer and solvent We first parameterized the IITT monomer and created a patch to create polymers with arbitrary numbers of units. The motifs present in these types of donor-acceptor polymers are often not optimized by standard force fields. Therefore, a rigorous parameterization from electronic structure calculations is necessary.63 For monomer parameterization, we used Force Field Toolkit (FFTK)64 to prepare the input structures for quantum mechanical (QM) calculations. All QM calculations were carried out in the Gaussian software.65 First, we optimized the geometry of the monomer and then computed the charges in presence of CHB to account for the solventmonomer dipole effect. For both CHB and IITT, the parameterization was performed using the CHARMM force field66 definition. We broke the molecule into three parts for the torsion scan because electronic structure calculation for an IITT monomer with 158 atoms is computationally expensive. We scanned the torsion angles with 5˚ iterations. The details of the IITT torsion scan


Page 17 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


and how we fragment the molecule into parts (Figure S4) are in Supporting Information. To create the polymer out of the parameterized monomer, we created an NTER/CTER patch between terminal backbone atoms C1 and C61 in the monomer structure (Figure 1b; see Supplementary PDB file, IITT_monomer.pdb). To optimize the charges of the patch and the surrounding atoms, we optimized the charges of a trimer and used those charges in the patch. Optimizations, charge calculations, and torsion scans were performed using MP2/6-31 G* level of theory.67-68 2. Molecular dynamics simulation We performed MD simulations using NAMD 2.669 with the parameterized CHARMM27 force field.66 Each single polymer was solvated with CHB molecules in a box of 30 nm×30 nm×30 nm using Visual Molecular Dynamics (VMD)70 (Figure 1c). The reason we selected this size for the solvation box is the large initial length of a single polymer (e.g. for 15 units, the initial length is about 27 nm; Figure 1d). Each system was ﬁrst equilibrated for 10 ns under constant temperature (300 K) and constant pressure (1 atm) conditions (NPT ensemble). After equilibration, we transferred and solvated the shortened polymers (e.g. for 15 units, the length becomes about 15.7 nm; Figure 1e) within the box. Finally, the production run was performed for 50 ns using 1.0 fs time steps and the data were collected every 50 ps. The pressure was maintained at 1 atm using the Nosé-Hoover Langevin piston method,71 and the temperature at 300 K using Langevin dynamics with a damping coefficient of 0.5 ps–1. Short-range interactions were truncated at 12 Å with a smoothing function applied after 10 Å, and long-range electrostatic forces were calculated using the particle mesh Ewald (PME) method72 with a grid density of at least 1/Å3. For the gas phase simulations, the single polymer still exists in a periodic box of the same size but without



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 18 of 28

any solvent. For aqueous simulations, the CHB molecules are replaced by water molecules in the box. This work was supported by the National Science Foundation Designing Materials to Revolutionize and Engineer our Future (NSF DMREF) Award Number 1434799. K.L.G. was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. H.Y. acknowledges support from SLAC National Accelerator Laboratory. We acknowledge the use of the parallel computing resource Blue Waters provided by the University of Illinois and the National Center for Supercomputing Applications. Additionally, we would like to thank Professor Jian Qin for helpful discussion. Supporting Information Available: Additional normal mode analysis plots; details of torsional scan for force field parameterization. (PDF) Monomer structure used for simulation (PDB) 15-unit polymer in chlorobenzene solution. (MPEG) 15-unit polymer in gas phase. (MPEG) 15-unit polymer in aqueous solution. (MPEG) Notes † Author Contributions (F.L.L., A.B.F.) These authors contributed equally to this work. V.S.P. is a consultant & SAB member of Schrodinger, LLC and Globavir, sits on the Board of


Page 19 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Directors of Apeel Inc, Freenome Inc, Omada Health, Patient Ping, Rigetti Computing, and is a General Partner at Andreessen Horowitz. (1)

Burroughes, J. H.; Jones, C. A.; Friend, R. H. New Semiconductor Device Physics in

Polymer Diodes and Transistors. Nature 1988, 335, 137-141. (2)

Sirringhaus, H.; Tessler, N.; Friend, R. H. Integrated Optoelectronic Devices Based on

Conjugated Polymers. Science 1998, 280, 1741. (3)

Coakley, K. M.; McGehee, M. D. Conjugated Polymer Photovoltaic Cells. Chem. Mater.

2004, 16, 4533-4542. (4)

Günes, S.; Neugebauer, H.; Sariciftci, N. S. Conjugated Polymer-Based Organic Solar

Cells. Chem. Rev. 2007, 107, 1324-1338. (5)

Mayer, A. C.; Scully, S. R.; Hardin, B. E.; Rowell, M. W.; McGehee, M. D. Polymer-

Based Solar Cells. Mater. Today 2007, 10, 28-33. (6)

Mei, J.; Diao, Y.; Appleton, A. L.; Fang, L.; Bao, Z. Integrated Materials Design of

Organic Semiconductors for Field-Effect Transistors. J. Am. Chem. Soc. 2013, 135, 6724-6746. (7)

Diao, Y.; Shaw, L.; Bao, Z.; Mannsfeld, S. C. B. Morphology Control Strategies for

Solution-Processed Organic Semiconductor Thin Films. Energy Environ. Sci. 2014, 7, 21452159. (8)

Collins, B. A.; Gann, E.; Guignard, L.; He, X.; McNeill, C. R.; Ade, H. Molecular

Miscibility of Polymer−Fullerene Blends. J. Phys. Chem. Lett. 2010, 1, 3160-3166.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(9)

Page 20 of 28

Brabec, C. J.; Heeney, M.; McCulloch, I.; Nelson, J. Influence of Blend Microstructure

on Bulk Heterojunction Organic Photovoltaic Performance. Chem. Soc. Rev. 2011, 40, 11851199. (10) Chen, W.; Nikiforov, M. P.; Darling, S. B. Morphology Characterization in Organic and Hybrid Solar Cells. Energy Environ. Sci. 2012, 5, 8045-8074. (11) Fauvell, T. J.; Zheng, T.; Jackson, N. E.; Ratner, M. A.; Yu, L.; Chen, L. X. Photophysical and Morphological Implications of Single-Strand Conjugated Polymer Folding in Solution. Chem. Mater. 2016, 28, 2814-2822. (12) Root, S. E.; Jackson, N. E.; Savagatrup, S.; Arya, G.; Lipomi, D. J. Modelling the Morphology and Thermomechanical Behaviour of Low-Bandgap Conjugated Polymers and Bulk Heterojunction Films. Energy Environ. Sci. 2017, 10, 558-569. (13) Flory, P. J. Principles of Polymer Chemistry; Cornell University Press: Ithaca, N.Y.; 1953. (14) Nguyen, T.-Q.; Doan, V.; Schwartz, B. J. Conjugated Polymer Aggregates in Solution: Control of Interchain Interactions. J. Chem. Phys. 1999, 110, 4068-4078. (15) Nguyen, T.-Q.; Martini, I. B.; Liu, J.; Schwartz, B. J. Controlling Interchain Interactions in Conjugated Polymers: The Effects of Chain Morphology on Exciton−Exciton Annihilation and Aggregation in MEH−PPV Films. J. Phys. Chem. B 2000, 104, 237-255. (16) Cheng, P.; Yan, C.; Li, Y.; Ma, W.; Zhan, X. Diluting Concentrated Solution: A General, Simple and Effective Approach to Enhance Efficiency of Polymer Solar Cells. Energy Environ. Sci. 2015, 8, 2357-2364.


Page 21 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(17) Frost, J. M.; Cheynis, F.; Tuladhar, S. M.; Nelson, J. Influence of Polymer-Blend Morphology on Charge Transport and Photocurrent Generation in Donor−Acceptor Polymer Blends. Nano Lett. 2006, 6, 1674-1681. (18) Mendels, D.; Tessler, N. A Comprehensive Study of the Effects of Chain Morphology on the Transport Properties of Amorphous Polymer Films. Sci. Rep. 2016, 6, 29092. (19) Maturová, K.; van Bavel, S. S.; Wienk, M. M.; Janssen, R. A. J.; Kemerink, M. Morphological Device Model for Organic Bulk Heterojunction Solar Cells. Nano Lett. 2009, 9, 3032-3037. (20) Wodo, O.; Ganapathysubramanian, B. Modeling Morphology Evolution During SolventBased Fabrication of Organic Solar Cells. Comp. Mater. Sci. 2012, 55, 113-126. (21) Wodo, O.; Ganapathysubramanian, B. How Do Evaporating Thin Films Evolve? Unravelling Phase-Separation Mechanisms During Solvent-Based Fabrication of Polymer Blends. Appl. Phys. Lett. 2014, 105, 153104. (22) Müller, C.; Wang, E.; Andersson, L. M.; Tvingstedt, K.; Zhou, Y.; Andersson, M. R.; Inganäs, O. Influence of Molecular Weight on the Performance of Organic Solar Cells Based on a Fluorene Derivative. Adv. Funct. Mater. 2010, 20, 2124-2131. (23) Liu, C.; Wang, K.; Hu, X.; Yang, Y.; Hsu, C.-H.; Zhang, W.; Xiao, S.; Gong, X.; Cao, Y. Molecular Weight Effect on the Efficiency of Polymer Solar Cells. ACS Appl. Mater. Inter. 2013, 5, 12163-12167. (24) Xiao, Z.; Sun, K.; Subbiah, J.; Qin, T.; Lu, S.; Purushothaman, B.; Jones, D. J.; Holmes, A. B.; Wong, W. W. H. Effect of Molecular Weight on the Properties and Organic Solar Cell



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 22 of 28

Device Performance of a Donor-Acceptor Conjugated Polymer. Polym. Chem. 2015, 6, 23122318. (25) Gu, K. L.; Zhou, Y.; Gu, X.; Yan, H.; Diao, Y.; Kurosawa, T.; Ganapathysubramanian, B.; Toney, M. F.; Bao, Z. Tuning Domain Size and Crystallinity in Isoindigo/PCBM Organic Solar Cells via Solution Shearing. Org. Electron. 2017, 40, 79-87. (26) Lei, T.; Cao, Y.; Zhou, X.; Peng, Y.; Bian, J.; Pei, J. Systematic Investigation of Isoindigo-Based Polymeric Field-Effect Transistors: Design Strategy and Impact of Polymer Symmetry and Backbone Curvature. Chem. Mater. 2012, 24, 1762-1770. (27) Zhou, Y.; Kurosawa, T.; Ma, W.; Guo, Y.; Fang, L.; Vandewal, K.; Diao, Y.; Wang, C.; Yan, Q.; Reinspach, J.; et al. High Performance All-Polymer Solar Cell via Polymer Side-Chain Engineering. Adv. Mater. 2014, 26, 3767-3772. (28) Adachi, T.; Brazard, J.; Ono, R. J.; Hanson, B.; Traub, M. C.; Wu, Z.-Q.; Li, Z.; Bolinger, J. C.; Ganesan, V.; Bielawski, C. W.; et al. Regioregularity and Single Polythiophene Chain Conformation. J. Phys. Chem. Lett. 2011, 2, 1400-1404. (29) Jackson, N. E.; Kohlstedt, K. L.; Savoie, B. M.; Olvera de la Cruz, M.; Schatz, G. C.; Chen, L. X.; Ratner, M. A. Conformational Order in Aggregates of Conjugated Polymers. J. Am. Chem. Soc. 2015, 137, 6254-6262. (30) Hu, Z.; Haws, R. T.; Fei, Z.; Boufflet, P.; Heeney, M.; Rossky, P. J.; Vanden Bout, D. A. Impact of Backbone Fluorination on Nanoscale Morphology and Excitonic Coupling in Polythiophenes. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 5113-5118.


Page 23 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(31) Maskey, S.; Pierce, F.; Perahia, D.; Grest, G. S. Conformational Study of a Single Molecule of Poly para Phenylene Ethynylenes in Dilute Solutions. J. Chem. Phys. 2011, 134, 244906. (32) Stone, M. T.; Heemstra, J. M.; Moore, J. S. The Chain-Length Dependence Test. Acc. Chem. Res. 2006, 39, 11-20. (33) Bahar, I.; Lezon, T. R.; Bakan, A.; Shrivastava, I. H. Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins. Chem. Rev. 2010, 110, 1463-1497. (34) Bakan, A.; Meireles, L. M.; Bahar, I. ProDy: Protein Dynamics Inferred from Theory and Experiments. Bioinformatics 2011, 27, 1575-1577. (35) Bahar, I.; Atilgan, A. R.; Demirel, M. C.; Erman, B. Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability. Phys. Rev. Lett. 1998, 80, 2733-2736. (36) Kratky, O.; Porod, G. Röntgenuntersuchung Gelöster Fadenmoleküle. Recl. Trav. Chim. Pays-Bas 1949, 68, 1106-1122. (37) Aragon, S. R.; Pecora, R. Dynamics of Wormlike Chains. Macromolecules 1985, 18, 1868-1875. (38) Kuei, B.; Gomez, E. D. Chain Conformations and Phase Behavior of Conjugated Polymers. Soft Matter 2017, 13, 49-67. (39) Grosberg, A.; Khokhlov, A. Statistical Physics of Macromolecules; American Institute of Physics: New York, N.Y.; 1994. 23 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 24 of 28

(40) McGibbon, R. T.; Beauchamp, K. A.; Schwantes, C. R.; Wang, L.-P.; Hernández, C. X.; Harrigan, M. P.; Lane, T. J.; Swails, J. M.; Pande, V. S. MDTraj: A Modern, Open Library for the Analysis of Molecular Dynamics Trajectories. bioRxiv 2014 (41) Teraoka, I. Polymer Solutions: An Introduction to Physical Properties; John Wiley & Sons, Inc: New York, N.Y.; 2002. (42) Dünweg, B.; Kremer, K. Molecular Dynamics Simulation of a Polymer Chain in Solution. J. Chem. Phys. 1993, 99, 6983-6997. (43) Seol, Y.; Li, J.; Nelson, P. C.; Perkins, T. T.; Betterton, M. D. Elasticity of Short DNA Molecules: Theory and Experiment for Contour Lengths of 0.6–7 µm. Biophys. J. 2007, 93, 4360-4373. (44) Fytas, G.; Nothofer, H. G.; Scherf, U.; Vlassopoulos, D.; Meier, G. Structure and Dynamics of Nondilute Polyfluorene Solutions. Macromolecules 2002, 35, 481-488. (45) Grell, M.; Bradley, D. D. C.; Long, X.; Chamberlain, T.; Inbasekaran, M.; Woo, E. P.; Soliman, M. Chain Geometry, Solution Aggregation and Enhanced Dichroism in the Liquidcrystalline Conjugated Polymer Poly(9,9-dioctylfluorene). Acta Polym. 1998, 49, 439-444. (46) Roitman, D. B.; Wessling, R. A.; McAlister, J. Characterization of Poly(p-phenylene-cisbenzobisoxazole) in Methanesulfonic Acid. Macromolecules 1993, 26, 5174-5184. (47) McCulloch, B.; Ho, V.; Hoarfrost, M.; Stanley, C.; Do, C.; Heller, W. T.; Segalman, R. A. Polymer Chain Shape of Poly(3-alkylthiophenes) in Solution Using Small-Angle Neutron Scattering. Macromolecules 2013, 46, 1899-1907.


Page 25 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(48) Bi, X.; Ying, Q.; Qian, R. Intrinsic Viscosity Versus Molar Mass Relationship of Poly(3hexylthiophene) in Toluene. Makromol. Chem. 1992, 193, 2905-2914. (49) Heffner, G. W.; Pearson, D. S. Molecular Characterization of Poly(3-hexylthiophene). Macromolecules 1991, 24, 6295-6299. (50) Aime, J. P.; Bargain, F.; Schott, M.; Eckhardt, H.; Miller, G. G.; Elsenbaumer, R. L. Structural Study of Doped and Undoped Polythiophene in Solution by Small-Angle Neutron Scattering. Phys. Rev. Lett. 1989, 62, 55-58. (51) Heffner, G. W.; Pearson, D. S.; Gettinger, C. L. Characterization of Poly(3octylthiophene). I: Molecular Characterization in Dilute Solution. Polym. Eng. Sci. 1995, 35, 860-867. (52) de Gennes, P.-G. Scaling Concepts in Polymer Physics; Cornell University Press: Ithaca, N.Y.; 1979. (53) Fujita, H. Polymer Solutions; Elsevier: New York, N.Y.; 1990. (54) Hohlneicher, G.; Mueller, M.; Demmer, M.; Lex, J.; Penn, J. H.; Gan, L. X.; Loesel, P. D. 1,2-Diphenylcycloalkenes: Electronic and Geometric Structures in the Gas Phase, Solution, and Solid State. J. Am. Chem. Soc. 1988, 110, 4483-4494. (55) Raos, G.; Allegra, G. Chain Collapse and Phase Separation in Poor-Solvent Polymer Solutions: A Unified Molecular Description. J. Chem. Phys. 1996, 104, 1626-1645. (56) Opps, S. B.; Polson, J. M.; Risk, N. A. Discontinuous Molecular Dynamics Simulation Study of Polymer Collapse. J. Chem. Phys. 2006, 125, 194904.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 26 of 28

(57) Polson, J. M.; Opps, S. B.; Abou Risk, N. Theoretical Study of Solvent Effects on the Coil-Globule Transition. J. Chem. Phys. 2009, 130, 244902. (58) Kumar, P.; Mehta, A.; Mahurin, S. M.; Dai, S.; Dadmun, M. D.; Sumpter, B. G.; Barnes, M. D. Formation of Oriented Nanostructures from Single Molecules of Conjugated Polymers in Microdroplets of Solution: The Role of Solvent. Macromolecules 2004, 37, 6132-6140. (59) Sumpter, B. G.; Kumar, P.; Mehta, A.; Barnes, M. D.; Shelton, W. A.; Harrison, R. J. Computational Study of the Structure, Dynamics, and Photophysical Properties of Conjugated Polymers and Oligomers under Nanoscale Confinement. J. Phys. Chem. B 2005, 109, 76717685. (60) Traiphol, R.; Charoenthai, N.; Srikhirin, T.; Kerdcharoen, T.; Osotchan, T.; Maturos, T. Chain Organization and Photophysics of Conjugated Polymer in Poor Solvents: Aggregates, Agglomerates and Collapsed Coils. Polymer 2007, 48, 813-826. (61) Ebihara, Y.; Vacha, M. Relating Conformation and Photophysics in Single MEH-PPV Chains. J. Phys. Chem. B 2008, 112, 12575-12578. (62) Noriega, R.; Rivnay, J.; Vandewal, K.; Koch, F. P. V.; Stingelin, N.; Smith, P.; Toney, M. F.; Salleo, A. A General Relationship Between Disorder, Aggregation and Charge Transport in Conjugated Polymers. Nat. Mater. 2013, 12, 1038-1044. (63) DuBay, K. H.; Hall, M. L.; Hughes, T. F.; Wu, C.; Reichman, D. R.; Friesner, R. A. Accurate Force Field Development for Modeling Conjugated Polymers. J. Chem. Theory Comput. 2012, 8, 4556-4569.


Page 27 of 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(64) Mayne, C. G.; Saam, J.; Schulten, K.; Tajkhorshid, E.; Gumbart, J. C. Rapid Parameterization of Small Molecules Using the Force Field Toolkit. J. Comput. Chem. 2013, 34, 2757-2770. (65) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian09, Revision A.02; Gaussian Inc.: Wallingford, C.T., 2009. (66) Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; MondragonRamirez, C.; Vorobyov, I.; MacKerell, A. D.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. J. Phys. Chem. B 2010, 114, 7830-7843. (67) Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46, 618-622. (68) Hariharan, P. C.; Pople, J. A. The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. Theor. Chim. Acta 1973, 28, 213-222. (69) Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD. J. Comput. Chem. 2005, 26, 1781-1802. (70) Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graph. Model. 1996, 14, 33-38. (71) Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant Pressure Molecular Dynamics Simulation: The Langevin Piston Method. J. Chem. Phys. 1995, 103, 4613-4621.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 28 of 28

(72) Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089-10092.


Solution-Phase Conformation and Dynamics of Conjugated Isoindigo

Recommend Documents