Charge carrier dynamics in conducting polymer PEDOT using ab initio molecular dynamics simulations.

As conducting polymers become increasingly important in electronic devices, understanding their charge transport is essential for material and device development. Various semi-empirical approaches have been used to describe temporal charge carrier dynamics in these materials, but there have yet to be any theoretical approaches utilizing ab initio molecular dynamics. In this work, we develop a computational technique based on ab initio Car-Parrinello molecular dynamics to trace charge carrier temporal motion in archetypical conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT). Particularly, we analyze charge dynamics in a single PEDOT chain and in two coupled chains with different degrees of coupling and study the effect of temperature. In our model we first initiate a positively charged polaron (compensated by a negative counterion) at one end of the chain, and subsequently displace the counterion to the other end of the chain and trace polaron dynamics in the system by monitoring bond length alternation in the PEDOT backbone and charge density distribution. We find that at low temperature (T = 1 K) the polaron distortion gradually disappears from its initial location and reappears near the new position of the counterion. At the room temperature (T = 300 K), we find that the distortions induced by polaron, and atomic vibrations are of the same magnitude, which makes tracking the polaron distortion challenging because it is hidden behind the temperature-induced vibrations. The novel approach developed in this work can be used to study polaron mobility along and between the chains, investigate charge transport in highly doped polymers, and explore other flexible polymers, including n-doped ones.

A computational study of cellulose regeneration: Coarse-grained molecular dynamics simulations.

Understanding the microscopic mechanisms of regeneration of cellulose is prerequisite for engineering and controlling its material properties. In this paper, we performed coarse-grained Martini 3 molecular dynamics simulations of cellulose regeneration at a scale comparable to the experiments. The X-ray diffraction (XRD) curves were monitored to follow the structural changes of regenerated cellulose and trace formation of cellulose sheets and crystallites. The calculated coarse-grained morphologies of regenerated cellulose were backmapped to atomistic ones. After the backmapping we find that the regenerated coarse-grained cellulose structures calculated for both topology parameters of cellulose Iß and cellulose II/III, are transformed to cellulose II, where the calculated XRD curves exhibit the main peak at approximately 20-21 degrees, corresponding to the (110)/(020) planes of cellulose II. This result is in good quantitative agreement with the available experimental observations.

A computational study of cellulose regeneration: All-atom molecular dynamics simulations.

Processing natural cellulose requires its dissolution and regeneration. It is known that the crystallinity of regenerated cellulose does not match that of native cellulose, and the physical and mechanical properties of regenerated cellulose can vary dependent on the technique applied. In this paper, we performed all-atom molecular dynamics simulations attempting to simulate the regeneration of order in cellulose. Cellulose chains display an affinity to align with one another on the nanosecond scale; single chains quickly form clusters, and clusters then interact to form a larger unit, but the end results still lack that abundance of order. Where aggregation of cellulose chains occurs, there is some resemblance of the 1-10 surfaces found in Cellulose II, with certain indication of 110 surface formation. Concentration and simulation temperature show an increase of aggregation, yet it appears that time is the major factor in reclaiming the order of "crystalline" cellulose.

Microscopic Insight into the Structure-Processing-Property Relationships of Core-Shell Structured Dialcohol Cellulose Nanoparticles.

In the quest to develop sustainable and environmentally friendly materials, cellulose is a promising alternative to synthetic polymers. However, native cellulose, in contrast to many synthetic polymers, cannot be melt-processed with traditional techniques because, upon heating, it degrades before it melts. One way to improve the thermoplasticity of cellulose, in the form of cellulose fibers, is through chemical modification, for example, to dialcohol cellulose fibers. To better understand the importance of molecular interactions during melt processing of such modified fibers, we undertook a molecular dynamics study of dialcohol cellulose nanocrystals with different degrees of modification. We investigated the structure of the nanocrystals as well as their interactions with a neighboring nanocrystal during mechanical shearing, Our simulations showed that the stress, interfacial stiffness, hydrogen-bond network, and cellulose conformations during shearing are highly dependent on the degree of modification, water layers between the crystals, and temperature. The melt processing of dialcohol cellulose with different degrees of modification and/or water content in the samples was investigated experimentally by fiber extrusion with water used as a plasticizer. The melt processing was easier when increasing the degree of modification and/or water content in the samples, which was in agreement with the conclusions derived from the molecular modeling. The measured friction between the two crystals after the modification of native cellulose to dialcohol cellulose, in some cases, halved (compared to native cellulose) and is also reduced with increasing temperature. Our results demonstrate that molecular modeling of modified nanocellulose fibers can provide fundamental information on the structure-property relationships of these materials and thus is valuable for the development of new cellulose-based biomaterials.

The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles.

The structure and dynamics of networks formed by rod-shaped particles can be indirectly investigated by measuring the diffusion of spherical tracer particles. This method was used to characterize cellulose nanofibril (CNF) networks in both dispersed and arrested states, the results of which were compared with coarse-grained Brownian dynamics simulations. At a CNF concentration of 0.2 wt% a transition was observed where, below this concentration tracer diffusion is governed by the increasing macroscopic viscosity of the dispersion. Above 0.2 wt%, the diffusion of small particles (20-40 nm) remains viscosity controlled, while particles (100-500 nm) become trapped in the CNF network. Sedimentation of silica microparticles (1-5 µm) in CNF dispersions was also determined, showing that sedimentation of larger particles is significantly affected by the presence of CNF. At concentrations of 0.2 wt%, the sedimentation velocity of 5 µm particles was reduced by 99 % compared to pure water.

Why does solvent treatment increase the conductivity of PEDOT : PSS? Insight from molecular dynamics simulations.

Poly(3,4-ethylenedioxythiophene) : polystyrene sulfonate (PEDOT : PSS) is one of the most important conducting polymers. In its pristine form its electrical conductivity is low, but it can be enhanced by several orders of magnitude by solvent treatment, e.g. dimethyl sulfoxide (DMSO). There are various (and often conflicting) explanations of this effect suggested in the experimental literature, but its theoretical understanding based on simulation and modelling accounting for the complex realistic morphology of PEDOT : PSS is missing. Here, we report Martini coarse-grained molecular dynamics simulation for the DMSO solvent treatment of the PEDOT : PSS film. We show that during solvent treatment a part of the deprotonated PSS chains are dissolved in the electrolyte. After the solvent treatment and subsequent drying, the PEDOT-rich regions become closer to each other, with a part of the PEDOT chains penetrating into the PSS-rich regions. This leads to an efficient coupling between PEDOT-rich regions, leading to the enhancement of the conductivity. Another factor leading to the conductivity improvement is the π-π stacking enhancement resulting in more π-π stacks in the film and in the increased average size of PEDOT crystallites. Our results demonstrate that course-grained molecular dynamics simulations of a realistic system represent a powerful tool enabling theoretical understanding of important morphological features of conducting polymers, which, in turn, represents a prerequisite for materials design and improvement.

Exploiting mixed conducting polymers in organic and bioelectronic devices.

Efficient transport of both ionic and electronic charges in conjugated polymers (CPs) has enabled a wide range of novel electrochemical devices spanning applications from energy storage to bioelectronic devices. In this Perspective, we provide an overview of the fundamental physical processes which underlie the operation of mixed conducting polymer (MCP) devices. While charge injection and transport have been studied extensively in both ionic and electronic conductors, translating these principles to mixed conducting systems proves challenging due to the complex relationships among the individual materials properties. We break down the process of electrochemical (de)doping, the basic feature exploited in mixed conducting devices, into its key steps, highlighting recent advances in the study of these physical processes in the context of MCPs. Furthermore, we identify remaining challenges in further extending fundamental understanding of MCP-based device operation. Ultimately, a deeper understanding of the elementary processes governing operation in MCPs will drive the advancement in both materials design and device performance.

Tuning of the elastic modulus of a soft polythiophene through molecular doping.

Molecular doping of a polythiophene with oligoethylene glycol side chains is found to strongly modulate not only the electrical but also the mechanical properties of the polymer. An oxidation level of up to 18% results in an electrical conductivity of more than 52 S cm-1 and at the same time significantly enhances the elastic modulus from 8 to more than 200 MPa and toughness from 0.5 to 5.1 MJ m-3. These changes arise because molecular doping strongly influences the glass transition temperature Tg and the degree of π-stacking of the polymer, as indicated by both X-ray diffraction and molecular dynamics simulations. Surprisingly, a comparison of doped materials containing mono- or dianions reveals that - for a comparable oxidation level - the presence of multivalent counterions has little effect on the stiffness. Evidently, molecular doping is a powerful tool that can be used for the design of mechanically robust conducting materials, which may find use within the field of flexible and stretchable electronics.

Faradaic Pixels for Precise Hydrogen Peroxide Delivery to Control M-Type Voltage-Gated Potassium Channels.

H2 O2 plays a significant role in a range of physiological processes where it performs vital tasks in redox signaling. The sensitivity of many biological pathways to H2 O2 opens up a unique direction in the development of bioelectronics devices to control levels of reactive-oxygen species (ROS). Here a microfabricated ROS modulation device that relies on controlled faradaic reactions is presented. A concentric pixel arrangement of a peroxide-evolving cathode surrounded by an anode ring which decomposes the peroxide, resulting in localized peroxide delivery is reported. The conducting polymer (poly(3,4-ethylenedioxythiophene) (PEDOT), is exploited as the cathode. PEDOT selectively catalyzes the oxygen reduction reaction resulting in the production of hydrogen peroxide (H2 O2 ). Using electrochemical and optical assays, combined with modeling, the performance of the devices is benchmarked. The concentric pixels generate tunable gradients of peroxide and oxygen concentrations. The faradaic devices are prototyped by modulating human H2 O2 -sensitive Kv7.2/7.3 (M-type) channels expressed in a single-cell model (Xenopus laevis oocytes). The Kv7 ion channel family is responsible for regulating neuronal excitability in the heart, brain, and smooth muscles, making it an ideal platform for faradaic ROS stimulation. The results demonstrate the potential of PEDOT to act as an H2 O2 delivery system, paving the way to ROS-based organic bioelectronics.

How Long are Polymer Chains in Poly(3,4-ethylenedioxythiophene):Tosylate Films? An Insight from Molecular Dynamics Simulations.

Poly(3,4-ethylenedioxythiophene) (PEDOT) is one of the most important conductive polymers utilized in a variety of applications in organic electronics and bioelectronics and energy storage. PEDOT chains are believed to be rather short, but detailed knowledge of their length is missing because of the challenges in its experimental determination due to insolubility of PEDOT films. Here, we report a molecular dynamics (MD) study of in situ oxidative chemical polymerization and simultaneous crystallization of molecularly doped PEDOT focusing on the determination of its chain lengths at different polymerization temperatures. We find the average chain length to be 6, 7, and 11 monomers for 298, 323 and 373 K, respectively. At the same time, the length distribution is rather broad, for example, between 2 and 16 monomer units for T = 323 K. We demonstrate that the limiting factor determining the chain length is the diffusivity of the reactants (PEDOT monomers and oligomers). We also study the polymer film formation during solvent evaporation, and we find that although crystallization starts and proceeds already during the polymerization and doping phases, it mostly occurs during the evaporation phase. Finally, we believe that our results providing the oligomer chain length and polymerization and crystallization mechanisms obtained by means of MD "computational microscopy" provide an important insight into the morphology of PEDOT that cannot be obtained by other means.

Ion Diffusion through Nanocellulose Membranes: Molecular Dynamics Study.

One of the most promising applications of nanocellulose is for membranes for energy storage devices including supercapacitors, batteries, and fuel cells. Several recent studies reported the fabrication of cellulose-based membranes where ionic conductivity was confined to channels. So far, theoretical understanding of the effect of the nanoconfinement and surface charged groups on the diffusion coefficient of ions in cellulose nanochannels is missing. In the present study, we perform atomistic molecular dynamics simulations to provide this theoretical understanding and unravel mechanisms affecting the ionic diffusion in nanochannels. We demonstrate that the diffusion coefficient of ions in cellulose nanochannels is reduced in comparison to its bulk value. The change of the diffusion coefficient depends on the density of charged surface groups in nanochannels and the channel height, and it is primarily caused by the Coulomb interaction between the ions and the surface. We believe that our results reveal an important structure/property relationship in cellulose nanochannels, and they show that accounting for the dependence of the diffusion coefficient on the charge of the surface groups and channel height can be important for the Nernst-Plank-Poisson modeling of the ion conductivity in nanomembranes as well as for accurate fitting the experimental data to extract the material parameters.

PEDOT:PSS nano-particles in aqueous media: A comparative experimental and molecular dynamics study of particle size, morphology and z-potential.

PEDOT: PSS is the most widely used conducting polymer in organic and printed electronics. PEDOT: PSS films have been extensively studied to understand the morphology, ionic and electronic conductivity of the polymer. However, the polymer dispersion, which is used to cast or spin coat the films, is not well characterized and not well understood theoretically. Here, we study in detail the particle morphology, size, charge density and zeta potential (z-potential) by coarse-grained MD simulations and dynamic light scattering (DLS) measurements, for different pH levels and ionic strengths. The PEDOT:PSS particles were found to be 12 nm-19 nm in diameter and had a z-potential of -30 mV to -50 mV when pH was changed from 1.7 to 9, at an added NaCl concentration of 1 mM, as measured by DLS. These values changed significantly with changing pH and ionic strength of the solution. The charge density of PEDOT:PSS particles was also found to be dependent on pH and ionic strength. Besides, the distribution of different ions (PSS-, PEDOT+, Na+, Cl-) present in the solution is simulated to understand the particle morphology and molecular origin of z-potential in PEDOT:PSS dispersion. The trend in change of particle size, charge density and z- potential with changing pH and ionic strength are in good agreement between the simulations and experiments. Our results show that the molecular model developed in this work represents very well the PEDOT:PSS nano-particles in aqueous dispersion. With this study, we hope to provide new insight and an in-depth understanding of the morphology and z-potential evolution in PEDOT:PSS dispersion.

UV-to-IR Absorption of Molecularly p-Doped Polythiophenes with Alkyl and Oligoether Side Chains: Experiment and Interpretation Based on Density Functional Theory.

The UV-to-IR transitions in p-doped poly(3-hexylthiophene) (P3HT) with alkyl side chains and polar polythiophene with tetraethylene glycol side chains are studied experimentally by means of the absorption spectroscopy and computationally using density functional theory (DFT) and tight-binding DFT. The evolution of electronic structure is calculated as the doping level is varied, while the roles of dopant ions, chain twisting, and π-π stacking are also considered, each of these having the effect of broadening the absorption peaks while not significantly changing their positions. The calculated spectra are found to be in good agreement with experimental spectra obtained for the polymers doped with a molybdenum dithiolene complex. As in other DFT studies of doped conjugated polymers, the electronic structure and assignment of optical transitions that emerge are qualitatively different from those obtained through earlier "traditional" approaches. In particular, the two prominent bands seen for the p-doped materials are present for both polarons and bipolarons/polaron pairs. The lowest energy of these transitions is due to excitation from the valence band to a spin-resolved orbitals located in the gap between the bands. The higher-energy band is a superposition of excitation from the valence band to a spin-resolved orbitals in the gap and an excitation between bands.

Density Functional Theory Mechanistic Study on H2O2 Production Using an Organic Semiconductor Epindolidione.

Organic semiconductors have recently emerged as promising catalytic materials for oxygen reduction to hydrogen peroxide, H2O2, a chemical of great importance in industry as well as biology. While examples of organic semiconductor-mediated photocatalytic and electrocatalytic processes for H2O2 production become more numerous and improve in performance, fundamental understanding of the reaction mechanisms at play have been explored far less. The aim of the present work is to computationally test hypotheses of how selective oxygen reduction to H2O2 generally occurs on carbonyl dyes and pigments. As an example material, we consider epindolidione (EPI), an industrial pigment with demonstrated semiconductor properties, which photocatalytic activity in oxygen reduction reaction (ORR) and thereby producing hydrogen peroxide (H2O2) in low pH environment has been recently experimentally demonstrated. In this work, the ability of the reduced form of EPI, viz. EPI-2H (which was formed after a photoinduced 2e-/2H+ process), to reduce molecular triplet oxygen to peroxide and the possible mechanism of this reaction are computationally investigated using density functional theory. In the main reaction pathway, the reduction of O2 to H2O2 reaction occurs via abstraction of one of the hydrogen atoms of EPI-2H by triplet dioxygen to produce an intermediate complex consisting of the radicals of hydrogen peroxide (HOO•) and EPI-H• at the initial stage. HOO• thus released can abstract another hydrogen atom from EPI-H• to produce H2O2 and regenerates EPI; otherwise, it can enter another pathway to abstract hydrogen from a neighboring EPI-2H to form EPI-H• and H2O2. EPI, after reduction, thus plays in ORR the role of hydrogen atom transfer (HAT) agent via its OH group, similar to anthraquinone in the industrial process, while HAT from its amino hydrogen is found unfavorable.

Side Chain Redistribution as a Strategy to Boost Organic Electrochemical Transistor Performance and Stability.

A series of glycolated polythiophenes for use in organic electrochemical transistors (OECTs) is designed and synthesized, differing in the distribution of their ethylene glycol chains that are tethered to the conjugated backbone. While side chain redistribution does not have a significant impact on the optoelectronic properties of the polymers, this molecular engineering strategy strongly impacts the water uptake achieved in the polymers. By careful optimization of the water uptake in the polymer films, OECTs with unprecedented steady-state performances in terms of [µC* ] and current retentions up to 98% over 700 electrochemical switching cycles are developed.

Theoretical Rationalization of Self-Assembly of Cellulose Nanocrystals: Effect of Surface Modifications and Counterions.

The hierarchical self-assembly of cellulose nanocrystals (CNCs) is an important phenomenon occurring naturally in plant cell walls. Utilization of this assembly for advanced applications requires a fundamental theoretical understanding of interactions between the CNCs, which is still incomplete. Hence, in this work, we used molecular dynamics simulations to study the effect of surface modification on the interactions between the CNCs and the resulting bundling process. We consider two types of common surface modifications of native CNCs, sulfated CNCs (SCNCs) and TEMPO-oxidized CNCs (TCNCs), in the presence of two types of counterions, Na+ and Ca2+, in solution. We used the umbrella sampling method to calculate the potential of the mean force (PMF), and we found that the strength of interaction between the modified CNCs decreases, compared with the native CNCs. The strength of interaction for TCNCs is almost similar to that for SCNCs at the same level of surface substitution, whereas the type of counterion has a strong effect on the PMF with a higher interaction energy between the CNCs in the presence of a divalent counterion as compared to a monovalent counterion. Finally, we studied the self-assembly of CNCs into a hexagonal bundle for the native CNCs and sulfated CNCs focusing on the twist of the bundle, bound water inside the bundle, inter-CNC gap, and interaction energy between the CNCs in the bundle, and the effect of the counterions on the morphology of the bundle. The equilibrium spacing of the CNCs within the bundle is found to be consistent with the results of PMF calculations for the minimum separation distance between the respective crystal surfaces.

New Patchy Particle Model with Anisotropic Patches for Molecular Dynamics Simulations: Application to a Coarse-Grained Model of Cellulose Nanocrystal.

Self-assembly is ubiquitous in nature and underlies the formation of many complex systems from the molecular to the macroscopic scale. Kern-Frenkel-like patchy particles are powerful models to investigate this phenomenon by computational methods such as Monte Carlo or molecular dynamics simulations. However, in these models the interactions are mediated by circular patches at the particle surface, which can be hardly mapped to realistic systems, containing for instance faceted particles with rectangular surfaces. In this paper we extend the model to take into account such geometries, and we use it to build a supra coarse-grained model of the cellulose nanocrystal where the interactions are parametrized against all-atomistic molecular dynamics simulations. The formation of cholesteric ribbons and defects in cholesteric droplets of the cellulose nanocrystal are investigated and confirm experimental behavior reported in the literature. The flexibility of this new patchy particle model makes it a powerful tool to develop supra coarse-grained models of self-assembly for large space and time scales and should find a broad range of applications for self-assembly in chemical and biological systems.

Reversible Electronic Solid-Gel Switching of a Conjugated Polymer.

Conjugated polymers exhibit electrically driven volume changes when included in electrochemical devices via the exchange of ions and solvent. So far, this volumetric change is limited to 40% and 100% for reversible and irreversible systems, respectively, thus restricting potential applications of this technology. A conjugated polymer that reversibly expands by about 300% upon addressing, relative to its previous contracted state, while the first irreversible actuation can achieve values ranging from 1000-10 000%, depending on the voltage applied is reported. From experimental and theoretical studies, it is found that this large and reversible volumetric switching is due to reorganization of the polymer during swelling as it transforms between a solid-state phase and a gel, while maintaining percolation for conductivity. The polymer is utilized as an electroactive cladding to reduce the void sizes of a porous carbon filter electrode by 85%.

Why Is Pristine PEDOT Oxidized to 33%? A Density Functional Theory Study of Oxidative Polymerization Mechanism.

Currently, a theoretical understanding of thermodynamics and kinetics of the oxidative polymerization of poly(3,4-ethylenedioxythiophene) (best known as PEDOT) is missing. In the present study, step-by-step density functional theory calculations of the radical polymerization of PEDOT with tosylate counterions (PEDOT:TOS) using Fe3+(TOS-)3 as oxidant and dopant are performed. We calculate the Gibbs free energy for the conventional mechanism that consists of the polymerization of neutral PEDOT oligomers first, followed by their oxidation (doping). We also propose an alternative mechanism of polymerization, in which the already oxidized oligomers are used as reactants, leading to doped (oxidized) oligomers as products during polymerization. Our calculations indicate that the alternative mechanism is more efficient for longer PEDOT oligomers (chain length N > 6). We find that the oxidation of the EDOT monomer is the rate-limiting step for both mechanisms. Another focus of our study is the understanding of the maximum oxidation level that can be achieved during polymerization. Our calculations provide a theoretical explanation of "the magic number" of 33% for the oxidation level typically reported for the pristine (i.e., as-polymerized) materials and relate it to the change of the character of the bonds in the oligomers (aromatic to quinoid) that occurs at this oxidation level.

Computational microscopy study of the granular structure and pH dependence of PEDOT:PSS.

Computational microscopy based on Martini coarse grained molecular dynamics (MD) simulations of a doped conducting polymer poly(3,4-ethylenedioxythiophene)polystyrene sulfonate (best known as PEDOT:PSS) was performed focussing on the formation of the granular structure and PEDOT crystallites, and the effect of pH on the material morphology. The PEDOT:PSS morphology is shown to be sensitive to the initial distribution of PEDOT and PSS in the solution, and the results of the modelling suggest that the experimentally observed granular structure of PEDOT:PSS can be only obtained if the PEDOT/PSS solution is in the dispersive state in the initial crystallization stages. Variation of the pH is demonstrated to strongly affect the morphology of PEDOT:PSS films, altering their structure between granular-type and homogeneous. It also affects the size of crystallites and the relative arrangement of PEDOT and PSS chains. It is shown that the crystallites in PEDOT:PSS are smaller than those in PEDOT with molecular counterions such as PEDOT:tosylate, which is consistent with the available experimental data. The predicted changes of the PEDOT:PSS morphology with variation of the pH can be tested experimentally, and the calculated atomistic picture of PEDOT:PSS films (not accessible by conventional experimental techniques) is instrumental for understanding the material structure and building realistic models of PEDOT:PSS morphology.