Resistance switching of graphene by gate-controlled polarization reorientation of polyvinylidene fluoride in a field effect transistor.

Ferroelectric ß-phase crystals of a polyvinylidene fluoride (PVDF) polymer grown or deposited on a graphene channel of a field effect transistor would induce various degrees of electrostatic doping (i.e., various amounts of charge carriers) into graphene and in turn ON/OFF switching of the device, only if the electric field applied at the gate can reorient its polarization (i.e., the well-aligned F-to-H dipole moments perpendicular to the all-trans polymer backbone) around the polymer backbone. To assess the feasibility of achieving a ß-PVDF/graphene ferroelectric field effect transistor or memory device, we mimic (1) the electric-field-controlled PVDF polarization reversal (with density functional theory calculations and molecular dynamics simulations) and (2) the conductance switching of ß-PVDF/graphene by PVDF reorientations (F-, H- and FH-down) representing a cycle of gate-voltage sweep (with density functional theory combined with non-equilibrium Green's function formalism). The low energy barrier of the collective synchronous PVDF chain rotation around the backbone (0.22 eV per monomer) and the high electric field required to initiate the chain rotation (16 V nm-1) are compatible with the domain nucleation-growth theory and would support the polarization-induced resistance switching mechanism if the PVDF film is ultrathin and partially amorphous.

DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide.

Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis.

Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA.

Protamines are more arginine-rich and more basic than histones and are responsible for providing a highly compacted shape to the sperm heads in the testis. Phosphorylation and dephosphorylation are two events that occur in the late phase of spermatogenesis before the maturation of sperms. In this work, we have studied the effect of phosphorylation of protamine-like cationic peptides using all-atom molecular dynamics simulations. Through thermodynamic analyses, we found that phosphorylation reduces the binding efficiency of such cationic peptides on DNA duplexes. Peptide phosphorylation leads to a less efficient DNA condensation, due to a competition between DNA-peptide and peptide-peptide interactions. We hypothesize that the decrease of peptide bonds between DNA together with peptide self-assembly might allow an optimal re-organization of chromatin and an efficient condensation through subsequent peptide dephosphorylation. Based on the globular and compact conformations of phosphorylated peptides mediated by arginine-phosphoserine H-bonding, we furthermore postulate that phosphorylated protamines could more easily intrude into chromatin and participate to histone release through disruption of histone-histone and histone-DNA binding during spermatogenesis.

DNA-assisted assembly of cationic gold nanoparticles: Monte Carlo simulation.

DNA-assisted assembly of ligand-stabilized gold nanoparticles is studied using Monte Carlo simulations with coarse-grained models for DNA and AuNP. Their interaction in a periodic simulation box is described by a combination of electrostatic and pairwise hard core potentials. We first probe the self-assembly of AuNPs resulting in an ordered distribution on a single fixed DNA strand. Subsequently, the effective force calculated between a pair of parallel DNA in the presence of AuNPs shows the attraction between them at short distance associated to a stable equilibrium position. Finally, the osmotic pressure calculated in a compact DNA-AuNP lattice with various amounts of monovalent salt ions shows that an increasing amount of salt prevents aggregate formation.

Liquid crystal ordering of nucleic acids.

Several analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (φ). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions.

Ionic Liquid Designed for PEDOT:PSS Conductivity Enhancement.

Poly-3,4-ethylenedioxythiophene:polystyrenesulfonate (PEDOT:PSS) is a water-processable conducting polymer with promise for use in transparent flexible electrodes and thermoelectric devices, but its conductivity is not satisfactory. Its low conductivity is attributed to the formation of hydrophilic/insulating PSS outer layers encapsulating the conducting/hydrophobic p-doped PEDOT cores. Recently a significant conductivity enhancement has been achieved by adding ionic liquid (IL). It is believed that ion exchange between PEDOT:PSS and IL components helps PEDOT to decouple from PSS and to grow into large-scale conducting domains, but the exact mechanism is still under debate. Here we show through free energy calculations using density functional theory on a minimal model that the most efficient IL pairs are the least tightly bound ones with the lowest binding energies, which would lead to the most efficient ion exchange with PEDOT:PSS. This spontaneous ion exchange followed by nanophase segregation between PEDOT and PSS, with formation of a π-stacked PEDOT aggregate decorated by IL anions, is also supported by molecular dynamics performed on larger PEDOT:PSS models in solution. We also show that the most efficient IL anions would sustain the highest amount of charge carriers uniformly distributed along the PEDOT backbone to further enhance the conductivity, providing that they remain in the PEDOT domain after the ion exchange. Hence, our design principle is that the high-performance IL should induce not only an efficient ion exchange with PEDOT:PSS to improve the PEDOT morphology (to increase mobility) but also a uniform high-level p-doping of PEDOT (to enhance intrinsic conductivity). Based on this principle, a promising (electron-withdrawing, but bulky, soft, and hydrophobic) new IL pair is proposed.

Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study.

A polymeric network of 1-(4-tritylphenyl)urea (TPU) built via layer-by-layer cross-linking polymerization has been proposed to be an excellent mesh equipped with single-molecule-thick pores (i.e., cyclic poly-TPU rings), which can sieve glucose (∼0.7 nm) out of its mixture with urea for hemodialysis applications. Monte Carlo search for the lowest-energy conformation of various sizes of poly-TPU rings unravels the origin of narrow pore size distribution, which is around the sizes of dimer and trimer rings (0.3-0.8 nm). Flexible rings larger than the dimer and trimer rings, in particular tetramer rings, prefer a twisted conformation in the shape of the infinity symbol (∞, which looks like two dimer rings joined together) locked by a hydrogen bond between diphenylurea linker groups facing each other. Translocation energy profiles across these TPU rings reveal their urea-versus-glucose sieving mechanism: glucose is either too large (to enter dimers and twisted tetramers) or too perfectly fit (to exit trimers), leaving only a dimer-sized free space in the ring, whereas smaller-sized urea and water pass through these effective dimer-sized rings (bare dimers, twisted tetramers, and glucose-filled trimers) without encountering a substantial energy barrier or trap.

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC6H4)5HC60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

N-Alkylthienopyrroledione versus benzothiadiazole pulling units in push-pull copolymers used for photovoltaic applications: density functional theory study.

Low-band-gap push-pull copolymers are promising donor materials for bulk heterojunction organic solar cells. One of the best push-pull copolymers are composed of bridged dithiophene pushing units and benzothiadiazole (BT) pulling units, but BT has no proper position to accommodate alkyl side chains introduced to enhance the solubility of the resulting copolymers in organic solvents. On the other hand, N-alkylthienopyrroledione (TPD), which has an alkyl side chain attached to its pyrrole moiety, has been combined with various bridged dithiophene pushing units to give high-solubility donor polymers whose power conversion efficiencies are higher than those of the BT-based polymers especially after a morphology control. However, our well-validated time-dependent density functional theory calculation on the intrinsic (single-chain) electronic structure, which has been proved powerful to estimate the efficiency, gives a contradictory prediction that both polymers would show essentially the same efficiency. Intrigued by this, we subsequently perform density functional theory calculations on their π-stacked-pair models in a number of stacking configurations and conclude that the enhanced performance of the TPD-based polymers is ascribed to their enhanced inter-chain interaction resulting from their enhanced dipole moments in the push-pull direction. Enhanced morphological ordering (π-stacking and π-conjugation) in their solid films, which is not considered in electronic-structure calculations, would reduce the band gap (as proved by the low-energy shoulders in UV/vis absorption spectra), improve the charge transfer (as shown by the calculated transfer integral, transfer rate, and hole mobility), and enhance the power conversion efficiencies (as observed after a morphology control).

Lithium ion solvation by ethylene carbonates in lithium-ion battery electrolytes, revisited by density functional theory with the hybrid solvation model and free energy correction in solution.

Complex formation between lithium (Li(+)) ions and electrolyte molecules would affect the ionic conductivity through the electrolyte in lithium-ion batteries (LIBs). We hence revisit the solvation number of Li(+) in the most commonly used ethylene carbonate (EC) electrolyte. The solvation number n of Li(+)(EC)n in the first solvation shell of Li(+) is estimated on the basis of the free energy calculated by the density functional theory combined with a hybrid solvation model where the explicit solvation shell of Li(+) is immersed in a free volume of an implicit bulk solvent. This new hybrid solvation (implicit and explicit) model predicts the most probable solvation number (n = 4) and solvation free energy (-91.3 kcal mol(-1)) of Li(+) in a good agreement with those predicted by calculations employing simpler solvation models (either implicit or explicit). The desolvation (n = 2) of Li(0)(EC)n upon reduction near anodes is also well described with this new hybrid model.

D-A-D-type narrow-bandgap small-molecule photovoltaic donors: pre-synthesis virtual screening using density functional theory.

A new series of D-A-D-type small-molecule photovoltaic donors are designed and virtually screened before synthesis using time-dependent density functional theory calculations carefully validated against various polymeric and molecular donors. In this series of new design, benzodithiophene is kept as D to achieve the optimum highest-occupied molecular orbital energy level, while thienopyrroledione is initially chosen as A but later replaced by difluorinated benzodiathiazole or its selenide derivative to achieve the optimum band gap. The D-A-D core is end-capped by pyridone units which could not only enhance their self-assembly via hydrogen bonds but also play a role as an acceptor (A') to form an extended A'-D-A-D-A' small-molecule donor.

Dual function of a living polymerization initiator through the formation of a chain-end-protecting cluster: density functional theory calculation.

Sodium benzanilide (Na(+)BA(-)) initiators have opened a new route to living anionic polymerization of n-hexylisocyanate (HIC) with 100% yield and controlled molecular weight. The NaBA initiators not only provide initiation points for polymerization by attacking HIC monomers but also successfully prevent back-biting side reactions without any help from additives. Our hypothesis on this dual function of the NaBA initiators is that they self-assemble to form protection shields around the chain ends. Indeed, our density functional theory calculations performed under experimental conditions on the free energy of formation of (NaBA)n clusters of various sizes and conformations searched by Monte Carlo simulations show that the BA(-) moiety forms a stable complex with Na(+) in a fan-like circular-sector shape owing to its double binding sites (N(-)-C=O ↔ N=C-O(-)) and that the tightly-bound NaBA units spontaneously self-assemble to form small (NaBA)n clusters (n = 2 and 4). The growing end of the polymer chain [(BA)(HIC)n(-)], which resembles BA(-), would also assemble with n - 1 NaBA units to form an n-mer cluster. We expect that the chain end in this cluster would be more available to attack small HIC monomers coming into the cluster (leading to chain growth) rather than folding back to attack the middle of the chain (leading to cyclotrimerization to isocyanurates and depolymerization).

Active Sites of Mixed-Metal Core-Shell Oxygen Evolution Reaction Catalysts: FeO4 Sites on Ni Cores or NiN4 Sites in C Shells?

Water electrolysis for clean hydrogen production requires high-activity, high-stability, and low-cost catalysts for its particularly sluggish half-reaction, the oxygen evolution reaction (OER). Currently, the most promising of such catalysts working in alkaline conditions is a core-shell nanostructure, NiFe@NC, whose Fe-doped Ni (NiFe) nanoparticles are encapsulated and interconnected by N-doped graphitic carbon (NC) layers, but the exact OER mechanism of these catalysts is still unclear, and even the location of the OER active site, either on the core side or on the shell side, is still debated. Therefore, we herein derive a plausible active-site model for each side based on various experimental evidence and density functional theory calculations and then build OER free-energy diagrams on both sides to determine the active-site location. The core-side model is an FeO4-type (rather than NiO4-type) active site where an Fe atom sits on Ni oxide layers grown on top of the core surface during catalyst activation, whose facile dissolution provides an explanation for the activity loss of such catalysts directly exposed to the electrolyte. The shell-side model is a NiN4-type (rather than FeN4-type) active site where a Ni atom is intercalated into the porphyrin-like N4C site of the NC shell during catalyst synthesis. Their OER free-energy diagrams indicate that both sites require similar amounts of overpotentials, despite a complete shift in their potential-determining steps, i.e., the final O2 evolution from the oxophilic Fe on the core and the initial OH adsorption to the hydrophobic shell. We conclude that the major active sites are located on the core, but the NC shell not only protects the vulnerable FeO4 active sites on the core from the electrolyte but also provides independent active sites, owing to the N doping.

DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions.

Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.

Corrosion-driven droplet wetting on iron nanolayers.

The classical Evans' drop describes a drop of aqueous salt solution, placed on a bulk metal surface where it displays a corrosion pit that grows over time producing further oxide deposits from the metal dissolution. We focus here on the corrosion-induced droplet spreading using iron nanolayers whose semi-transparency allowed us to monitor both iron corrosion propagation and electrolyte droplet behavior by simple optical means. We thus observed that pits grow under the droplet and merge into a corrosion front. This front reached the triple contact line and drove a non radial spreading, until it propagated outside the immobile droplet. Such chemically-active wetting is only observed in the presence of a conductive substrate that provides strong adhesion of the iron nanofilm to the substrate. By revisiting the classic Evan's drop experiment on thick iron film, a weaker corrosion-driven droplet spreading is also identified. These results require further investigations, but they clearly open up new perspectives on substrate wetting by corrosion-like electrochemical reactions at the nanometer scale.

Protic Ionic Liquids for Intrinsically Stretchable Conductive Polymers.

Inspired by the classic hard-soft acid-base theory and intrigued by a theoretical prediction of spontaneous ion exchange between poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and hard-cation-soft-anion ionic liquid (IL), we treat PEDOT:PSS with a new IL composed of a protic (i.e., extremely hard) cation (3-methylimidazolium, p-MIM+) and an extremely soft anion (tetracyanoborate, TCB-). In fact, this protic IL (p-MIM:TCB) accomplishes the same levels of ion-exchange-mediated PEDOT-PSS separation, PEDOT-rich nanofibril formation, and electrical conductivity enhancement (∼2500 S/cm) as its aprotic counterpart (EMIM:TCB with 1-ethyl-3-methylimidazolium), the best IL used for this purpose so far. Furthermore, p-MIM:TCB significantly outperforms EMIM:TCB in terms of improving the stretchability (i.e., the highest tensile strain) of the PEDOT:PSS thin film. This enhancement is a result of the aromatic and protic cation p-MIM+, which acts as a molecular adhesive holding the exchanged ion pairs (PEDOT+:TCB----p-MIM+:PSS-) via ionic intercalation (at the surface of TCB--decorated PEDOT+ clusters) and hydrogen bonding (to PSS-), in which washing p-MIM+ out of the film degrades the stretchability while keeping the morphology. Our results offer molecular-level insight into the morphological, electrical, and mechanical properties of PEDOT:PSS and a molecular-interaction-based enhancement strategy that can be used for intrinsically stretchable conductive polymers.

Supramolecular assemblies of lipid-coated polyelectrolytes.

We reveal the existence of a general class of supramolecular assemblies made up of lipid-coated polyelectrolytes including the celebrated lipid-nucleic acid complexes. With the aid of high-resolution cryo-electron microscopy, we unveil the nanoscale internal organization of assemblies generated with a wide range of synthetic and biological polyelectrolytes, several of them being investigated in this context for the first time, namely, poly(styrene sulfonic acid), carboxylmethylcellulose, and filamentous actin. Using an original coarse-grained model representing lipid-coated polyelectrolytes as semiflexible tubes, we thoroughly explored the morphologies resulting from the self-assembly process as a function of tube lengths and rigidities; the computed structures are fully consistent with the experimental observations. In particular, we found a strong extension of the correlation range of the order parameter as the rigidity of the lipid-coated polyelectrolytes increases. Electrostatic interactions provide a stabilizing mechanism leading to finite-size equilibrium assemblies. These assemblies may constitute a generic route for interfacing polyelectrolytes to living cells to perform gene delivery, for instance.

Hard-Cation-Soft-Anion Ionic Liquids for PEDOT:PSS Treatment.

A promising conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) experiences significant conductivity enhancement when treated with proper ionic liquids (ILs). Based on the hard-soft-acid-base principle, we propose a combination of a hydrophilic hard cation A+ (instead of the commonly used 1-ethyl-3-methyl imidazolium, EMIM+) and a hydrophobic soft anion X- (such as tetracyanoborate, TCB-) as the best ILs for this purpose. Such ILs would decouple hydrophilic-but-insulating PSS- from conducting-but-hydrophobic PEDOT+ most efficiently by strong interactions with hydrophilic A+ and hydrophobic X-, respectively. Such a favorable ion exchange between PEDOT+:PSS- and A+:X- ILs would allow the growth of conducting PEDOT+ domains decorated by X-, not disturbed by PSS- or A+. Using density functional theory calculations and molecular dynamics simulations, we demonstrate that a protic cation- (aliphatic N-alkyl pyrrolidinium, in particular) combined with the hydrophobic anion TCB- indeed outperforms EMIM+ by promptly leaving hydrophobic TCB- and strongly binding to hydrophilic PSS-.

Three-dimensional structure and multistable optical switching of triple-twisted particle-like excitations in anisotropic fluids.

Control of structures in soft materials with long-range order forms the basis for applications such as displays, liquid-crystal biosensors, tunable lenses, distributed feedback lasers, muscle-like actuators and beam-steering devices. Bistable, tristable and multistable switching of well-defined structures of molecular alignment is of special interest for all of these applications. Here we describe the facile optical creation and multistable switching of localized configurations in the molecular orientation field of a chiral nematic anisotropic fluid. These localized chiro-elastic particle-like excitations--dubbed 'triple-twist torons'--are generated by vortex laser beams and embed the localized three-dimensional (3D) twist into a uniform background. Confocal polarizing microscopy and computer simulations reveal their equilibrium internal structures, manifesting both skyrmion-like and Hopf fibration features. Robust generation of torons at predetermined locations combined with both optical and electrical reversible switching can lead to new ways of multistable structuring of complex photonic architectures in soft materials.

Aluminum oxide formation at Al/La(1-x)Sr(x)MnO3 interface: a computational study for resistance random access memory applications.

Resistance random access memory (ReRAM) is emerging as a next-generation nonvolatile memory. One of the most promising materials for the ReRAM application is a composite of a reactive metal [such as aluminum (Al)] and a mixed-valance manganite [such as La(1-x)Ca(x)MnO3 (LCMO) and La(1-x)Sr(x)MnO3 (LSMO)]. One of the current hypotheses regarding the origin of the resistive switching of such systems is a voltage-controlled reversible formation of a high-resistance aluminum oxide (AlO(x)) layer at the Al/LC(S)MO interface through oxygen migration from LC(S)MO. To validate this hypothesis, quantum mechanics (density functional theory) calculations were carried out on an atomistic model of the resistive-switching phenomena at the Al/LSMO interface (the composite systems of Al/LSMO and AlO(x)/LSMO) as well as on the component materials such as Al, AlO(x), LaMnO3, LaMnO(3-delta), La(1-x)Sr(x)MnO3, and La(1-x)Sr(x)MnO(3-delta). The changes in the structure, energy, and electronic structure of these systems during the oxygen vacancy formation in LSMO, the oxygen migration through the Al/LSMO interface, and the AlO(x) formation were investigated.