Mass spectrometry imaging of untreated wet cell membranes in solution using single-layer graphene.

We report a means by which atomic and molecular secondary ions, including cholesterol and fatty acids, can be sputtered through single-layer graphene to enable secondary ion mass spectrometry (SIMS) imaging of untreated wet cell membranes in solution at subcellular spatial resolution. We can observe the intrinsic molecular distribution of lipids, such as cholesterol, phosphoethanolamine and various fatty acids, in untreated wet cell membranes without any labeling. We show that graphene-covered cells prepared on a wet substrate with a cell culture medium reservoir are alive and that their cellular membranes do not disintegrate during SIMS imaging in an ultra-high-vacuum environment. Ab initio molecular dynamics calculations and ion dose-dependence studies suggest that sputtering through single-layer graphene occurs through a transient hole generated in the graphene layer. Cholesterol imaging shows that methyl-ß-cyclodextrin preferentially extracts cholesterol molecules from the cholesterol-enriched regions in cell membranes.

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.

Effect of Bulky Atom Substitution on Backbone Coplanarity and Electrical Properties of Cyclopentadithiophene-Based Semiconducting Polymers.

The effect of atomic substitution on the optoelectronic properties of a coplanar donor-acceptor (D-A) semiconducting polymer (SPs), prepared using cyclopentadithiophene (CDT) and 2,1,3-benzothiadiazole (BT) moieties, is investigated. By substituting a carbon atom in the BT unit with CF or C-Cl, two random D-A SPs are prepared, and their optoelectronic properties are thoroughly investigated. Density functional theory calculations demonstrate that the fluorinated polymer has a slightly smaller dihedral angle (Ï´ = 0.6°) than the pristine polymer (Ï´ = 1.9°) in its lowest-energy conformation, implying efficient charge transport through the coplanar backbone of the fluorinated polymer. However, the chlorinated polymer shows the lowest energy at a relatively larger dihedral angle (Ï´ = 139°) due to the steric hindrance induced by bulky chlorine atoms in the backbone, thereby leading to thin-film morphology, which is unfavorable for charge transport. Consequently, the fluorinated polymer yields the highest field-effect mobility (µ) of 0.57 cm2 V-1 s-1 , slightly higher than that of the pristine polymer (µ = 0.33 cm2 V-1 s-1 ), and the extended device lifetime of organic field-effect transistors over 12 d without any encapsulation layers. The results of this study provide design guidelines for air-stable D-A SPs.

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.

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( FL) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the FL dependence (i.e., FL-dependent and FL-independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the FL ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( FvdW) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

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.

Unraveling the Magnesium-Ion Intercalation Mechanism in Vanadium Pentoxide in a Wet Organic Electrolyte by Structural Determination.

Magnesium batteries have received attention as a type of post-lithium-ion battery because of their potential advantages in cost and capacity. Among the host candidates for magnesium batteries, orthorhombic α-V2O5 is one of the most studied materials, and it shows a reversible magnesium intercalation with a high capacity especially in a wet organic electrolyte. Studies by several groups during the last two decades have demonstrated that water plays some important roles in getting higher capacity. Very recently, proton intercalation was evidenced mainly using nuclear resonance spectroscopy. Nonetheless, the chemical species inserted into the host structure during the reduction reaction are still unclear (i.e., Mg(H2O)n2+, Mg(solvent, H2O)n2+, H+, H3O+, H2O, or any combination of these). To characterize the intercalated phase, the crystal structure of the magnesium-inserted phase of α-V2O5, electrochemically reduced in 0.5 M Mg(ClO4)2 + 2.0 M H2O in acetonitrile, was solved for the first time by the ab initio method using powder synchrotron X-ray diffraction data. The structure was tripled along the b-axis from that of the pristine V2O5 structure. No appreciable densities of elements were observed other than vanadium and oxygen atoms in the electron density maps, suggesting that the inserted species have very low occupancies in the three large cavity sites of the structure. Examination of the interatomic distances around the cavity sites suggested that H2O, H3O+, or solvated magnesium ions are too big for the cavities, leading us to confirm that the intercalated species are single Mg2+ ions or protons. The general formula of magnesium-inserted V2O5 is Mg0.17HxV2O5, (0.66 ≤ x ≤ 1.16). Finally, density functional theory calculations were carried out to locate the most plausible atomic sites of the magnesium and protons, enabling us to complete the structure modeling. This work provides an explicit answer to the question about Mg intercalation into α-V2O5.

RRM domain of Arabidopsis splicing factor SF1 is important for pre-mRNA splicing of a specific set of genes.

KEY MESSAGE: The RNA recognition motif of Arabidopsis splicing factor SF1 affects the alternative splicing of FLOWERING LOCUS M pre-mRNA and a heat shock transcription factor HsfA2 pre-mRNA. Splicing factor 1 (SF1) plays a crucial role in 3' splice site recognition by binding directly to the intron branch point. Although plant SF1 proteins possess an RNA recognition motif (RRM) domain that is absent in its fungal and metazoan counterparts, the role of the RRM domain in SF1 function has not been characterized. Here, we show that the RRM domain differentially affects the full function of the Arabidopsis thaliana AtSF1 protein under different experimental conditions. For example, the deletion of RRM domain influences AtSF1-mediated control of flowering time, but not the abscisic acid sensitivity response during seed germination. The alternative splicing of FLOWERING LOCUS M (FLM) pre-mRNA is involved in flowering time control. We found that the RRM domain of AtSF1 protein alters the production of alternatively spliced FLM-ß transcripts. We also found that the RRM domain affects the alternative splicing of a heat shock transcription factor HsfA2 pre-mRNA, thereby mediating the heat stress response. Taken together, our results suggest the importance of RRM domain for AtSF1-mediated alternative splicing of a subset of genes involved in the regulation of flowering and adaptation to heat stress.

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms.

KEY MESSAGE: The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice.

MAIN CONCLUSION: OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response through the modulation of three flowering-time genes ( Ehd1, Hd3a , and RFT1 ) in rice. Plant NUCLEAR FACTOR Y (NF-Y) transcription factors control numerous developmental processes by forming heterotrimeric complexes, but little is known about their roles in flowering in rice. In this study, it is shown that some subunits of OsNF-YB and OsNF-YC interact with each other, and among them, OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response of rice. Protein interaction studies showed that the physical interactions occurred between the three OsNF-YC proteins (OsNF-YC2, OsNF-YC4 and OsNF-YC6) and three OsNF-YB proteins (OsNF-YB8, OsNF-YB10 and OsNF-YB11). Repression and overexpression of the OsNF-YC2 and OsNF-YC4 genes revealed that they act as inhibitors of flowering only under long-day (LD) conditions. Overexpression of OsNF-YC6, however, promoted flowering only under LD conditions, suggesting it could function as a flowering promoter. These phenotypes correlated with the changes in the expression of three rice flowering-time genes [Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1)]. The diurnal and tissue-specific expression patterns of the subsets of OsNF-YB and OsNF-YC genes were similar to those of CCT domain encoding genes such as OsCO3, Heading date 1 (Hd1) and Ghd7. We propose that OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response by interacting directly with OsNF-YB8, OsNF-YB10 or OsNF-YB11 proteins in rice.

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.

A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana.

During initial spliceosome assembly, SF1 binds to intron branch points and interacts with U2 snRNP auxiliary factor 65 (U2AF65). Here, we present evidence indicating that AtSF1, the Arabidopsis SF1 homolog, interacts with AtU2AF65a and AtU2AF65b, the Arabidopsis U2AF65 homologs. A mutant allele of AtSF1 (At5g51300) that contains a T-DNA insertion conferred pleiotropic developmental defects, including early flowering and abnormal sensitivity to abscisic acid. An AtSF1 promoter-driven GUS reporter assay showed that AtSF1 promoter activity was temporally and spatially altered, and that full AtSF1 promoter activity required a significant proportion of the coding region. DNA chip analyses showed that only a small proportion of the transcriptome was altered by more than twofold in either direction in the AtSF1 mutant. Expression of the mRNAs of many heat shock proteins was more than fourfold higher in the mutant strain; these mRNAs were among those whose expression was increased most in the mutant strain. An RT-PCR assay revealed an altered alternative splicing pattern for heat shock transcription factor HsfA2 (At2g26150) in the mutant; this altered splicing is probably responsible for the increased expression of the target genes induced by HsfA2. Altered alternative splicing patterns were also detected for the transcripts of other genes in the mutant strain. These results suggest that AtSF1 has functional similarities to its yeast and metazoan counterparts.

Observation of molecular orbital gating.

The control of charge transport in an active electronic device depends intimately on the modulation of the internal charge density by an external node. For example, a field-effect transistor relies on the gated electrostatic modulation of the channel charge produced by changing the relative position of the conduction and valence bands with respect to the electrodes. In molecular-scale devices, a longstanding challenge has been to create a true three-terminal device that operates in this manner (that is, by modifying orbital energy). Here we report the observation of such a solid-state molecular device, in which transport current is directly modulated by an external gate voltage. Resonance-enhanced coupling to the nearest molecular orbital is revealed by electron tunnelling spectroscopy, demonstrating direct molecular orbital gating in an electronic device. Our findings demonstrate that true molecular transistors can be created, and so enhance the prospects for molecularly engineered electronic devices.

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).