pinecone/core-2020-05-10-deduplication huggingface dataset:
Supercapacitors Based on  c‐ Type Cytochromes Using Conductive Nanostructured Networks of Living Bacteria

Supercapacitors have attracted interest in energy storage because they have the potential to complement or replace batteries. Here, we report that  c ‐type cytochromes, naturally immersed in a living, electrically conductive microbial biofilm, greatly enhance the device capacitance by over two orders of magnitude. We employ genetic engineering, protein unfolding and Nernstian modeling for in vivo demonstration of charge storage capacity of  c ‐type cytochromes and perform electrochemical impedance spectroscopy, cyclic voltammetry and charge–discharge cycling to confirm the pseudocapacitive, redox nature of biofilm capacitance. The biofilms also show low self‐discharge and good charge/discharge reversibility. The superior electrochemical performance of the biofilm is related to its high abundance of cytochromes, providing large electron storage capacity, its nanostructured network with metallic‐like conductivity, and its porous architecture with hydrous nature, offering prospects for future low cost and environmentally sustainable energy storage devices.     Living supercapacitors:  The capacitance of an electrode‐based device can be enhanced 100‐fold using the redox chemistry of  c ‐type cytochromes naturally embedded in an electrically conductive network of living bacteria (see picture). This study demonstrates the unique survival strategy by metal‐respiring bacteria when electron acceptors are temporarily unavailable and suggests a novel method for supercapacitive energy storage using self‐renewing microbes
Label-Free Live-Cell Imaging of Nucleic Acids Using Stimulated Raman Scattering Microscopy

Imaging of nucleic acids is important for studying cellular processes such as cell division and apoptosis.  A noninvasive label-free technique is attractive.  Raman spectroscopy provides rich chemical information based on specific vibrational peaks.  However, the signal from spontaneous Raman scattering is weak and long integration times are required, which drastically limits the imaging speed when used for microscopy.  Coherent Raman scattering techniques, comprising coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microscopy, overcome this problem by enhancing the signal level by up to five orders of magnitude.  CARS microscopy suffers from a nonresonant background signal, which distorts Raman spectra and limits sensitivity.  This makes CARS imaging of weak transitions in spectrally congested regions challenging.  This is especially the case in the fingerprint region, where nucleic acids show characteristic peaks.  The recently developed SRS microscopy is free from these limitations; excitation spectra are identical to those of spontaneous Raman and sensitivity is close to shot-noise limited.  Herein we demonstrate the use of SRS imaging in the fingerprint region to map the distribution of nucleic acids in addition to proteins and lipids in single salivary gland cells of Drosophila larvae, and in single mammalian cells.  This allows the imaging of DNA condensation associated with cell division and opens up possibilities of imaging such processes in vivo.Chemistry and Chemical Biolog
Ground state and excitation spectra of a strongly correlated lattice by
  the coupled cluster method

We apply Coupled Cluster Method to a strongly correlated lattice and develop
the Spectral Coupled Cluster equations by finding an approximation to the
resolvent operator, that gives the spectral response for an certain class of
probe operators. We apply the method to a $MnO_2$ plane model with a parameters
choice which corresponds to previous experimental works and which gives a
non-nominal symmetry ground state.
  We show that this state can be observed using our Spectral Coupled Cluster
Method by probing the Coupled Cluster solution obtained from the nominal
reference state. In this case one observes a negative energy resonance which
corresponds to the true ground state
Modification of electrode surfaces by self-assembled monolayers of thiol-terminated oligo(phenyleneethynylene)s.\ud

The wire-like properties of four S-(4-{2-[4-(2-phenylethynyl)phenyl]ethynyl}phenyl) thioacetate derivatives, PhC≡CC6H4C≡CC6H4SAc (1), H2NC6H4C≡CC6H4C≡CC6H4SAc (2), PhC≡CC6H2(OMe)2C≡CC6H4SAc (3) and AcSC6H4C≡CC6H4C≡CC6H4SAc (4) (Figure 1), all of which possess a high degree of conjugation along the oligo(phenyleneethynylene) (OPE) backbone, were investigated as self-assembled monolayers (SAMs) on gold and platinum electrodes by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The redox probe [Fe(CN)6]4− was used in both the CV and impedance experiments. The results indicate that the thiolates derived from thioacetate-protected precursor molecules 1 and 2 form well-ordered monolayers on a gold electrode, whereas SAMs derived from 3 and 4 exhibit randomly distributed pinholes. The electron tunnelling resistance and fractional coverage of SAMs of all four compounds were examined using electron tunnelling theory. The analysis of the results reveal that the well-ordered SAMs of 1 and 2 exhibit higher charge-transfer resistance in comparison to the defect-ridden SAMs of 3 and 4. The additional steric bulk offered by the methoxy groups in 3 is likely to prevent efficient packing within the SAM, leading to a microelectrode behaviour, when assembled on a gold electrode surface. The protected dithiol derivative 4 probably binds to the surface through both terminal groups which prevents dense packing and leads to the formation of a monolayer with randomly distributed pinholes. Atomic force microscopy (AFM) was used to examine the morphology of the monolayers, and height images gave root-mean-square (RMS) roughness′s which are in agreement with the proposed SAM structures
Electron Transfer between Hydrogen-Bonded Pyridylphenols and a Photoexcited Rhenium(I) Complex

Two pyridylphenols with intramolecular hydrogen bonds between the phenol and pyridine units have been synthesized, characterized crystallographically, and investigated by cyclic voltammetry and UV/Vis spectroscopy. Reductive quenching of the triplet metal-to-ligand charge-transfer excited state of the [Re(CO)3(phen)(py)]+ complex (phen=1,10-phenanthroline, py=pyridine) by the two pyridylphenols and two reference phenol molecules is investigated by steady-state and time-resolved luminescence spectroscopy, as well as by transient absorption spectroscopy. Stern–Volmer analysis of the luminescence quenching data provides rate constants for the bimolecular excited-state quenching reactions. H/D kinetic isotope effects for the pyridylphenols are on the order of 2.0, and the bimolecular quenching reactions are up to 100 times faster with the pyridylphenols than with the reference phenols. This observation is attributed to the markedly less positive oxidation potentials of the pyridylphenols with respect to the reference phenols (≈0.5 V), which in turn is caused by proton coupling of the phenol oxidation process. Transient absorption spectroscopy provides unambiguous evidence for the photogeneration of phenoxyl radicals, that is, the overall photoreaction is clearly a proton-coupled electron-transfer process
Synthesis, photophysics and nonlinear optical properties of stilbenoid pyrimidine-based dyes bearing methylenepyran donor groups.

International audienceThe nonlinear properties and the photophysical behavior of two π-conjugated chromophores that incorporate an electron-deficient pyrimidine core (A) and γ-methylenepyrans as terminal donor (D) groups have been thoroughly investigated. Both dipolar and quadrupolar branching strategies are explored and rationalized on the basis of the Frenkel exciton model. Even though a cooperative effect is clearly observed if the dimensionality is increased, the nonlinear optical (NLO) response of this series is moderate if one considers the nature of the D/A couple and the size of the chromophores (as measured by the number of π electrons). This effect was attributed to a disruption in the electronic conjugation within the dyes' scaffold for which the geometry deviates from planarity owing to a noticeable twisting of the pyranylidene end-groups. This latter structural parameter also has a strong influence on the excited-state dynamics, which leads to a very efficient fluorescence quenching
Super-resolution microscopy: going live and going fast

Super-resolution microscopy is increasingly becoming an important\ud
tool for biological research, providing valuable information at the\ud
nanometer length scales inside cells and tissues. In the past decade\ud
numerous technological advancements have transformed superresolution\ud
microscopes into powerful tools of discovery. While the first\ud
super-resolution images took several hours to acquire, recent\ud
progress has led to tremendous improvement in acquisition speed,\ud
enabling researchers to probe dynamic processes in living cells with\ud
unprecedented spatiotemporal resolution. This mini-review focuses\ud
on the recent developments in live-cell super-resolution microscopy\ud
and its biological applications.Peer ReviewedPostprint (author's final draft
Spatially Selective Heteronuclear Multiple‐Quantum Coherence Spectroscopy for Biomolecular NMR Studies

Spatially selective heteronuclear multiple‐quantum coherence (SS HMQC) NMR spectroscopy is developed for solution studies of proteins. Due to “time‐staggered” acquisitioning of free induction decays (FIDs) in different slices, SS HMQC allows one to use long delays for longitudinal nuclear spin relaxation at high repetition rates. To also achieve high intrinsic sensitivity, SS HMQC is implemented by combining a single spatially selective  1 H excitation pulse with nonselective  1 H 180° pulses. High‐quality spectra were obtained within 66 s for a 7.6 kDa uniformly  13 C, 15 N‐labeled protein, and within 45 and 90 s for, respectively, two proteins with molecular weights of 7.5 and 43 kDa, which were uniformly  2 H, 13 C, 15 N‐labeled, except for having protonated methyl groups of isoleucine, leucine and valine residues.     Expect longer delays:  Spatially selective (SS) HMQC NMR spectroscopy is presented for solution studies of proteins. Using SS HMQC allows one to employ long delays for longitudinal nuclear spin relaxation at high repetition rates for acquisition of free induction decays. This technique is applied to uniformly  13 C, 15 N‐labeled and uniformly  2 H, 13 C, 15 N‐labeled (but methyl group protonated) proteins with molecular weights of 7.5 and 43 kDa
Synthesis and Electrocatalytic Properties of H2SO4-Induced (100) Pt Nanoparticles Prepared in Water-in-Oil Microemulsion

The increasing number of applications for shape-controlled metal nanoparticles (NPs) has led to the need for easy, cheap, and scalable methodologies. We report the synthesis of (100) preferentially oriented Pt NPs, with a particle size of 9 nm, by using a water-in-oil microemulsion method. The specific surface structure of the NPs is induced by the presence of H2SO4 in the water phase of the microemulsion. Interestingly, the results reported herein show how increasing amounts of H2SO4 lead to the formation of Pt NPs containing a larger amount of (100) sites on their surface. This preferential surface orientation is confirmed electrochemically by using the so-called hydrogen adsorption/desorption process. In addition, transmission electron microscopy measurements confirm the presence of cubic-like Pt NPs. Finally, the electrocatalytic properties of the Pt NPs are evaluated towards ammonia and CO electro-oxidations, which are (100) structure-sensitive reactions.This work has been financially supported by the MCINN-FEDER (Spain) (project CTQ 2010-16271), Generalitat Valenciana (project PROMETEO/2009/045) and in part by NASA-URC Grant No. NNX10AQ17A and NSF-NSEC Center for Hierarchical Manufactur-ing Grant No. CHM-CMMI-0531171. R. M-R is grateful to the Becas Iberoamérica, Santander Universidades-España 2012 and PR-LSAMP Bridge to Doctorate Fellowship programs
Interactive Chemical Reactivity Exploration

Elucidating chemical reactivity in complex molecular assemblies of a few
hundred atoms is, despite the remarkable progress in quantum chemistry, still a
major challenge. Black-box search methods to find intermediates and
transition-state structures might fail in such situations because of the
high-dimensionality of the potential energy surface. Here, we propose the
concept of interactive chemical reactivity exploration to effectively introduce
the chemist's intuition into the search process. We employ a haptic pointer
device with force-feedback to allow the operator the direct manipulation of
structures in three dimensions along with simultaneous perception of the
quantum mechanical response upon structure modification as forces. We elaborate
on the details of how such an interactive exploration should proceed and which
technical difficulties need to be overcome. All reactivity-exploration concepts
developed for this purpose have been implemented in the Samson programming
environment.Comment: 36 pages, 14 figure
From double-four-ring germanosilicates to new zeolites : in silico investigation

The authors acknowledge financial support from the Grant Agency of the Czech Republic (Center of Excellence—P106/12/G015). R.E.M. thanks the Royal Society for provision of an industry fellowship and the E.P.S.R.C. for funding (EP/K025112/1).To date, the majority of zeolites have been prepared by the solvothermal route using organic structure directing agents. Two new zeolites with structural codes PCR and OKO were recently prepared from UTL germanosilicate by removal of the double-four ring (D4R) connecting the dense two-dimensional layers [Nature Chem. 2013, 5, 628]. The corresponding experimental protocol, Assembly-Disassembly-Organization-Reassembly (ADOR), is explored in this contribution with an in silico investigation. The structure and properties of hypothetical zeolites that could be obtained from zeolites with IWW, IWV, IWR, ITR, and ITH topologies using the ADOR protocol are reported based on a computational investigation. A total of 20 new structures are presented together with their characteristics.PostprintPeer reviewe
Understanding Quantum Confinement of Charge Carriers in Layered 2D Hybrid Perovskites

International audienceLayered hybrid organic perovskites (HOPs) structures are a class of low-cost two-dimensional materials that exhibit out- standing optical properties, related to dielectric and quantum confinement effects. Whereas modeling and understanding of quantum confinement are well developed for conventional semiconductors, such knowledge is still lacking for 2D HOPs. In this work, concepts of effective mass and quantum well are carefully investigated and their applicability to 2D HOPs is dis- cussed. For ultrathin layers, the effective-mass model fails. Ab- sence of superlattice coupling and importance of non-parabo- licity effects prevents the use of simple empirical models based on effective masses and envelope function approxima- tions. An alternative method is suggested in which 2D HOPs are treated as composite materials, and a first-principles ap- proach to the calculation of band offsets is introduced. These findings might also be relevant for other classes of layered 2D functional materials
Ring currents in benzo- and benzocyclobutadieno-annelated biphenylene derivatives

The effect of benzo and benzocyclobutadieno annelation on the current density induced in a series of biphenylene deriva- tives is examined at the B3LYP/cc-pVDZ level of theory, by using the CTOCD-DZ method. Angular benzo annelation in- creases, whereas linear benzo annelation decreases the intensi- ty of paratropic (antiaromatic) current density along the four-membered ring of biphenylene. The opposite effect is found for benzocyclobutadieno annelation. It is shown that the extent of local aromaticity of the four-membered ring in biphe- nylene congeners can vary from highly antiaromatic to nonaro- matic, as a result of different modes of annelation
Billion-Fold Enhancement in Sensitivity of Nuclear Magnetic Resonance Spectroscopy for Magnesium Ions in Solution

Beta-nuclear magnetic resonance (NMR) spectroscopy is highly
sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. Beta-NMR has previously been successfully applied in the fields of nuclear and solid-state physics. In this work, beta-NMR is applied, for the first time, to record an NMR spectrum for a species in solution. 31Mg b-NMR spectra are measured for as few as 10^7 magnesium ions in ionic liquid (EMIM-Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that beta-NMR is applicable
for the analysis of species in solution, and thus represents
a novel spectroscopic technique for use in general
chemistry and potentially in biochemistry.status: publishe
A Poly(3,4-ethylenedioxypyrrole)–Au@WO3-Based Electrochromic Pseudocapacitor

A poly(3,4-ethylenedioxypyrrole)–gold nanoparticle (Au)–tungsten oxide (PEDOP–Au@WO3) electrochromic supercapacitor electrode capable of optically modulating solar energy while simultaneously storing/releasing energy (in the form of charge) was fabricated for the first time. WO3 fibers, 50 to 200 nm long and 20 to 60 nm wide, were synthesized by a hydrothermal route and were electrophoretically deposited on a conducting substrate. Au nanoparticles and PEDOP were coated over WO3 to yield the PEDOP–Au@WO3 hybrid electrode. The inclusion of Au in the hybrid was confirmed by X-ray diffraction, Raman spectroscopy, and energy-dispersive X-ray analyses. The nanoscale electronic conductivity, coloration efficiency, and transmission contrast of the hybrid were found to be significantly greater than those of pristine WO3 and PEDOP. The hybrid showed a high specific discharge capacitance of 130 F g−1 during coloration, which was four and ten times greater than the capacitance achieved in WO3 or PEDOP, respectively. We also demonstrate the ability of the PEDOP–Au@WO3 hybrid, relative to pristine PEDOP, to perform as a superior counter electrode in a solar cell, which is attributed to a higher work function. The capacitance and redox switching capability of the hybrid decreases insignificantly with cycling, thus establishing the viability of this multifunction hybrid for next-generation sustainable devices such as electrochromic psuedocapacitors because it can concurrently conserve and store energy
Fluorescence energy transfer enhancement in aluminum nanoapertures

Zero-mode waveguides (ZMWs) are confining light into attoliter volumes,
enabling single molecule fluorescence experiments at physiological micromolar
concentrations. Among the fluorescence spectroscopy techniques that can be
enhanced by ZMWs, F\"{o}rster resonance energy transfer (FRET) is one of the
most widely used in life sciences. Combining zero-mode waveguides with FRET
provides new opportunities to investigate biochemical structures or follow
interaction dynamics at micromolar concentration with single molecule
resolution. However, prior to any quantitative FRET analysis on biological
samples, it is crucial to establish first the influence of the ZMW on the FRET
process. Here, we quantify the FRET rates and efficiencies between individual
donor-acceptor fluorophore pairs diffusing in aluminum zero-mode waveguides.
Aluminum ZMWs are important structures thanks to their commercial availability
and the large literature describing their use for single molecule fluorescence
spectroscopy. We also compare the results between ZMWs milled in gold and
aluminum, and find that while gold has a stronger influence on the decay rates,
the lower losses of aluminum in the green spectral region provide larger
fluorescence brightness enhancement factors. For both aluminum and gold ZMWs,
we observe that the FRET rate scales linearly with the isolated donor decay
rate and the local density of optical states (LDOS). Detailed information about
FRET in ZMWs unlocks their application as new devices for enhanced single
molecule FRET at physiological concentrations
Intra- and Intermolecular Dispersion Interactions in [n]Cycloparaphenylenes: Do They Influence Their Structural and Electronic Properties?

Cycloparaphenylenes (CPPs) are nanosized structures with unique isolated and bulk properties, and are synthetic targets for the template-driven bottom-up synthesis of carbon nanotubes. Thus, a systematic understanding of the supramolecular order at the nanoscale is of utmost relevance for molecular engineering. In this study, it is found that intramolecular noncovalent (dispersion) interactions must be taken into account for obtaining accurate estimates of the structural and optoelectronic properties of [n]CPP compounds, and their influence as the number of repeat units increases from n=4 to n=12 is also analyzed, both in the gas phase and in solution. The supramolecular self-assembly, for which both intra- and intermolecular noncovalent interactions are relevant, of [6]CPP is also investigated by calculating the binding energies of dimers taken along several crystal directions. These are also used to estimate the cohesive energy of the crystal, which is compared to the value obtained by means of dispersion-corrected DFT calculations using periodic boundary conditions. The reasonable agreement between both computational strategies points towards a first estimate of the [6]CPP cohesive energy of around 50 kcal mol−1.This work is supported by the “Ministerio de Economia y Competitividad” of Spain and the “European Regional Development Fund” through projects CTQ2011-27253, CTQ2014-55073P and FIS2012-35880
X-ray Photoelectron Spectroscopy of Pyridinium-Based Ionic Liquids: Comparison to Imidazolium- and Pyrrolidinium-Based Analogues

We investigate eight 1-alkylpyridinium-based ionic liquids of the form [CnPy][A] by using X-ray photoelectron spectroscopy (XPS). The electronic environment of each element of the ionic liquids is analyzed. In particular, a reliable fitting model is developed for the C 1s region that applies to each of the ionic liquids. This model allows the accurate charge correction of binding energies and the determination of reliable and reproducible binding energies for each ionic liquid. Shake-up/off phenomena are determinedfor both C 1s and N 1s spectra. The electronic interaction between cations and anions is investigated for both simple ionic liquids and an example of an ionic-liquid mixture; the effect of the anion on the electronic environment of the cation is also explored. Throughout the study, a detailed comparison is made between [C8Py][A] and analogues including 1-octyl-1-methylpyrrolidinium- ([C8C1Pyrr][A]), and 1-octyl-3-methylimidazolium- ([C8C1Im][A]) based samples, where X is common to all ionic liquids
Hydrodynamic microgap voltammetry under Couette flow conditions:electrochemistry at a rotating drum in viscous poly(ethylene glycol)

Electrochemical processes in highly viscous media such as poly(ethylene glycol) (herein PEG200) are interesting for energy-conversion applications, but problematic due to slow diffusion causing low current densities. Here, a hydrodynamic microgap experiment based on Couette flow is introduced for an inlaid disc electrode approaching a rotating drum. Steady-state voltammetric currents are independent of viscosity and readily increased by two orders of magnitude with further potential to go to higher rotation rates and nanogaps. A quantitative theory is derived for the prediction of currents under high-shear Couette flow conditions and generalised for different electrode shapes. The 1,1′-ferrocene dimethanol redox probe in PEG200 (D=1.4×10−11 m2 s−1) is employed and data are compared with 1) a Levich-type equation expressing the diffusion–convection-limited current and 2) a COMSOL simulation model providing a potential-dependent current trace