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  • Teaching Vibrational Spectra to Assign Themselves
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-21
    Paul Houston, Brian L. Van Hoozen, Jr., Qu Chen, Qi Yu, Joel M. Bowman

    A new paradigm for assigning vibrational spectra is described. Instead of proceeding from potential to Hamiltonian to eigenvalues/eigenvectors/intensities to spectrum, the new method goes ``backwards'' directly from spectrum to eigenvectors. The eigenvectors then ``assign'' the spectrum, in that they identify the basis states that contribute to each eigenvalue. To start, we demonstrate an algorithm that can obtain useful estimates of the eigenvectors connecting a real, symmetric Hamiltonian to its eigenvalues even if the only available information about the Hamiltonian is its diagonal elements. When this algorithm is augmented with information about transition intensities, it can be used to assign a complex vibrational spectrum using only information about 1) eigenvalues (the peak centers of the spectrum) and 2) a harmonic basis set (taken to be the diagonal elements of the Hamiltonian). Examples will be discussed, including application to the vibrationally complex spectral region of the formic acid dimer.

    更新日期:2018-05-21
  • How many Ritonavir cases are there still out there?
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-17
    Marcus Neumann, Jacco van de Streek

    Based on a thorough and critical analysis of the commercial crystal structure prediction studies of 41 pharmaceutical compounds, we conclude that for between 15 to 45% of all small-molecule drugs currently on the market the most stable experimentally observed polymorph is not the thermodynamically most stable crystal structure and that the appearance of the latter is kinetically hindered.

    更新日期:2018-05-17
  • Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-16
    Mikołaj Jan Janicki, Rafał Szabla, Jiri Sponer, Robert Władysław Góra

    2-aminoimidazole (2-AIM) was proposed as a plausible nucleotide activating group in a nonenzymatic copying and polymerization of short RNA sequences under prebiotically plausible conditions. One of the key selection factors controlling the lifespan and importance of organic molecules on the early Earth is ultraviolet radiation from the young Sun. Therefore, to assess suitability of 2-AIM for prebiotic chemistry, we performed non-adiabatic molecular dynamics simulations and static explorations of potential energy surface of the photoexcited 2-AIM-(H2O)5 cluster by means of the algebraic diagrammatic construction method to the second-order [ADC(2)]. Our quantum mechanical simulations demonstrate that 1πσ∗ excited states play a crucial role in the radiationless deactivation of UV-excited 2-AIM-(H2O)5 system. More precisely, electron-driven proton transfer (EDPT) along water wires is the only photorelaxation pathway leading to the formation of 1πσ∗/S0 conical intersections. The availability of this mechanism and lack of destructive photochemistry indicate that microhydrated 2-AIM is characterized by substantial photostability and resistance to prolonged UV irradiation.

    更新日期:2018-05-17
  • Adventures in boron chemistry - the prediction of novel ultra-flexible boron oxide frameworks
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-16
    Neil Allan, Harvey J. A. Dale, Judy N Hart, Frederik Claeyssens

    Recent periodic density functional calculations have predicted the existence of ultra-flexible low-energy forms of boron oxides in which rigid boron-oxygen heterocycles are linked by flexible B-O-B bridges. The minima in the energy landscapes of these frameworks are remarkably broad, with widths in excess of those of many hybrid metal-organic frameworks. Enormous changes in cell volume, which can exceed a factor of two, are accompanied by negligible changes in energy. Here we explore the underlying reasons for this behaviour using molecular electronic-structure calculations, periodic density functional theory and template-based geometric simulations. The angular flexibility of the B-O-B bridge depends only upon the geometry of the local B2O5 unit, remaining independent of the configuration of neighbouring bridges. Unique cooperativity between bending and twisting motions of the bridges leads to considerable anisotropy in framework flexibility. Exceptional flexibility is conferred not only by the intrinsic bending flexibility of the bridges but crucially by the relaxation of torsional constraints when B3O3 rings are present. We test these conclusions by showing how the flexibility of the frameworks can be tuned by decoration with isoelectronic rings. The new nanoporous boron oxides in this work are predicted to be potential novel guest-host materials because of their flat energy landscapes. Furthermore, such structures can be generated systematically from silicates by substitution of B2O54- for SiO44-. A borate analogue of β-cristobalite is shown to be isoenergetic with the known B2O3-I polymorph. We raise the possibility of new families of boron-containing covalent organic frameworks and zeolite analogues.

    更新日期:2018-05-16
  • Curve Crossing in a Manifold of Coupled Electronic States: Direct Quantum Dynamics Simulations of Formamide
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-16
    Kaite Eryn Spinlove, Gareth Richings, Mike A Robb, Graham Worth

    Quantum dynamics simulations are an important tool to evaluate molecular behaviour including the, often key, quantum nature of the system. In this paper we present an algorithm that is able to simulate the time-evolution of a molecule after photo-excitation into a manifold of states. The Direct Dynamics variational Multi-Configurational Gaussian (DD-vMCG) method circumvents the computational bottlenecks problems of traditional grid-based methods by computing the potential energy functions on-the-fly, i.e. only where required. Unlike other commonly used direct dynamics methods, DD-vMCG is fully quantum mechnical. Here, the method is combined with a novel on-the-fly diabatisation scheme to simulate the short-time dynamics of the key molecule formamide and its acid analogue formimidic acid. This is a challenging test system due to the nature and large number of excited-states and eight coupled states are included in the calculations. It is shown that the method is able to provide unbiased information on the product channels open after excitation at different energies and demonstrates the potential to be a practical scheme, limited mainly by the quality of the quantum chemistry used to describe the excited states.

    更新日期:2018-05-16
  • The Importance of Configurational Disorder in Crystal Structure Prediction: The Case of Loratadine
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-15
    Grahame Robert Woollam, Marcus Neumann, Trixie Wagner, Roger J Davey

    Loratadine, an over the counter antihistamine medication, has two known monotropically related polymorphs, both of which feature disorder. A combined experimental and computational approach using variable temperature single crystal X-ray diffraction (VT-SCXRD) analysis and dispersion corrected density functional theory (DFT-D) reveals that the nature of the disorder in both forms is markedly different and cannot be described by a simple isolated-site model with thermally populated conformations in either of the two cases. In Form I, the ethyl carbamate functionality adopts two different configurations with adjacent moieties interacting along one-dimensional chains. The most stable arrangement features alternating configurations, but because of the low energetic cost of stacking faults the domain sizes are short and an average crystal structure is observed experimentally. The configurational free energy of the disordered structure is lower than the energy of the two corresponding ordered crystal structures, but the energy decrease is dominated by the lower lattice energy of the alternating arrangement with a small entropic contribution. In Form II, the flexible cycloheptane bridge adopts two different configurations. The disorder is not an equilibrium property and instead frozen-in during the crystallisation process. The configurational free energy of the disordered structure falls in between the lattice energies of the two corresponding ordered structures. The two ordered components of each disordered structure are all found in a crystal structure prediction (CSP) study with the GRACE programme. However, the experimentally observed stability relationship is only reproduced when the energy contribution of disorder is taken into account. The disordered model of Form I is found to be lower in energy than all other predicted structures and there is no indication of a missing, thermodynamically more stable form. The case of loratadine demonstrates that experimentally observed disorder close to 50/50 does not necessarily correspond to a free energy decrease by kTln2.

    更新日期:2018-05-15
  • Introductory Lecture Supported Cluster Catalysts Synthesized to be Small, Simple, Selective, and Stable
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-11
    Erjia Guan, Chia-Yu Fang, Dong Yang, Liang Wang, Fengshou Xiao, Bruce C Gates

    Molecular metal complexes on supports have drawn wide attention as catalysts offering new properties and opportunities for precise synthesis to make uniform catalytic species that can be understood in depth. Here we highlight advances in research with catalysts that are a step more complex than those incorporating single, isolated metal atoms on supports. These more complex catalysts consist of supported noble metal clusters and supported metal oxide clusters, with emphasis placed on some of the simplest and best-defined of these catalysts, made by precise synthesis, usually with organometallic precursors. Characterization of these catalysts by spectroscopic, microscopic, and theoretical methods is leading to rapid progress in fundamental understanding of catalyst structure and function and to expansion of this class of materials. The simplest supported metal clusters incorporate two metal atoms each—they are pair-site catalysts. These and clusters containing several metal atoms have reactivities determined by the metal nuclearity, the ligands on the metal, and the supports, which themselves are ligands. Metal oxide clusters are included in the discussion, with Zr6O8 clusters that are nodes in metal-organic frameworks being among those understood the best. The surface and catalytic chemistry of these metal oxide clusters are distinct from those of bulk zirconia. A challenge in using any supported cluster catalysts is associated with their possible sintering, and recent research shows how metal nanoparticles can be encapsulated in sheaths with well-defined structures—zeolites—that make them highly resistant to sintering.

    更新日期:2018-05-12
  • Excited state dynamics and time-resolved photoelectron spectroscopy of para-xylylene
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-11
    Kevin Issler, Anja Röder, Lionel Poisson, Ingo Fischer, Roland Mitrić, Jens Petersen

    We investigated the excited-state dynamics of \textit{para}-xylylene using a combination of field-induced surface hopping simulations and time-resolved ionisation experiments. Our simulations predict an ultrafast decay of the initially excited bright state (S$_2$/S$_3$) to the S$_1$ state on a sub-100-fs time scale, followed by return to the ground state within $\sim$1 ps. This is accompanied by a transient change of the biradical character of the molecule, as monitored by calculating natural orbital occupation numbers. Specifically, the initially low biradicality is increased by electronic excitation as well as by vibrational activation. Experimentally, \textit{para}-xylylene was generated by pyrolysis from [2,2]paracyclophane and excited with 266 nm into the S$_2$/S$_3$ bright state. The subsequent dynamics was followed using ionisation as the probe step, with both mass spectra and photoelectron spectra recorded as a function of pump-probe delay. The observed decay of photoelectron and photoion intensities closely matches the theoretical predictions and is consistent with the sequential mechanism found in the simulations. This mechanism exhibits characteristic signatures in both time-resolved mass and photoelectron spectra, in particular in the appearance of fragment ions that are exclusively generated from the S$_1$ state. This allows for a separation of the S$_2$ and S$_1$ dynamics in the photoelectron and mass spectra. An excellent agreement between the observed and the simulated ion signal is observed.

    更新日期:2018-05-12
  • Multiple pulse coherent dynamics and wave packet control of the N2 a" 1Σg+ dark state by attosecond four wave mixing
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-08
    Erika Rose Warrick, Ashley Fidler, Wei Cao, Etienne Bloch, Daniel M Neumark, Stephen R Leone

    Nonlinear multidimensional spectroscopy is ubiquitous in the optical and radio-frequency regimes as a powerful tool to access structure and dynamics. The extension of this technique into the extreme ultraviolet (XUV) with attosecond pulses holds the promise of probing electronic dynamics and correlations with unprecedented time and spatial resolution. In this work, we use noncollinear four-wave mixing of a weak XUV attosecond pulse train (11-17 eV) and few- femtosecond NIR pulses (800 nm) to spectroscopically and dynamically probe the dipole-forbidden double-well potential of the a" 1Σg+ electronic state of nitrogen. The results demonstrate optical coupling of the inner and outer limits of the initially XUV-prepared vibrational wave packet in the valence character b' 1∑u+ state to the inner and outer wells, respectively, of the a" 1Σg+ double well state by 800 nm light. Two four-wave mixing schemes with different pulse timing sequences and noncollinear beam geometries are used (one NIR pulse collinear and one NIR pulse noncollinear versus both NIR pulses noncollinear to the XUV) to measure the a" dark state energetic structure and to control the dynamical preparation and motion of a dark state wave packet by selective population of either the inner Rydberg or outer valence-character potential well. Experimental measurements of the a" 1Σg+ outer well vibrational spacing and anharmonicity closely match the values theoretically predicted for this previously unobserved state.

    更新日期:2018-05-09
  • Nanoengineering ABO₃ Active Sites from low-energy routes (TX100-stabilised Water-in-Oil Microemulsions, Surface Segregation and Surface Complexation on Colloidal AlOOH/Sol-gel Al2O3 Surfaces) for Pollution Control Catalysis
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-08
    Paul Anthony Sermon, Myles Worsley, Sabine Roesch, Cindy Thatcher, Patrick N. Forrest

    It is shown that water-in-oil microemulsions (m/e or μE) can produce BaCeO3 (BCO) and LaCoO3 (LCO) precursors. The nanoparticles (NPs) adsorb on AlOOH sols, in much the same way as Turkevich previously immobilised platinum group metal sols. BCO is active in CO and propane oxidation and NO removal under stoichiometric exhaust conditions, but LCO is a better oxidation catalyst. Activity was also seen when Ba,Ce and La,Co are inserted into/segregate at the surface of AlOOH/Al2O3. However, there is only formation of low levels of BCO, CAO, LCO and LAO perovskites, along with aluminates and separate oxides. The complexing of cations by AlOOH surface-held oxalate ions, albeit with different efficiencies, has also been explored. All three routes yield active catalysts with micro-domains of crystallinity; microemulsions produce the best defined perovskite NPs, but even those from surface segregation have higher turnover numbers than traditional Pt catalysts. Perovskite NPs may open up green chemistry for air pollution control that are consistent with a circular economy.

    更新日期:2018-05-08
  • TopoFF : MOF structure prediction using specifically optimized blue prints
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-04
    Julian Keupp, Rochus Schmid

    For the structure prediction of MOFs and related crystalline framework materials we have proposed the Reversed Topological Approach (RTA), where the default embedding of a topology is used as a blueprint. The optimal rotational insertion of the building blocks (BBs) at the fixed vertex positions of the blueprint is performed by minimizing the target function of the average angle deviation (AAD). Here we extend this idea by pre-optimizing the maximum symmetry embedding of a topology in order to minimize the overall mean AAD for the given set of BBs. By this fast and essentially parameter free topoFF method, the vertex positions and cell parameters of the blueprint are further optimized in order to fit the structural needs of the BBs, which speeds up the overall search for the energetically most favorable structure. In addition, different topologies can be ranked in a quantitative and intuitive way. The definition and implementation of topoFF is explained and its application for the RTA based structure prediction of MOFs is demonstrated on a number of instructive examples.

    更新日期:2018-05-05
  • ROY Revisited, Again: The Eighth Solved Structure
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-02
    Melissa Tan, Alexander Shtukenberg, Shengcai Zhu, Wenqian Xu, Eric Dooryhee, Shane M Nichols, Michael David Ward, Bart Kahr, Qiang Zhu

    X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å,, β = 118.23(1)○. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0○ and 44.9○. These angles fall between those previously determined for the red and orange forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.

    更新日期:2018-05-03
  • Water permeation across artificial I-quartet membrane channels: from structure to disorder
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-02
    Samuel Murail, Tudor Vasiliu, Andrei Neamtu, Mihail Dumitru Barboiu, Fabio Sterpone, Marc Baaden

    Aquaporins allow fast water transport across membranes (~108-109 water molecules/s/channel), with complete exclusion of ions thanks to an hourglass structure with a narrowest constriction of 2.8 Å. Few synthetic channels have been designed to mimic this high water permeability, and none reject ions at a significant level. Recent works on designed self-assembling alkylureido-ethylimidazole compounds forming imidazole-quartet channels (I-quartets), have shown high water permeability across lipid bilayers and total ionic-rejection [1]. I-quartets are promising candidates for further development of artificial water channels (AWC). However the molecular mechanism of water permeation as well as I-quartet organization and stability in a membrane environment need to be fully understood to guide optimal AWC design. Here, we use a wide range of all-atom molecular dynamics (MD) simulations to understand the structure/activity relationships of the artificial I-quartet water channels. Four different I-quartet channels with varying alkyl chain length or chirality have been studied in a complex fully hydrated lipid bilayer environment at both microsecond and nanosecond scale. Microsecond simulations shows two distinct behaviors; (i) two out of four of the self-assembled I-quartets embedded within lipid bilayers maintain chiral dipolar oriented water wires, but also undergo strong reorganization of the crystal shape, (ii) the two other I-quartets channels completely lose the crystal packing organization, nonetheless keeping a water transport activity. Short MD simulations with higher time resolution were conducted to characterize the dynamic properties of water molecules in these model channels and provided a detailed hypothesis on the molecular mechanism of water transport. The ordered confined water was characterized with quantitative measures of hydrogen-bond life-time and single particle dynamics, showing discrepancy within I-quartets channels. We will further discuss the underlying assumptions, currently based on self-aggregation simulations and crystal patches embedded in lipid bilayer simulations and attempt to describe possible alternative approaches to computationally capture the water permeation mechanism and the self-assembly process of these AWC. [1] Licsandru et al. JACS (2016), 138(16), 5403-5409.

    更新日期:2018-05-02
  • Quantum and Classical IR Spectra of (HCOOH)2, (DCOOH)2 and (DCOOD)2 using Ab Initio Potential Energy and Dipole Moment Surfaces
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-02
    Qu Chen, Joel M. Bowman

    The accurate quantum mechanical description of the vibrational dynamics and IR spectra of molecules is illustrated here for the formic acid dimer, (HCOOH)2 and isotopologues (DCOOH)2 and (DCOOD)2 in full dimensionality. The calculations make use of recent full-dimensional ab initio potential energy and dipole moment surfaces and are done with the code MULTIMODE. IR spectra are reported for the three dimers and also compared to available experimental spectra. In addition, standard classical and “semiclassially prepared” quasiclassical molecular dynamics calculations of the IR spectra of these complexes are reported and compared to the quantum spectra and also experiment. These comparisons indicate good accuracy of the MD spectra for sharp bands but not for the complex O-H stretch band, where the complex molecular dynamics band is upshifted from experiments by roughly 300 cm1. For the the fully deuterated dimer (DCOOD)2, the quantum spectral band for O-D stretch sharpens relative to the O-H spectral bands in (HCOOH)2 and (DCOOH)2; however, the molecular dynamics OD stretch band does not exhibit this sharpening.

    更新日期:2018-05-02
  • Proton transfer in a guanine–cytosine base pair analogue studied by NMR spectroscopy and PIMD simulation
    Faraday Discuss. (IF 3.588) Pub Date : 2018-05-02
    Radek Pohl, Ondrej Socha, Petr Slavicek, Michal Sala, Paul Hodgkinson, Martin Dracinsky

    It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium-isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of nuclei by electrons. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts bring a unique possibility to study NQEs and to evaluate the accuracy of computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.

    更新日期:2018-05-02
  • Real-time determination of aggregated alpha-synuclein induced membrane disruption at neuroblastoma cells using scanning ion conductance microscopy
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-30
    Stephanie Wong Su, Andy Chieng, Jacob Parres-Gold, Megan Chang, Yixian Wang

    Parkinson's disease (PD) is recognized as the second most common neurodegenerative disorder and has affected approximately one million people in the United States alone. A large body of evidence has suggested that deposition of aggregated alpha-synuclein (α-Syn), a brain protein abundant near presynaptic termini, in intracellular protein inclusions (Lewy bodies) results in neuronal cell damage and ultimately contributes to the progression of PD. However, the exact mechanism is still unclear. One hypothesis is that α-Syn aggregates disrupt the cell membrane's integrity, eventually leading to cell death. We used scanning ion conductance microscopy (SICM) to monitor the morphological changes of SH-SY5Y neuroblastoma cells and observed dramatic disruption of the cell membrane after adding α-Syn aggregates to the culturing media. This work demonstrates that SICM can be applied as a new approach to studying cytotoxicity of α-Syn aggregates.

    更新日期:2018-05-01
  • Driven Water/Ion Transport through Narrow Nanopores: a Molecular Dynamics Perspective
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-30
    Rob D. Coalson

    Atomistic Molecular Dynamics (MD) simulations provide numerous insights into the process whereby water is driven through a narrow nanopore (diameter on the order of a few water molecules) by application of hydrostatic pressure. If there are ions in the water, e.g., from dissolved salt, these may be swept along with the flowing water. If the surface of the nanopore is charged, electrostatic interaction between the surface charges and the ions as well as with partial charges on the water molecules will influence the details of the water/ion flow through the channel. Water and ion permeability depend on the geometry of the channel and the degree to which it is charged. Interesting collective features of the water molecules such as water wires that form along the pore axis and rings of water molecules that can insert into the pore perpendicular to the channel axis strongly influence the permeation process, thus emphasizing the importance of molecular level interactions in the mechanism of water and ion flow through conduits with dimensions on the molecular scale.

    更新日期:2018-04-30
  • Protein-protein interactions in AQP regulation – biophysical characterization of AQP0-CaM and AQP2-LIP5 complex formation
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-25
    Stefan Kreida, Jennifer Virginia Roche, Caroline Olsson, Sara Linse, Susanna Törnroth-Horsefield

    Protein-protein interactions play important roles in regulating human aquaporins (AQP) by gating as well as trafficking. While structural and functional studies have provided detailed knowledge of AQP transport mechanism, selectivity as well as gating by conformational changes of loops or termini, the mechanism behind how protein-protein interactions control AQP-mediated water transport through cellular membranes remain poorly characterized. Here we explore the interaction between two human AQPs and regulatory proteins: the interaction between AQP0 and calmodulin, which mediates AQP0 gating, as well as the interaction between AQP2 and LIP5, which is involved in trafficking. Using microscale thermophoresis (MST) and fluorescence anisotropy, two methods that have the advantage of low sample consumption and detergent compatibility, we show that the interactions can be studied using both full-length AQPs and AQP peptides corresponding to the regulatory protein binding sites. However, full-length AQPs gave better reproducibility between methods and for the first time revealed that AQP0 binds CaM in a cooperative manner, which was not seen in experiments using peptides. Our study highlights that, while peptides are great tools for locating binding sites and pinpointing interacting residues, full-length proteins may give additional insights, such as binding mechanism, allostery and cooperativity, which are important parameters for understanding protein-protein interactions in the cellular context.

    更新日期:2018-04-25
  • Probing Ion Current in Solid-Electrolytes at the Meso- and Nanoscale
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-23
    Joseph Martinez, David Ashby, Cheng Zhu, Bruce Dunn, Lane A Baker, Zuzanna Siwy

    We present experimental approaches to probe ionic conductivity of solid electrolytes at meso- and nanoscales. Silica ionogel based electrolytes have emerged as an important class of solid electrolytes because they maintain both fluidic and high conductivity states at the nanoscale, but at the macroscale they are basically solid. Single mesopores in polymer films are shown to serve as templates for cast ionogels. Ionic conductivity of the ionogels was probed by two experimental approaches. In the first approach, the single-pore/ionogel membranes were placed between two chambers of a conductivity cell, in a set-up similar to that used for investigating liquid electrolytes. The second approach involved depositing contacts directly onto the membrane and measuring conductivity without bulk solution present. Ionic conductivity determined by the two methods was in excellent agreement with macroscopic measurements, which suggested that electrochemical properties of ionogel based electrolytes are preserved at the mesoscale, and ionogels can be useful in designing meso-scaled energy-storage devices.

    更新日期:2018-04-24
  • Impact of PEG additives and pore rim functionalization on water transport through sub-1-nm carbon nanotube porins
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-20
    Ramya Tunuguntla, Andrew Yuheng Hu, Yuliang Zhang, Aleksandr Noy

    Carbon nanotubes represent one of the most interesting examples of a nanofluidic channel that combines extremly small diameters with atomically smooth walls and well-defined chemical functionalities at the pore entrance. In the past, sub-1-nm diameter carbon nanotube porins (CNTPs) embedded in a lipid membrane matrix demonstrated extremely high water permeabilities and strong ion selectivities. In this work, we explore additional factors that can influence transport in these channels. Specifically, we use stopped-flow transport measurements to focus on the effect of chemical modifications of the CNT rims and chaotropic polyethyleneglycol (PEG) additives on CNTP water permeability and Arrenius activation energy barriers for water transport. We show that PEG, especially in its more chaotropic coiled configuration, enhances the water transport and reduces the associated activation energy. Removal of the static charges on the CNTP rim by converting -COOH groups to neutral methylamide groups also reduces the activation energy barriers and enhances water transport rates.

    更新日期:2018-04-20
  • Parameterization and Atomistic Simulations of Biomimetic Membranes
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-18
    Daniel Ryan Barden, Harish Vashisth

    Biomimetic membranes, designed by combining proteins or protein-mimics with self-assembled block copolymers, are emerging as novel hybrid materials with applications in the next generation of sensing and separation devices. However, designing such membranes requires a fundamental understanding of atomic-scale interactions between biological channel proteins and their non-native polymeric membrane environment as it affects their stability and function. In principle, all-atom molecular dynamics (MD) simulations are well-suited to probe atomistic details of channel/membrane interactions, but the absence of interatomic potentials is a major limiting factor in conducting such simulations. To alleviate this, we have developed CHARMM force-field compatible parameters and conducted all-atom explicit-solvent MD simulations of biomimetic membranes composed of block copolymers of poly(butadiene), poly(isoprene), and poly(ethylene oxide). Consistent with scaling laws and literature data, we report measurements on several structural properties that inform on molecular-scale features of chain conformations. Finally, we report simulations of a synthetic transport channel in selected membranes and characterize its functional behavior by measuring single-channel water permeability. We suggest that the interatomic potentials and membrane models reported here could be useful in studies of other proteins as well as for deriving potentials for coarse-grained models to permit future simulations of large-scale protein/polymer membranes.

    更新日期:2018-04-19
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  • Computational studies on ground and excited state charge transfer properties of peptidomimetics
    Faraday Discuss. (IF 3.588) Pub Date : 2018-01-23
    Sherin Joy, Vommina V Sureshbabu, Ganga Periyasamy
    更新日期:2018-04-17
  • The role of water molecules in phototransduction of retinal proteins and G protein-coupled receptors
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-20
    Elena Lesca, Valérie Panneels, Gebhard F. X. Schertler
    更新日期:2018-04-17
  • Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-15
    D. Agathangelou, Y. Orozco-Gonzalez, M. del Carmen Marín, P. P. Roy, J. Brazard, H. Kandori, K.-H. Jung, J. Léonard, T. Buckup, N. Ferré, M. Olivucci, S. Haacke
    更新日期:2018-04-17
  • Protein charge transfer absorption spectra: an intrinsic probe to monitor structural and oligomeric transitions in proteins
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-13
    Mohd. Ziauddin Ansari, Amrendra Kumar, Dileep Ahari, Anurag Priyadarshi, Padmavathi Lolla, Rashna Bhandari, Rajaram Swaminathan
    更新日期:2018-04-17
  • Photochemical relaxation pathways of S6-methylthioinosine and O6-methylguanosine in solution
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-07
    Brennan Ashwood, Luis A. Ortiz-Rodríguez, Carlos E. Crespo-Hernández
    更新日期:2018-04-17
  • Probing the excited state dynamics of Venus: origin of dual-emission in fluorescent proteins
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-06
    Shaina Dhamija, Bhisham Thakur, Purnananda Guptasarma, Arijit K. De
    更新日期:2018-04-17
  • Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-06
    Yuyuan Zhang, Kimberly de La Harpe, Mahesh Hariharan, Bern Kohler
    更新日期:2018-04-17
  • A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-03
    Veniamin A. Borin, Christian Wiebeler, Igor Schapiro
    更新日期:2018-04-17
  • Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-01
    Subhas C. Bera, Tapas Paul, A. N. Sekar Iyengar, Padmaja P. Mishra
    更新日期:2018-04-17
  • Optically sensing phospholipid induced coil–helix transitions in the phosphoinositide-binding motif of gelsolin
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-01
    Samsuzzoha Mondal, Amitava Chandra, Ravindra Venkatramani, Ankona Datta
    更新日期:2018-04-17
  • Engineered photoproteins that give rise to photosynthetically-incompetent bacteria are effective as photovoltaic materials for biohybrid photoelectrochemical cells
    Faraday Discuss. (IF 3.588) Pub Date : 2017-11-01
    Juntai Liu, Vincent M. Friebe, David J. K. Swainsbury, Lucy I. Crouch, David A. Szabo, Raoul N. Frese, Michael R. Jones
    更新日期:2018-04-17
  • 更新日期:2018-04-17
  • Photoinduced formation mechanism of the thymine–thymine (6–4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study
    Faraday Discuss. (IF 3.588) Pub Date : 2017-10-24
    Angelo Giussani, Irene Conti, Artur Nenov, Marco Garavelli
    更新日期:2018-04-17
  • Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates
    Faraday Discuss. (IF 3.588) Pub Date : 2017-10-24
    Javier Segarra-Martí, Vishal K. Jaiswal, Ana Julieta Pepino, Angelo Giussani, Artur Nenov, Shaul Mukamel, Marco Garavelli, Ivan Rivalta
    更新日期:2018-04-17
  • 更新日期:2018-04-17
  • Exploring oligomeric state of the serotonin1A receptor utilizing photobleaching image correlation spectroscopy: implications for receptor function
    Faraday Discuss. (IF 3.588) Pub Date : 2017-10-06
    Hirak Chakraborty, Md. Jafurulla, Andrew H. A. Clayton, Amitabha Chattopadhyay
    更新日期:2018-04-17
  • Chiral self-assembly of fullerene clusters on CT-DNA templates
    Faraday Discuss. (IF 3.588) Pub Date : 2017-10-05
    Sandeepa Kulala Vittala, Joshy Joseph
    更新日期:2018-04-17
  • 更新日期:2018-04-17
  • Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution
    Faraday Discuss. (IF 3.588) Pub Date : 2017-09-18
    Pratip Chakraborty, Tolga N. V. Karsili, Barbara Marchetti, Spiridoula Matsika
    更新日期:2018-04-17
  • Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation
    Faraday Discuss. (IF 3.588) Pub Date : 2017-09-12
    Akos Banyasz, Tiia Ketola, Lara Martínez-Fernández, Roberto Improta, Dimitra Markovitsi
    更新日期:2018-04-17
  • Gold nanorods decorated with a cancer drug for multimodal imaging and therapy
    Faraday Discuss. (IF 3.588) Pub Date : 2017-09-12
    Resmi V. Nair, Hema Santhakumar, Ramapurath S. Jayasree
    更新日期:2018-04-17
  • Fluorescent excimers and exciplexes of the purine base derivative 8-phenylethynyl-guanine in DNA hairpins
    Faraday Discuss. (IF 3.588) Pub Date : 2017-09-01
    Kristen E. Brown, Arunoday P. N. Singh, Yi-Lin Wu, Lin Ma, Ashutosh K. Mishra, Brian T. Phelan, Ryan M. Young, Frederick D. Lewis, Michael R. Wasielewski
    更新日期:2018-04-17
  • Computational Modelling of Solvent Effects in a Prolific Solvatomorphic Porous Organic Cage
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    David P McMahon, Andrew Stephenson, Samantha Y Chong, Marc Little, James T. A. Jones, Andrew I Cooper, Graeme Matthew Day

    Crystal structure prediction methods can enable the in silico design of functional molecular crystals, but solvent effects can have a major influence on relative lattice energies, sometimes thwarting predictions. This is particularly true for porous solids, where solvent included in the pores can have an important energetic contribution. We present a Monte Carlo solvent insertion procedure for predicting the solvent filling of porous structures from crystal structure prediction landscapes, tested using a highly solvatomorphic porous organic cage molecule, CC1. Using this method, we can understand why the predicted global energy minimum structure for CC1 is never observed from solvent crystallisation. We also explain the formation of three different solvatomorphs of CC1 from three structurally-similar chlorinated solvents. Calculated solvent stabilisation energies are found to correlate with experimental results from thermogravimetric analysis, suggesting a future computational framework for a priori materials design that factors in solvation effects.

    更新日期:2018-04-16
  • Predicting the Structures and Associated Phase Transitions Mechanisms in Disordered Crystals via a Combination of Experimental and Theoretical Methods
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Michael T Ruggiero, Johanna Kölbel, Qi Li, J. Axel Zeitler

    Disordered materials make up a large portion of condensed phase systems, but the difficulties in describing their structures and molecular dynamics limit their potential applications. Disordered crystalline systems, also known as plastic crystals, offer a unique perspective into these factors because the system retains a degree of crystallinity, reducing the degrees of freedom that must be explored when interpreting the results. However, while disordered crystals do diffract X-rays, it is difficult to fully resolve a meaningful crystalline structure, with the best scenario resulting in lattice parameters. In this study, we use a combination of experimental terahertz time-domain spectroscopy, and theoretical solid-state ab initio density functional theory and molecular dynamics simulations to fully elucidate the structures and associated dynamics of organic molecular solids. The results highlight that this combination provides a complete description of the energetic and mechanistic pathways involved in the formation of disordered crystals, and highlights the importance of low-frequency dynamics on their properties. Finally, with structures fully determined and validated by the experimental results, recent progress into anharmonic calculations, namely the quasi-harmonic approximation method, enables full temperature and pressure-dependent properties to be understood within the framework of the potential energy hyper-surface structure.

    更新日期:2018-04-16
  • A study of dynamic nanoscale corrosion initiation events by HS-AFM
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Stacy Moore, Robert Burrows, Loren Picco, Tomas Martin, Scott Greenwell, Thomas Scott, Oliver Payton

    Atomic force microscopes (AFMs) are capable of high-resolution mapping of structures and the measurement of mechanical properties at nanometre scales within gaseous, liquid and vacuum environments. The contact mode high-speed AFM (HS-AFM) developed at Bristol Nano Dynamics Ltd. operates at speeds orders of magnitude faster than conventional AFMs, and is capable of capturing multiple frames per second. This allows for direct observation of dynamic events in realtime, with nanometre lateral resolution and subatomic height resolution. HS-AFM is a valuable tool for the imaging of nanoscale corrosion initiation events, such as metastable pitting, grain boundary (GB) dissolution and short crack formation during stress corrosion cracking (SCC). Within this study HS-AFM was combined with SEM and FIB milling to produce a multifaceted picture of localised corrosion events occurring on thermally sensitised AISI 304 stainless steel in an aqueous solution of 1% sodium chloride (NaCl). HS-AFM measurements were performed in situ by imaging within a custom built liquid cell with parallel electrochemical control. The high resolution of the HS-AFM allowed for measurements to be performed at individual reaction sites, i.e. at specific GB carbide surfaces. Topographic maps of the sample surface allowed for accurate measurements of the dimensions of pits formed. Using these measurements it was possible to calculate, and subsequently model, the volumes of metal reacting with respect to time, and so the current densities and ionic fluxes at work. In this manner, the local electrochemistry at nanoscale reaction sites may be reconstructed.

    更新日期:2018-04-16
  • Continuous synthesis of hollow silver-palladium nanoparticles for catalytic applications
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Ke-Jun Wu, Yunhu Gao, Laura Torrente-Murciano

    Hollow bimetallic nanoparticles exhibit unique surface plasmonic properties, enhanced catalytic activities and high photo-thermal conversion efficiencies amongst other properties, however, their research and further deployment are currently limited by their complicated multi-step syntheses. This paper presents a novel approach for their continuous synthesis with controllable and tuneable sizes and compositions. This robust manufacturing tool, consisting of coiled flow inverter (CFI) reactors connected in series, allows for the first time the tempo- and spatial- separation of the initial formation of silver seeds and their subsequent galvanic displacement reaction in the presence of a palladium precursor, leading to the full control of both steps separately. We have also demonstrated that coupling the galvanic replacement and co-reduction leads to a great kinetic enhancement of the system leading to a high yield process of hollow bimetallic nanoparticles, directly applicable to other metal combinations.

    更新日期:2018-04-16
  • Effects of heat treatment atmosphere on the structure and activity of Pt3Sn nanoparticle electrocatalysts: a characterisation case study
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Haoliang Huang, Abu Bakr Ahmed Amine Nassr, Veronica Celorrio, Sarah Frances Rebecca Taylor, Vinod Kumar Puthiyapura, Christopher Hardacre, Dan Brett, Andrea E Russell

    Comprehensive identification of the phases and atomic configurations of bimetallic nanoparticle catalysts are critical in understanding structure-properties relationships in catalysis. However, control of the structure, whilst retaining the same composition, is challenging. Here, the same carbon supported Pt3Sn catalyst is annealed under air, Ar and H2 resulting in variation of the extent of alloying of the two components. The atmosphere-induced extent of alloying is characterised using a variety of methods including TEM, XRD, XPS, XANES, and EXAFS and is defined as the fraction of Sn present as Sn0 (XPS and XANES) or the ratio of the calculated composition of the bimetallic particle to the nominal composition according to the stoichiometric ratio of the preparation (TEM, XRD, and EXAFS) . The values obtained depend on the structural method used, but the trend air < Ar < H2 annealed samples is consistent. These results are then used to provide insights regarding the electrocatalytic activity of Pt3Sn catalysts for CO, methanol, ethanol, and 1-butanol oxidation and the roles of alloyed Sn and SnO2.

    更新日期:2018-04-16
  • Water and Hydrophobic Gates in Ion Channels and Nanopores
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Shanlin Rao, Charlotte Lynch, Gianni Klesse, Georgia E Oakley, Phillip Stansfeld, Stephen Tucker, Mark Sansom

    Ion channel proteins form nanopores in biological membranes which allow the passage of ions and water molecules. Hydrophobic constrictions in such pores can form gates, i.e. energetic barriers to water and ion permeation. Molecular dynamics simulations of water in ion channels may be used to assess whether a hydrophobic gate is closed (i.e. impermeable to ions) or open. If there is an energetic barrier to water permeation then it is likely that a gate will also be impermeable to ions. Simulations of water behaviour have been used to probe hydrophobic gates in two recent ion channel structures: BEST1 and TMEM175. In each of these channels a narrow region is formed by three consecutive rings of hydrophobic sidechains and in both cases such analysis demonstrates that the crystal structures correspond to a closed state of the channel. In silico mutations of BEST1 have also been used to explore the effect of changes in the hydrophobicity of the gating constriction, demonstrating that substitution of hydrophobic sidechains by more polar sidechains results in an open gate which allows water permeation. A possible open state of the TMEM175 channel was modelled by in silico expansion of the hydrophobic gate resulting in wetting of the pore and free permeation of potassium ions through the channel. Finally, a preliminary study suggests that a hydrophobic gate motif can be transplanted in silico from the BEST1 channel into a simple β-barrel pore template. Overall, these results suggest that simulations of the behaviour of water in hydrophobic gates can reveal important design principles for the engineering of gates in novel biomimetic nanopores.

    更新日期:2018-04-16
  • Electric field mediated separation of water-ethanol mixture in carbon-nanotubes integrated to nanoporous graphene membrane
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-16
    Manash Pratim Borthakur, Dipankar Bandyopadhyay, Gautam Biswas

    We investigate the influence of an applied electric field on the separation of water-ethanol solution inside a carbon nanotube (CNT) using a series of molecular dynamics simulations. The electric field is applied at an angle with respect to the axis of the CNT. The study uncovers that with the application of a ‘small-angle’ electric field (e.g. smaller ), the water molecules exhibit preferential occupancy inside the CNT, whereas application of the same at a ‘wide-angle’ mode (e.g. higher ) fills the CNT with ethanol molecules in place of water. Remarkably, the direction of the electric field plays a pivotal role because the field exerts a contrasting influence on the behaviours of the water and ethanol molecules. The water dipoles are favourably aligned at small values of creating an ordered water structure inside the CNT. Increasing disrupts the water dipole orientation and leads to preferential occupancy of the CNT by ethanol molecules. An in-depth analysis on the simulated systems unveil that, at lower values of , multiple layers of water molecules are physically adsorbed near the CNT walls, which is found to diminish as is increased. In comparison, at higher magnitudes of , the ethanol molecules are preferentially adsorbed inside the CNT. The average interaction energy per ethanol (water) molecule is found to enhance (reduce) when is monotonically increased, which can be ascribed to the promotion (reduction) of intermolecular hydrogen bonding capacity of the ethanol (water) molecules at larger values of . Consequently, inside the CNT, the average occupancy of water molecules decreases and ethanol molecules increases, as is monotonically increased, leading to the separation of ethanol-water mixture. The proposed methodology can convert an equimolar mixture (1:1) of ethanol-water into a concentrated one (14:1) when the electric field is applied orthogonal to the axis of the CNT. The separation efficiency is found to improve with the increase in intensity of the externally applied electric field.

    更新日期:2018-04-16
  • Zeolite structure determination using genetic algorithms and geometry optimisation.
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-13
    Xuehua Liu, Soledad Valero Cubas, Estefania Argente, German Sastre

    A recently presented software, zeoGAsolver, based on genetic algorithms, with domain- dependent crossover and selection operators that maintain the size of the population in successive iterations while improving the average fitness. Using the density, cell parameters, and symmetry (or candidate symmetries) of a zeolite sample whose resolution can not be achieved by analysis of the XRD (X-Ray Diffraction) data, the software attempts to locate the coordinates of the T-atoms of the zeolite unit cell employing a function of 'fitness' (F), which is defined through the different contributions to the 'penalties' (P) as F = 1/(1+P). While testing the software to find known zeolites such as LTA (Zeolite A), AEI (SSZ-39), ITW (ITQ-12) and others, the algorithm has found not only most of the target zeolites but also seven new hypothetical zeolites whose feasibility is confirmed by energetic and structural criteria.

    更新日期:2018-04-13
  • Functionalised Microscale Nanoband Edge Electrode (MNEE) Arrays; the systematic quantitative study of hydrogels grown on nanoelectrode biosensor arrays for enhanced sensing in biological media
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-12
    Andrew Piper, Ben Alston, Dave Adams, Andrew R Mount

    Nanoelectrodes and nanoelectrode arrays show enhanced diffusion and greater Faradaic current densities and signal-to-noise ratios than macro and microelectrodes, which can lead to enhanced sensing and detection. One example is the microsquare nanoband edge electrode (MNEE) array system, readily formed through microfabrication and whose quantitative response has been established electroanalytically. Hydrogels have been shown to have applications in drug delivery, tissue engineering, and anti-biofouling; some also have the ability to be grown electrochemically. Here, we combine these two emerging technologies to demonstrate the principles of a hydrogel-coated nanoelectrode array biosensor that is resistant to biofouling. We first electrochemically grow and analyze hydrogels on MNEE arrays. The structure of these gels is shown by imaging to be electrochemically controllable, reproducible and structurally hierarchical. This structure is determined by the MNEE array diffusion fields, consistent with the established hydrogel formation reaction, and varies in structural scale from nano (early time, near electrode growth) to micro (for isolated elements in the array) to macro (when there is array overlap) with distance from the electrode, forming a hydrogel mesh of increasing density on progression from solution to electrode. There is also increased hydrogel structural density observed at electrode corners, attributable to enhanced diffusion. The resulting hydrogel structure can be formed on (and is firmly anchored to/through) an established clinically relevant biosensing layer without compromising detection. It is also shown to be capable, through proof-of-principal model protein studies using Bovine serum albumin (BSA), of preventing protein biofouling whilst enabling smaller molecules such as DNA to pass through the hydrogel matrix and be sensed. Together, this demonstrates a method for developing reproducible, quantitative electrochemical nanoelectrode biosensors able to sense selectively in real-world sample matrices through the tuning of their interfacial properties.

    更新日期:2018-04-12
  • Data-driven learning and prediction of inorganic crystal structures
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-12
    Volker L. Deringer, Davide M Proserpio, Gabor Csanyi, Chris J. Pickard

    Crystal-structure prediction algorithms, including ab initio random structure searching (AIRSS), are intrinsically limited by the huge computational cost of the underlying quantum-mechanical methods. We have recently shown that a novel class of machine-learning (ML) based interatomic potentials can provide a way out: by performing a high-dimensional fit to the ab initio energy landscape, these potentials reach comparable accuracy but are orders of magnitude faster. In this paper, we develop our approach, dubbed Gaussian approximation potential based random structure searching (GAP-RSS), towards a more general tool for exploring configuration space and predicting structures. We present a GAP-RSS interatomic potential model for elemental phosphorus, which identifies and correctly “learns” the orthorhombic black phosphorus (A17) structure without prior knowledge of any crystalline allotropes. Using the tubular structure of fibrous phosphorus as an example, we then discuss the limits of free searching, and discuss a possible way forward that combines a recently proposed fragment analysis with GAP-RSS. Examples of possible tubular (1D) and extended (3D) hypothetical allotropes of phosphorus as found by GAP-RSS are discussed. We believe that in the future, ML potentials can become versatile and routine computational tools for materials discovery and design.

    更新日期:2018-04-12
  • Molecular dynamics simulations of carbon nanotube porins in lipid bilayers
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-11
    Martin Vögele, Jürgen Köfinger, Gerhard Hummer

    Artificial channels made of carbon nanotube (CNT) porins are promising candidates for applications in filtration and molecular delivery devices. Their symmetric shape and high mechanical, chemical, and thermal stability ensure well-defined transport properties, and at the same time make them ideal model systems for more complicated membrane protein pores. As the technology to produce and tune CNTs advances, simulations can aid in the design of customized membrane porins. Here we concentrate on CNTs embedded in lipid membranes. To derive design guidelines, we systematically studied the interaction of CNT porins with their surrounding lipids. For our simulations, we developed an AMBER- and Lipid14-compatible parameterization scheme for CNTs with different chirality and with functional groups attached to their rim, and a flexible coarse-grained description for open-ended CNTs fitting to the MARTINI lipid model. We found that the interaction with lipid acyl chains is independent of the CNT chirality and the chemical details of functional groups at the CNT rims. The latter, however, are important for the interactions with lipid head groups, and for water permeability. The orientation and permeability of the pore are mainly determined by how well its hydrophobicity pattern matches the membrane. By identifying the factors that determine the structure both of isolated CNTs in lipid membranes and of CNT clusters, we set the foundation for a targeted design of CNT-membrane systems.

    更新日期:2018-04-12
  • CO oxidation over supported gold nanoparticles as revealed by operando grazing incidence X-ray scattering analysis
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-09
    Yaroslav Odarchenko, David James Martin, Thomas Arnold, Andrew Michael Beale

    The mechanism of carbon monoxide oxidation over gold was explored using a model planar catalyst consisting of monodisperse gold nanoparticles periodically arranged on a single crystal SiO2/Si(111) substrates using a combination of Grazing Incidence Small Angle X-ray Scattering and Grazing Incidence X-ray Diffraction (GISAXS/GIXD) under reaction conditions. It is shown that nanoparticle composition, size and shape change when the catalyst is exposed to reactive gases. During CO oxidation, the particle’s submergence depth with respect to the surface decreases due to the removal of gold oxide at the metal-support edge, meanwhile the particle ‘flattens’ to maximise the number of the reaction sites along its perimeter. The effect of the CO concentration on the catalyst structure is also discussed. Our results support the dual catalytic sites mechanism whereby CO is activated on the gold surface whereas molecular oxygen is dissociating at the gold-support interface.

    更新日期:2018-04-09
  • Accelerating CALYPSO Structure Prediction by Data-driven Learning of Potential Energy Surface
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-06
    Qunchao Tong, Lantian Xue, Jian Lv, Yanchao Wang, Yanming Ma

    Ab initio structure prediction methods have been nowadays widely used as powerful tools for structure search and material discovery. However, they are generally restricted to small systems owing to the heavy computational cost of underlying density functional theory (DFT) calculations on structure optimizations. In this work, by combining state-of-art machine learning (ML) potential with our in-house developed CALYPSO structure prediction method, we developed two acceleration schemes for structure prediction toward large systems, in which ML potential is pre-constructed to fully replace DFT calculations or trained in an on-the-fly manner from scratch during the structure searches. The developed schemes have been applied to medium- and large-sized boron clusters, both of which are challenging cases for either construction of ML potentials or extensive structure searches. Experimental structures of B36 and B40 clusters can be readily reproduced, and the putative global minimum structure for B84 cluster is proposed, where the computational cost is substantially reduced by ~1 - 2 orders of magnitude if compared with full DFT-based structure searches. Our results demonstrate a viable route for structure prediction toward large systems via the combination of state-of-art structure prediction methods and ML techniques.

    更新日期:2018-04-06
  • 2D Graphene Oxide Channel for Water Transport
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-05
    Baoxia Mi, Sunxiang Zheng, Qingsong Tu

    Layer-stacked graphene oxide (GO) membranes, in which unique two-dimensional (2D) water channels are formed between two neighboring GO nanosheets, have demonstrated great potential for aqueous phase separation. Subjects of crucial importance are to fundamentally understand the interlayer spacing (i.e., channel height) of GO membranes in aqueous environment, elucidate the mechanisms for water transport within such 2D channels, and precisely controlling the interlayer spacing to tune the membrane separation capability for targeted applications. In this investigation, we used an integrated quartz crystal mass balance (QCM-D) and ellipsometry to experimentally monitor the interlayer spacing of GO, reduced GO and crosslinked GO, respectively, in aqueous solution, and found that crosslinking can effectively prevent GO from swelling and precisely control the interlayer spacing. We then used molecular dynamics simulation to study the mass transport inside the 2D channels, and prove that the chemical functional groups on GO plane dramatically slow down water transport in the channels. Our findings on GO structure and water transport provide a necessary basis for further tailoring and optimizing the design and fabrication of GO membranes in various separation applications.

    更新日期:2018-04-06
  • Hyperpolarised NMR to Follow Water Proton Transport through Membrane Channels via Exchange with Biomolecules
    Faraday Discuss. (IF 3.588) Pub Date : 2018-04-05
    Viorel Vasile Nastasa, Cristina Stavarache, Anamaria Hanganu, Adina Coroaba, Alina Nicolescu, Calin Deleanu, Aude Sadet, Paul Vasos

    Water uptake in vesicles and subsequent exchange between water protons and amide -NH protons in amino acids can be followed by a new, highly sensitive, avatar of magnetic resonance spectroscopy: dynamic nuclear polarisation (DNP)-enhanced NMR in the liquid state. Water hydrogen atoms are detected prior to and after their transfer to molecular sites in peptides and proteins featuring highly-accessible proton-exchangeable groups, as is the case for the -NH groups of intrinsically disordered proteins. The detection of amide proton-water proton exchange can be modulated by membrane-crossing rates, when a membrane channel is interposed. We hyperpolarised water proton spins via dynamic nuclear polarisation followed by sample dissolution (d-DNP) and transferred the created polarisation to -NH groups with high solvent accessibility in an intrinsically disordered protein domain. This domain is the membrane anchor of c-Src kinase, whose activity controls cell proliferation. The hindrance of effective water proton transfer rate constants observed in free solvent when a membrane-crossing step is involved is discussed. This study aims to assess the feasibility of using recently-introduced hyperpolarised (DNP-enhanced) NMR to assess water membrane crossing dynamics.

    更新日期:2018-04-05
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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