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Methods are described for the preparation and high-performance liquid chromatography (HPLC) analysis of monobromobimane derivatives of low molecular weight thiols in extracts of biological samples. Typical problems encountered in the development and application of these methods are discussed. Analysis of mung bean extract is used as an example.
Ab initio molecular dynamics liquid-quench simulations and hybrid density functional calculations are performed to model the effects of room-temperature atomic fluctuations and photo-illumination on the structural and electronic properties of amorphous sub-stoichiometric In 2 O 2.96 . A large configurational ensemble is employed to reliably predict the distribution of localized defects as well as their response to the thermal and light activation. The results reveal that the illumination effects on the carrier concentration are greater in amorphous configurations with shorter In–O bond length and reduced polyhedral sharing as compared to the structures with a more uniform morphology. Further, the obtained correlation between the photo-induced carrier density and the reduction in the number of fully coordinated In-atoms implies that metal oxides with a significant fraction of crystalline/amorphous interfaces would show a more pronounced response to illumination. Photo-excitation also produces In–O 2 –In defects that have not been previously found in sub-stoichiometric amorphous oxides; these defects are responsible for carrier instabilities due to overdoping.
Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary ion mass spectrometry (SIMS) has been recognized as a powerful technique for both two-dimensional (2D) and 3D molecular imaging. Sample fixations (e. g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be non-trivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed in situ liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in in situ liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuum-compatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar 1800 + ion on ice has been determined as 1500 (± 8%) water molecules per Ar 1800 + ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Finally, taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.
Abstract Quasicrystals exhibit long-range order but lack translational symmetry. When grown as single crystals, they possess distinctive and unusual properties owing to the absence of grain boundaries. Unfortunately, conventional methods such as bulk crystal growth or thin film deposition only allow us to synthesize either polycrystalline quasicrystals or quasicrystals that are at most a few centimeters in size. Here, we reveal through real-time and 3D imaging the formation of a single decagonal quasicrystal arising from a hard collision between multiple growing quasicrystals in an Al-Co-Ni liquid. Through corresponding molecular dynamics simulations, we examine the underlying kinetics of quasicrystal coalescence and investigate the effects of initial misorientation between the growing quasicrystalline grains on the formation of grain boundaries. At small misorientation, coalescence occurs following rigid rotation that is facilitated by phasons. Our joint experimental-computational discovery paves the way toward fabrication of single, large-scale quasicrystals for novel applications.
Sulfur has been proposed as the dominant composition for the volcanic material on Io. Sulfur is a complex element which forms many intramolecular and intermolecular allotropes exhibiting a variety of physical properties. Cyclo-S8 sulfur is the most abundant and stable molecular form. The important molecular species within liquid sulfur change in concentration with temperature. Concentrations of the allotropes control the physical properties of the melt. Discontinuities in density, viscosity, and thermal properties reflect the polymerization process within liquid sulfur. Variations in the melting point are related to autodissociation of the liquid. Many solids forms of sulfur have been identified but only orthorhombic alpha and monoclinic beta sulfur, both composed of cyclo-S8 sulfur, are stable under terrestrial conditions. Physical properties of solid sulfur are dependent on the allotrope and, in some cases, the thermal history. Three natural terrestrial sulfur flows are described: (1) Siretoko-Iosan, Japan; (2) Volcan Azufre, Galapagos Islands; and (3) Mauna Loa, Hawaii. All of the flows are associated with fumarolic areas and are considered to have formed by the melting and mobilization of sulfur deposits. Surface textures of the flows indicate a behavior of molten sulfur similar to that of silicate lava. Channels, rivulets, and lobate edges were described for the flows. The solidification of man-made sulfur flows formed as part of the Frasch mining process by which sulfur is removed from the subsurface in a liquid state is described.
Liquid and solid molecular hydrogen has been levitated using a pair of small superconducting solenoids. The hydrogen samples, up to 3 mm in dimension, were trapped in a magnetic potential having either a discrete minimum or a minimum in the form of a ring 1 cm in diameter. The hydrogen could be moved about in the magnetic trap by applying an electric field.
While establishing the basis for a 'Technology 2000' product plan several years ago we plugged in the usual factors contributing toward product success: price/performance justifiable; profitable, warranting high quality maintenance, enhancement, and specific property improvement; narrow inventory requirements; and raw material integrable backwards with easily variable properties (molecular weight, functionality, and isomer control). We resolved this by selecting radical functional, low molecular weight polybutadiene liquid polymers. Encouraged by the need for solid rocket binders, several companies embarked on various perceptions of binder performance requirements over four decades ago. Initially dominated by progress of liquid polysulfides, soon a few settled primarily upon polybutadiene based binders. Such an approach in a few instances was exploited quite viably with a series of functional group terminated liquid polybutadienes: hydroxyl, mercaptan, carboxyl, vinyl, and amine. Good results are obtained for oligomers, liquid polymers, and their hybrids. The only significant limits on compounded products has been solvent resistance and oxidative sensitivity, unless sufficient proportion of sulfide or nitrile moiety is incorporated. For convenience, they have been grouped under the trademarks Nylane, Seamax, Oligomax, and Castomax.
Oligomers are prepared by heating solid ethylene-propylene rubber in container that retains solid and permits liquid product to flow out as it is formed. Molecular weight and viscosity of liquids can be predetermined by process temperature. Copolymers have low viscosity for given molecular weight.
In this work, we use molecular dynamics simulations to evaluate the behavior of toluene (TOL) and p-xylene (XYL) within three different solvents: n -hexane (HEX), n -heptane (HEP), and a thermally-robust ionic liquid (triphenyl-p-phenyl sulfonyl phenyl phosphonium + bis(trifluoromethylsulfonyl)imide (TPSP + Tf 2 N)). Several different temperatures are explored, while the solvation structures, energetics, and dynamics of TOL and XYL are evaluated. The solvation free energy (ΔG solv ) and transfer free energy (ΔG transfer ) of TOL and XYL are calculated using thermodynamic integration (TI). The transfer free energy of XYL from HEP/HEX to TPSP + Tf 2 N is more favorable than that of TOL over the entire temperature range, while the transfer of both TOL and XYL becomes less favorable as the temperature increases. The diffusion rates of TOL and XYL are lower in the ionic liquid when compared to HEP and HEX, but the thermal stability of TPSP + Tf 2 N may allow for higher operating temperatures and accelerated mass transport rates.
An interfacial study is performed using ab initio molecular dynamics (AIMD) simulations to elucidate the electrochemical interfacial stability of an ionic liquid (IL) as component of an electrolyte in contact with a Li-metal anode when an additive, vinylene carbonate (VC), is added to the electrolyte. The IL electrolyte is composed of 1-butyl-1-methylpyrrolidinium bis(fluoro-sulfonyl)-imide (PYR14 + FSI − ) with lithium bis(trifluoromethane-sulfonyl)imide salt (Li + TFSI − ) in a 8:2 concentration ratio. Reactions observed at the interface electrolyte/Li-metal during the AIMD simulations are verified by electronic structure calculations using density functional theory calculations considering a continuum solvent model. We found that the addition of VC to the IL prevents further reduction of the counter-ion TFSI − and retards reduction of FSI − in comparison to the case when the additive VC is absent. The PYR14 + reduction is never observed with or without the additive. The 1st, 2nd, and 3rd electron affinities of the PYR14 + are −0.08, −0.36 and −3.65 eV, indicating little to large repulsive behavior against electrons. The opposite is observed for the two negative ions, FSI − and TFSI − , which yield 1st electron affinities of 1.73 and 1.83 eV, respectively. Reactions obtained under open circuit conditions. Dissociation mechanisms are presented for all IL components reduced at the IL/Li-metal interface.
To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquidlike motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally, the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall, our findings increase our understanding of the connection between molecular motions and diffraction data and therefore advance efforts to extract information about functionally important motions from crystallography experiments.
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We present a method based on sinusoidal approach to equilibrium molecular dynamics (SAEMD) to compute the thermal conductivity of liquids Similar to nonequilibrium molecular dynamics, and unlike equilibrium simulations based on the Green-Kubo formalism, the method only requires the calculation of forces and total energies. The evaluation of heat fluxes and energy densities is not necessary, thus offering the promise of efficiently implementing first principles simulations based on density functional theory or deep molecular dynamics. Our approach is a generalization of SAEMD for solids, where the thermal conductivity is computed in the steady state, instead of a transient regime, thus properly taking into account diffusive terms in the heat equation. We present results for liquid water at ambient conditions and under pressure and discuss simulation requirements to obtain converged values of the thermal conductivity as a function of size and simulation time.
Here we review the current understanding of molecular interactions that govern liquid-liquid phase separation (LLPS) of biological condensates. The connection between sequence, chain conformation, and phase separation of intrinsically disordered proteins (IDPs) and their model polyampholytes is discussed. In particular, we highlight how the charge pattern influences the conformation and phase behavior of natural IDPs. We then describe recent results from theoretical treatments of polyampholytes implementing random phase approximation, field-theoretic simulations, and transfer matrix theory that show an increase in charge segregation results in an increased tendency to phase separate.
Molecular ionic composites (MICs), made from ionic liquids and a rigid-rod polymer poly(2,2'-disulfonyl-4,4'-benzidine terephthalamide) (PBDT), are a new type of rigid gel electrolyte that combine fast ion transport with high thermal stability and mechanical strength. In this work, a MIC electrolyte membrane is prepared that is composed of PBDT, lithium bis(trifluoromethylsulfonyl)imide (LiTFSI), and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (Pyr 14 TFSI) in a mass ratio of 10:10:80. The ionic conductivity at 25 °C is 0.56 mS cm –1 with no added flammable/volatile components. Although the polymer content is only 10 wt%, this MIC membrane is rigid with a tensile modulus of 410 MPa at room temperature. The MIC membrane remains stable and rigid at 200 °C with the shear storage modulus (G') only slightly decreasing by 35%. Li/MIC/LiFePO 4 cells demonstrate stable cycling performance over a wide temperature range from 23 to 150 °C. The specific discharge capacity at 100 and 150 °C at 1 C rate exceeds 160 mAh g –1 . The discharge capacity retention is 99% after 50 cycles at 150 °C. Furthermore, this stable battery performance shows that this low polymer content MIC membrane qualifies for use as a solid electrolyte in lithium metal batteries operating over a wide temperature range.
The benefits of liquid crystal polymers and polyetherimides are combined in an all-aromatic thermoplastic liquid crystalline polyetherimide. Because of the unique molecular structure, all-aromatic thermotropic liquid crystal polymers exhibit outstanding processing properties, excellent barrier properties, low solubilities and low coefficients of thermal expansion in the processing direction. These characteristics are combined with the strength, thermal, and radiation stability of polyetherimides.
Solid hydrogen particles have been selected as a means of storing atomic propellants in future launch vehicles (refs. 1 to 2). In preparation for this, hydrogen particle formation in liquid helium was tested experimentally. These experiments were conducted to visually characterize the particles and to observe their formation and molecular transformations (aging) while in liquid helium. The particle sizes, molecular transformations, and agglomeration times were estimated from video image analyses. The experiments were conducted at the NASA Glenn Research Center in the Supplemental Multilayer Insulation Research Facility (SMIRF, ref. 3). The facility has a vacuum tank, into which the experimental setup was placed. The vacuum tank prevented heat leaks and subsequent boiloff of the liquid helium, and the supporting systems maintained the temperature and pressure of the liquid helium bath where the solid particles were created. As the operation of the apparatus was developed, the hydrogen particles were easily visualized. The figures (ref. 1) show images from the experimental runs. The first image shows the initial particle freezing, and the second image shows the particles after the small particles have agglomerated. The particles finally all clump, but stick together loosely. The solid particles tended to agglomerate within a maximum of 11 min, and the agglomerate was very weak. Because the hydrogen particles are buoyant in the helium, the agglomerate tends to compact itself into a flat pancake on the surface of the helium. This pancake agglomerate is easily broken apart by reducing the pressure above the liquid. The weak agglomerate implies that the particles can be used as a gelling agent for the liquid helium, as well as a storage medium for atomic boron, carbon, or hydrogen. The smallest particle sizes that resulted from the initial freezing experiments were about 1.8 mm. About 50 percent of the particles formed were between 1.8 to 4.6 mm in diameter. These very small particle sizes are encouraging for future formation experiments, where simpler operations will reduce the costs of production.
Porous liquids (PLs) represent a unique platform for molecular separations by combining permanent porosity with liquid-phase mobility. However, it remains a formidable challenge to construct and stabilize PLs with sub-5 Å pores using readily available porous host and liquid media. Here, we report the construction of cyclodextrin (CD)-derived PLs enabled by in situ solvation shell formation. The acid–base neutralization reaction between CD and an organic base was leveraged to generate a thin ionic solvation shell around the CD host, effectively liquefying CD and preventing its segregation in the liquid base medium while preserving accessible molecular-scale cavities. Spectroscopic analysis, neutron scattering, density functional theory calculations, and molecular dynamics simulations collectively confirm the structural evolution and existence of abundant internal porosity in PLs. The unique architectures of CD-derived PLs enable highly selective encapsulation of fluorinated alkanes and significantly enhanced uptake of inert gases. This facile and generalizable strategy enables construction of high-quality PLs with engineered ultramicroporosity to facilitate molecular separations.