A polarizable ion model for the structure of molten CuI

The results are reported of the molecular dynamics simulations of the coherent static structure factor of molten CuI at 938 K using a polarizable ion model. This model is based on a rigid ion potential to which the many body interactions due to the anions induced polarization are added. The calculated structure factor reproduces the clear sharp prepeak observed in neutron diffraction data. The corresponding partial structure factors and the related radial distribution functions calculated by molecular dynamics are compared with those found in the literature derived from a combination of neutron and x-ray diffraction data with the aid of the reverse Monte Carlo simulation technique, as well as those calculated by ab initio MD simulations.     

Structure factor and thermodynamics of rigid dendrimers in solution

The "polymer reference interaction site model" (PRISM) integral equation theory is used to determine the structure factor of rigid dendrimers in solution. The theory is quite successful in reproducing experimental structure factors for various dendrimer concentrations. In addition, the structure factor at vanishing scattering vector is calculated via the compressibility equation using scaled particle theory and fundamental measure theory. The results as predicted by both theories are systematically smaller than the experimental and PRISM data for platelike dendrimers.     

Molecular dynamics study of polarizable ion models for molten AgBr

Three different polarizable ion models for molten AgBr have been studied by molecular dynamics simulations. The three models are based on a rigid ion model (RIM) with a pair potential of the type proposed by Vashishta and Rahman for alpha-AgI, to which the induced dipole polarization of the ions is added. In the first (PIM1) the dipole moments are only induced by the local electric field, while in the other two (PIM1s and PIM2s) a short-range overlap induced polarization opposes the electrically induced dipole moments. In the PIM1 and the PIM1s only the anions are assumed polarizable, while in the PIM2s both species are polarizable. Long molecular dynamics simulations show that the PIM2s is an unphysical model since, for some improbable but possible critical configurations, the ions become infinitely polarized. The results of using the PIM1, the PIM1s, as well as those of the simple RIM, have been compared for the static structure and ionic transport properties. The PIM1 reproduces the broad main peak of the total structure factor present in the neutron diffraction data, although the smoothed three-peak feature of this broad peak is slightly overestimated. The structural results for the PIM1s are intermediate between those for the RIM and the PIM1, but fail to reproduce the experimental features within the broad principal peak. Concerning the ionic transport properties, the value of the conductivity obtained using PIM1 is in good agreement with experimental values, while the self-diffusion coefficients and the conductivity for the PIM1s are lower than the corresponding values using the PIM1 and the RIM.     

Poisson-Boltzmann与Donnan模型计算压实膨润土孔隙水与外部溶液间离子平衡的差异性比较

压实膨润土孔隙水与外部溶液之间的离子平衡是影响离子在压实膨润土中扩散的影响因素之一, 表征这一平衡的离子平衡系数可用压实膨润土的宏观属性参数通过Donnan 模型计算得到. 通过对膨润土主体矿物蒙脱石的TOT层结构单元进行简化, 构建了一个压实膨润土的单类孔隙结构模型, 辅以一个尺度变量H, 用Poisson-Boltzmann (PB)理论模型计算上述离子平衡系数. 对比计算结果, 发现PB模型计算的离子平衡系数总是大于Donnan模型的结果, 而参数H是联系这两种模型之间的桥梁. 通过对参数H取极限H→0, 实现了从PB模型到Donnan 模型的数学变换, 并从机理上讨论了两种模型之间的差异及其在实际扩散问题中的应用.分析表明PB模型更符合离子在压实膨润土中扩散的实际情况, 更适于处理实际扩散问题.     

Neutron diffraction data and molecular dynamics simulations of the molten mixture Ag(Br0.7I0.3)

The structure factors of the ionic liquid mixture Ag(Br(0.7)I(0.3)) at three temperatures, 723, 923, and 1023 K, as well as of the pure molten AgI at 923 K and the pure molten AgBr at 773 and 923 K, were studied experimentally and by means of molecular dynamics simulations. The experiments were carried out using the high intensity total scattering time-of-flight spectrometer, HIT-II, at the KENS spallation neutron source in Japan. The experimental data are very reliable, with the possible exception of the small momentum transfer region, whose accessibility is limited by neutron energy and detector positions. The simulations made use of the semiempirical rigid ion potentials of the Vashishta-Rahman [Phys. Rev. Lett. 40, 1337 (1978)] type using a new set of parameters appropriate for the mixture. Within the known constraints of the pairwise rigid ion potentials, the simulated structure factors are in fair agreement with experiment. The results for the pair distribution functions suggest that the molten mixture retains the superionic character found in previous calculations of both the AgI and AgBr melts. This suggestion is confirmed by the results for the self-diffusion coefficients. Values obtained for the ionic conductivities are also presented.     

Molecular dynamics study of polarization effects on AgI

Three different models of AgI are studied by molecular dynamics simulations. The first one is the rigid ion model (RIM) with the effective pair potential of the Vashishta and Rahman form and the parametrization proposed by Shimojo and Kobayashi. The other two are polarizable ion models in which the induced polarization effects have been added to the RIM effective pair potential. In one of them (PIM1), only the anions are assumed to be polarizable by the local electric field. In the other one (PIM2s), the silver polarization is also included, and a short-range overlap-induced polarization opposes the electrically induced dipole moments. This short-range polarization is proved to be necessary to avoid overpolarization when both species are assumed to be polarizable. The three models reproduce the superionic character of alpha-AgI at 573 K and the liquid behavior of molten AgI at 923 K. The averaged spatial distribution of the cations in the alpha-phase obtained for PIM1 appears to be in better agreement with experimental data analysis. The PIM1 also reproduces the structure factor prepeak at about 1 A(-1) observed from neutron diffraction data of molten AgI. The three models retain in the liquid phase the superionic character of alpha-AgI, as the mobility of the cations is significantly larger than that for the anions. The ionic conductivity for the polarizable ion models is in better agreement with experimental data for alpha-AgI and molten AgI.     

Natural Soft/Rigid Superlattices as Anodes for High‐Performance Lithium‐Ion Batteries

Volume expansion and poor conductivity are two major obstacles that hinder the pursuit of the lithium‐ion batteries with long cycling life and high power density. Herein, we highlight a misfit compound PbNbS₃ with a soft/rigid superlattice structure, confirmed by scanning tunneling microscopy and electrochemical characterization, as a promising anode material for high performance lithium‐ion batteries with optimized capacity, stability, and conductivity. The soft PbS sublayers primarily react with lithium, endowing capacity and preventing decomposition of the superlattice structure, while the rigid NbS₂ sublayers support the skeleton and enhance the migration of electrons and lithium ions, as a result leading to a specific capacity of 710 mAh g^?1 at 100 mA g^?1, which is 1.6 times of NbS₂ and 3.9 times of PbS. Our finding reveals the competitive strategy of soft/rigid structure in lithium‐ion batteries and broadens the horizons of single‐phase anode material design.     

X-ray diffraction from the uniaxial and biaxial nematic phases of bent-core mesogens

X-ray diffraction patterns for the uniaxial and biaxial nematic phases exhibited by rigid bent-core mesogens were calculated using a simple model for the molecular form factor and a modified Lorentzian structure factor. The X-ray diffraction patterns depend strongly on the extent of the alignment of the molecular axes as well as the orientation of molecular planes. The X-ray diffraction can be unequivocally used to identify the biaxial nematic phase, study the uniaxial-biaxial phase transition, and estimate the order parameters of the nematic phase.     

X‐ray diffraction from the uniaxial and biaxial nematic phases of bent‐core mesogens

X‐ray diffraction patterns for the uniaxial and biaxial nematic phases exhibited by rigid bent‐core mesogens were calculated using a simple model for the molecular form factor and a modified Lorentzian structure factor. The X‐ray diffraction patterns depend strongly on the extent of the alignment of the molecular axes as well as the orientation of molecular planes. The X‐ray diffraction can be unequivocally used to identify the biaxial nematic phase, study the uniaxial–biaxial phase transition, and estimate the order parameters of the nematic phase.     

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.     

A structural analysis of lead hydroxyvanadinite

Hydroxyvanadinite, Pb(10)(VO(4))(6)(OH)(2), was prepared by the co-precipitation method and analyzed by X-ray absorption spectroscopy (XANES, EXAFS), infrared spectroscopy, Raman scattering and X-ray diffraction (XRD). The results showed that the structure is very similar to that of vanadinite, Pb(10)(VO(4))(6)Cl(2), with space group P6(3)/m (176) and cell parameters a = 10.2242(3) A and c = 7.4537(2) A. A Rietveld refinement of the structure was performed using vanadinite as the starting model and fixing the geometry of the vanadate ion as a rigid body. First-principles Density Functional embedded cluster models are developed to analyze electronic structures, bonding, and densities of states. Interaction of Pb with the OH channel anion is examined in detail, as an important structural feature. A periodic band structure approach was used to obtain a further estimate of relaxed atomic coordinates.     

Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment

Immobilized lanthanide ions offer the opportunity to refine structures of proteins and the complexes they form by using restraints obtained from paramagnetic NMR experiments. We report the design, synthesis, and spectroscopic evaluation of the lanthanide chelator, Caged Lanthanide NMR Probe 5 (CLaNP-5) readily attachable to a protein surface via two cysteine residues. The probe causes tunable pseudocontact shifts, alignment, paramagnetic relaxation enhancement, and luminescence, by chelating it to the appropriate lanthanide ion. The observation of single shifts and the finding that the magnetic susceptibility tensors obtained from shifts and alignment analyses are highly similar strongly indicate that the probe is rigid with respect to the protein backbone. By placing the probe at various positions on a model protein it is demonstrated that the size and orientation of the magnetic susceptibility tensor of the probe are independent of the local protein environment. Consequently, the effects of the probe are readily predictable using a protein structure only. These findings designate CLaNP-5 as a protein probe to deliver unambiguous high quality structural restraints in studies on protein-protein and protein-ligand interactions.     

Rigid organic nanodisks of controlled size: A catanionic formulation

We show that organic rigid nanodisks of controlled size can be produced using a balanced pair of ionic surfactant molecules in a catanionic system. The counter-ion for the cationic surfactant is hydroxide. The counter-ion of the anionic surfactant is the hydronium ion. Close to equimolarity, counter-ions from water molecules: fluid solutions of ultra-low conductivity are obtained. This is solution contains rigid disks of thickness 4 nm: chains are frozen and surfaces are covered by ion pairs formed by the headgroups. The overall size of the disks is continuously adjustable from micrometer to nanometer size and is controlled by the excess of one of the two single chain surfactants involved. Unbound dispersed, nematic and lamellar structures are detected and located in the ternary equilibrium phase diagram at room temperature.     

Transmembrane ion transport by calixarenes and their derivatives

Regulation of transmembrane ion transport is a vital aspect of bioinorganic chemistry. To understand how this highly selective process occurs, how it can become impaired and how impairment may be treated, model compounds are useful tools. Several systems are presently being explored but one of the most widely applicable combines a rigid macrocycle, capable of size-based ion recognition, with membrane-spanning substituents that allow the target ions to traverse a phospholipid bilayer. The calixarene class of macrocycles is ideally suited to this task. This article sets out the biological background to transmembrane ion transport, the methods available to study the phenomenon, examples of model compounds, and proposes areas of further study.     

Local order in aqueous NaCl solutions and pure water: X-ray scattering and molecular dynamics simulations study

The microstructures of pure water and aqueous NaCl solutions over a wide range of salt concentrations (0-4 m) under ambient conditions are characterized by X-ray scattering and molecular dynamics (MD) simulations. MD simulations are performed with the rigid SPC water model as a solvent, while the ions are treated as charged Lennard-Jones particles. Simulated data show that the first peaks in the O...O and O...H pair correlation functions clearly decrease in height with increasing salt concentration. Simultaneously, the location of the second O...O peak, the signature of the so-called tetrahedral structure of water, gradually disappears. Consequently, the degree of hydrogen bonding in liquid water decreases when compared to pure fluid. MD results also show that the hydration number around the cation decreases as the salt concentration increases, which is most likely because some water molecules in the first hydration shell are occasionally substituted by chlorine. In addition, the fraction of contact ion pairs increases and that of solvent-separated ion pairs decreases. Experimental data are analyzed to deduce the structure factors and the pair correlation functions of each system. X-ray results clearly show a perturbation of the association structure of the solvent and highlight the appearance of new interactions between ions and water. A model of intermolecular arrangement via MD results is then proposed to describe the local order in each system, as deduced from X-ray scattering data.     

Rigid Lipid Membranes and Nanometer Clefts: Motifs for the Creation of Molecular Landscapes

Amphiphilic lipids associate in water spontaneously to form micelles, vesicles, monolayers, or biological membranes. These aggregates are soft and their shape can be changed easily. They behave like complex fluids because they are merely held together by weak, nondirected forces. The most important characteristic of these monolayers is their ability to dissolve hydrophobic molecules in the form of freely movable monomers. The fluid molecular layers are not suitable to anchor the components of chain reactions. However, if the alkyl chains are replaced by rigid skeletons or if the head groups are connected through intermolecular interactions, the aggregates become rigid and their fluid solvent character is lost. The construction of chiral surfaces by synkinesis (synthesis of noncovalent compounds) and of enzyme‐type surface clefts of defined size can now be carried out by using rigid lipid membranes. Monolayers and nanometer pores on solid substrates attain sharp edges, and upright nanometer columns on smooth surfaces no longer dissipate. Five examples illustrate the advantages of using rigid molecular assemblies: 1) Cationic domains of rigid edge amphiphiles in fluid membranes act as manipulable ion channels. 2) Spherical micelles, micellar helical fibers, and vesicular tubes can be dried and stored as stable material. Molecular landscapes form on smooth surfaces. 3) α,ω‐Diamide bolaamphiphiles form rigid nanometer‐thick walls on smooth surfaces and these barriers cannot be penetrated by amines. Around steroids and porphyrins, they form rigid nanometer clefts whose walls and water‐filled centers can be functionalized. 4) The structure of rigid oligophenylene‐ and quinone monolayers on electrodes can be changed drastically and reversibly by changing the potential. 5) 10¹⁰ Porphyrin cones on a 1‐cm² gold electrode can be controlled individually by AFM‐ and STM‐tips and investigated by electrochemical, photochemical, and mechanical means. In summary, rigid monolayers and bilayers allow the formation of a great variety of membrane structures that cannot be obtained from classical fluid alkyl amphiphiles.     

Structure-based prediction of the conductance properties of ion channels

The HOLE procedure allows the prediction of the absolute conductance of an ion channel model from its structure. The original prediction method uses an empirically corrected Ohmic method. It is most successful, with predictions being reliable to within a factor of two. A new modification of the procedure is presented in which the self-diffusion coefficients of water molecules from molecular dynamics simulation are used to replace the empirical correction factor. A "prediction" of the conductance for the porin OmpF by the new method is made and shown to be very close to the experimental value. HOLE also allows the prediction of the effect that the addition of non-electrolyte polymers will have on channel conductance. The method has great potential to yield structural information from data provided by single channel recordings but needs further validation by making measurements on channels of known structure. Preliminary results are given of single channel records establishing the effects of non-electrolytes on the conductance of gramicidin D channels. As an example of the potential uses of the procedure application is made to examine the oligomerization of alpha-toxin (alpha-hemolysin) channels. A model for the alpha-toxin hexamer, based on the crystal structure for the heptamer, is generated using molecular mechanics methods. The compatibility of the structures with single channel conductance data is assessed using HOLE.     

Computational study of the texture formation in mesophase pitch-based carbon fibres

This paper studies the thermal relaxation phenomena after melt-extrusion of a rigid discotic uniaxial nematic mesophase pitch using mathematical modelling and computer simulation. The Ericksen and Landau-de Gennes continuum theories are used to investigate the structure development and texture formation across mesophase pitch-based carbon fibres. The two-dimensional model captures five types of transverse patterns, which match the commonly observed textures for mesophase pitch-based carbon fibres. They are: random, zig-zagged radial, radial, quasi-onion and onion. These textures represent the various combinations possible from the interplay between structure (i.e. texture) development and cooling during the fibre spinning process. During the thermal relaxation after the cessation of extensional flow the discotic nematic molecules store elastic free energy decays. The distorted nematic molecular profiles reorient to release the stored elastic free energy. The difference in time scales for molecular reorientation and thermal relaxation result in different transverse textures. The rate at which the fibres are cooled is the main factor in controlling the structure development. A slow cooling rate would permit the nematic discotic molecules to reorient to a well-developed (radial or onion) texture. The random texture is a result of rapid quenching. The numerical results are consistent with published experimental observations.     

Molecular dynamics study of polarizable point dipole models for molten sodium iodide

The structure, the ionic transport properties, and the dynamics of long-wavelength charge-density fluctuations, for two polarizable point dipole models of molten NaI, have been studied by molecular dynamics simulations. These models are based on a rigid ion potential to which the induced dipole polarization of the anions is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and short-range damping interactions that oppose the electrically induced dipole moments. The two polarizable ion models differ only in the range of the damping polarization interactions. The influence of the induced anion polarization on the different properties of simulated molten NaI is discussed.     

Monitoring the mechanical properties of the solid electrolyte interphase(SEI) using electrochemical quartz crystal microbalance with dissipation

Stable solid electrolyte interphase(SEI) has been well established to be critical for the reversible operation of Li(ion) batteries,yet our understanding of its mechanical properties currently remains incomplete.Here,we used an electrochemical quartz crystal microbalance combined with dissipation monitoring(EQCM-D) to investigate SEI formation.By quantitatively estimating in-situ,the change in mass,shear modulus,and viscosity of the SEI,we show that the SEI formation in propylene carbonate(PC)-and ethylene carbonate/diethyl carbonate(EC/DEC)-based electrolytes involves the growth of a rigid laye r followed by a viscoelastic layer,whereas a distinct "one-layer" rigid model is applicable to the SEI formulated in tetraethylene glycol dimethyl ether(TEGDME)-based electrolyte.With the continuous formation of the SEI,its shear modulus decreases accompanied by an increase in viscosity.In TEGDME,the lightest/thinnest SEI(mass lower than in PC by a factor of nine) yet having the greatest stiffness(more than five times that in PC) is obtained.We attribute this behavior to differences in the chemical composition of the SEIs,which have been revealed by tracking the mass-change-per-mole-of-electrontransferred using EQCM-D and further confirmed by X-ray photoelectron spectroscopy.