Inherent structures for soft long-range interactions in two-dimensional many-particle systems

We generate inherent structures, local potential-energy minima, of the "k-space overlap potential" in two-dimensional many-particle systems using a cooling and quenching simulation technique. The ground states associated with the k-space overlap potential are stealthy (i.e., completely suppress single scattering of radiation for a range of wavelengths) and hyperuniform (i.e., infinite wavelength density fluctuations vanish). However, we show via quantitative metrics that the inherent structures exhibit a range of stealthiness and hyperuniformity depending on the fraction of degrees of freedom χ that are constrained. Inherent structures in two dimensions typically contain five-particle rings, wavy grain boundaries, and vacancy-interstitial defects. The structural and thermodynamic properties of the inherent structures are relatively insensitive to the temperature from which they are sampled, signifying that the energy landscape is relatively flat along the directions sampled, with wide shallow local minima and devoid of deep wells. Using the nudged-elastic-band algorithm, we construct paths from ground-state configurations to inherent structures and identify the transition points between them. In addition, we use point patterns generated from a random sequential addition (RSA) of hard disks, which are nearly stealthy, and examine the particle rearrangements necessary to make the configurations absolutely stealthy. We introduce a configurational proximity metric to show that only small local, but collective, particle rearrangements are needed to drive initial RSA configurations to stealthy disordered ground states. These results lead to a more complete understanding of the unusual behaviors exhibited by the family of "collective-coordinate" potentials to which the k-space overlap potential belongs.     

Modeling the allosteric effect: modification of the tautomerism by intermolecular interactions and extension to molecular wires

B3LYP/6−31G(d) and B3LYP/6−311++G(d,p) calculations were carried out on quinolone and its four azaderivatives (15 tautomers), five wire models (10 tautomers) for proton transfer formed of anthracenol and azaacridines and the corresponding five crown ethers (ten tautomers) in the anthracenol part. The wires are formed by four carbon atoms existing either as cumulenes (pentaene) or polyynes (diyne). On these structures the effect of hydrogen bonds with HF as hydrogen bond donor, protonation on the aza N atoms and coordination with Li⁺ on the same positions were studied. The resulting energies were analyzed taking into account proximity effects.     

Application of standard DFT theory for nonbonded interactions in soft matter: prototype study of poly-para-phenylene

We present a detailed analysis of the application of density functional theory (DFT) methods to the study of structural properties of molecular and supramolecular systems, using as a paradigmatic example three para-phenylene-based systems: isolated biphenyl, single chain poly-para-phenylene, and crystalline biphenyl. We use different functionals for the exchange correlation potential, the local density (LDA), and generalized gradient approximations (GGA), and also different basis sets expansions, localized, plane waves (PW), and mixed (localized plus PW), within the reciprocal space formulation for the hamiltonian. We find that regardless of the choice of basis functions, the GGA calculations yield larger interring distances and torsion angles than LDA. For the same XC approximation, the agreement between calculations with different basis functions lies within 1% (LDA) or 0.5% (GGA) for distances, and while PW and mixed basis calculations agree within 1 degrees for torsion angles, the localized basis results show larger angles by approximately 8 degrees and a nonmonotonic dependence on basis size, with differences within 6 degrees. The most prominent features, namely the torsion between rings for isolated molecule and infinite chain, and planarity for the molecule in crystalline environment, are well reproduced by all DFT calculations.     

Hard–soft modeling parallel factor analysis to solve equilibrium processes

PARAFAC model is the most famous model for analyzing three‐way data. However, this method does not converge to chemically meaningful solutions when applied to three‐way problems involving rank overlap profiles at least in one mode. Rank overlap can be simply found where components have similar spectral profiles or analytes appearing in identical proportions throughout an experiment. However, an appropriate selection of the initial parameters and constraints such as non‐negativity and unimodality can still make PARAFAC model useful in this regard. Although such constraints reduce rotational freedom in PARAFAC solution, they are generally insufficient to wholly eliminate the rotational problem. The goal of the present paper is to incorporate hard modeling constraint in the soft‐modeled PARAFAC algorithm to overcome non‐uniqueness problem in the equilibrium processes involving linearly dependent factors at least in one mode. The hard constraint is introduced to force some or all of the concentration profiles to fulfill an equilibrium model that is refined at each iteration cycle of the optimization process of PARAFAC. The proposed approach is called hard–soft PARAFAC (HSPARAFAC). When the rank overlap species obeys equilibrium model in HSPARAFAC, the unique results are obtained even in the presence of non‐modeled interferences. The new modification in the treatment of equilibrium data sets yields more satisfactory results than the exclusive PARAFAC algorithm. Simulated and real examples with rank overlap problem are used to confirm this statement. Copyright © 2011 John Wiley & Sons, Ltd.     

Molecular topological index: An extension to heterosystems

The molecular topological index (MTI), recently introduced by Schultz, is extended to heterosystems. In order to test the utility of this formulation of the MTI, the index is used to set up the structure-property model for boiling points of alkyl alcohols. This model is comparable to related models based on the connectivity index and on the Wiener index.Dedicated to Professor Frank Harary on the occasion of his 70th birthday.     

Intermolecular interactions as controlling factor for water sorption into polymer membranes

A multidisciplinary approach was used for delineating the mechanisms controlling water sorption into modified block co-poly-(ether/amide) (PEBAX) membranes. In particular, incorporation of aromatic sulfonamide (KET) into the polymer matrix led to a nonlinear increase of water sorption in the membrane. The modification in sorption was accompanied by a nonlinear behavior in membrane surface energies. Infrared analysis revealed a different availability and accessibility of free polar groups supporting the formation of hydrogen bonding as a function of modifier concentration. A combination of both experimental and theoretical procedures was used to analyze the molecular processes of water sorption on PEBAX membranes. Molecular dynamics (MD) and quantum chemical (QC) calculations demonstrated that the formation of KET-KET dimers in the polymeric matrix led to a decrease in the interaction energy between water and modifiers. In addition, no variations in the dipole moments of water-dimer structures were found in comparison to a single KET and water-KET molecule. The formation of water-dimer complexes at higher concentration of modifier decreases the number of the dipole moment, thus preventing the polarization of polymer chains.     

Plant protein-polysaccharide interactions in solutions: application of soft particle analysis and light scattering measurements

The soft particle analysis theory was applied to plant proteins and polysaccharides in solution, to determine the charge density of these polymers and the depth of the layer accessible by counterions according to pH conditions. In addition to the macromolecule shape characterized by light scattering measurements, these properties are also correlated with the optimum coacervation condition, so as to establish the prevalent plant protein-polysaccharide interactions governing the coacervate formation. Globulin was found to be highly charged and spherically shaped. The best coacervation condition was obtained at the pH value, which corresponds to the protein conformation with a dense and compact accessible layer. On the contrary, for the alpha gliadin, bearing a lower charge, a more extended conformation seems to be more favourable. For the plant proteins studied, the coacervation seems to be controlled by the structure of the counter polyanion used: from our model, it turns out that the rod-like structure of arabic gum observed at acidic pH allows the interaction with plant proteins to form coacervates, contrary to the highly charged and spherical structure of alginate.     

Collision models for spectral line shapes: explicit parity considerations

The Voigt line shape is standardly used for interpolating between gaussian and lorentzian line shapes as the gas pressure increases. This is equivalent to modelling the collision processes by one relaxation rate. Deviations from the Voigt line shape are obtained by using more detailed forms for the collision model. Here it is shown that parity considerations motivate a class of collision models, and resulting line shapes, that have not been previously considered.     

Collision cross sections for protein ions

A method for the determination of cross sections for gas-phase protein ions, based on the energy loss of ions as they pass through a collision gas, is described. A simple model relates the energy loss to the number of collisions and hence the cross section. Results from a Monte Carlo model that support the validity of this approach are described. Experimental cross sections are reported for motilin, ubiquitin, cytochrome c, myoglobm, and bovine serum albumin. Cross sections range from approximately 800 Ų for motilin to approximately 14,000 Ų for bovine serum albumin and generally increase with the number of charges on the ion. Cytochrome c ions from aqueous solution show somewhat smaller cross sections than ions formed from solutions of higher organic content, suggesting that the gas-phase ions may retain some memory of their solution conformation.     

Molecular interactions of cord factor with dipalmitoylphosphatidylcholine monolayers: implications for lung surfactant dysfunction in pulmonary tuberculosis

Molecular interactions between mycobacterial cell wall lipid, cord factor (CF) and the abundant surfactant lipid, dipalmitoylphosphatidylcholine (DPPC) were investigated using Langmuir monolayers at physiological temperatures (37 degrees C). Surface topography of the films was visualized by atomic force microscopy (AFM). Thermodynamic behavior of the mixed monolayers was evaluated by investigating the molecular area excess, excess Gibbs free energy of mixing and maximum compressibility modulus (SCM(max)). Cord factor formed immiscible and thermodynamically unstable monolayers with DPPC. Monolayer presence of cord factor altered the physical state of DPPC monolayers from liquid condensed to liquid expanded with the lowering of SCM(max) from 160 to 40 mN/m, respectively. AFM imaging exhibited smooth homogenous surface topography of DPPC films which in the presence of cord factor was markedly altered with the appearance of aggregates and increased surface roughness. The results highlight the capacity of cord factor to disturb DPPC monolayer organization and structure. Interfacial presence of cord factor results in DPPC monolayer fluidization. Lung surfactant function is attributed to its ability to form well packed low compressibility films. Such molecular interactions suggest a dysfunction of lung surfactant in pulmonary tuberculosis due to surfactant monolayer fluidization.     

Energy screening for the incremental scheme: application to intermolecular interactions

A systematic screening procedure for small contributions in the incremental expansion of the correlation energy is presented. The performance of the proposed scheme is checked for the calculation of intermolecular interactions in realistic test systems as large as a guanine-cytosine base pair. It is found that the computational cost for the incremental expansion can be reduced considerably without significant loss of accuracy. Typically, the errors of the systems investigated here amount to <3.4, 0.22, and 0.06% for second-, third-, and fourth-order expansions, respectively. For almost all cases, the error in the total correlation energy can be kept below 1 kcal/mol with respect to the canonical CCSD result if the incremental series is truncated in a proper way.     

Use of surface plasmon resonance for studies of protein-protein and protein-phospholipid membrane interactions. Application to the binding of factor VIII to von Willebrand factor and to phosphatidylserine-containing membranes.

The surface plasmon resonance phenomenon is used for real time measurements of protein-protein and protein-membrane interactions. In the present study two surface plasmon resonance-based binding assays permitting study of the interaction of coagulation factor VIII (fVIII) with von Willebrand factor (vWf) and phospholipid have been developed. These interactions of fVIII are required for maintenance of fVIII concentration in circulation and for the assembly of the functional factor Xase complex, respectively. With these binding assays, the role of the light chain (LCh) in fVIII binding to vWf and to immobilized phospholipid monolayers and intact vesicles containing 25% phosphatidylserine (PS) and 4% PS was examined. The finding that Kd of LCh binding to vWf (3.8 nM) is 9.5 times higher than that of fVIII (0.4 nM), indicates that the heavy chain (HCh) is required for the maximal affinity of fVIII for vWf. In contrast, affinities of LCh for 25/75 PS/phosphatidylcholine (PC) monolayers and 4/76/20 PSPC-phosphatidylethanolamine (PE) vesicles are similar to that of fVIII, indicating that LCh is solely responsible for these interactions. It was also examined how removal of the acidic region affects the binding affinity of the remaining part of LCh for vWf and phospholipid. It was demonstrated that the loss of the LCh acidic region upon thrombin cleavage leads to an 11 and 160-fold increase in the dissociation rate constant (k(off) value) and a 165 and 1500-fold increase in the Kd value of the binding of fVIII fragment A3-C1-C2 to vWf compared to that of LCh and fVIII, respectively. In contrast, the binding affinity of A3-C1-C2 for PS-containing membranes was 8-11-fold higher than that of LCh. Possible conformational change(s) in C2 domain upon removal of the acidic region were studied using anti-fVIII monoclonal antibody NMC-VIII/5 with an epitope within the C2 domain of LCh as a probe. The determined lower binding affinity of A3-C1-C2 for NMC-VIII/5 immobilized to a sensor chip than that of LCh, indicates that these conformational changes do occur.     

Particle-particle particle-mesh method for dipolar interactions: on error estimates and efficiency of schemes with analytical differentiation and mesh interlacing

The interlaced and non-interlaced versions of the dipolar particle-particle particle-mesh (P(3)M) method implemented using the analytic differentiation scheme (AD-P(3)M) are presented together with their respective error estimates for the calculation of the forces, torques, and energies. Expressions for the optimized lattice Green functions, and for the Madelung self-forces, self-torques and self-energies are given. The applicability of the theoretical error estimates are thoroughly tested and confirmed in several numerical examples. Our results show that the accuracy of the calculations can be improved substantially when the approximate (mesh computed) Madelung self-interactions are subtracted. Furthermore, we show that the interlaced dipolar AD-P(3)M method delivers a significantly higher accuracy (which corresponds approximately to using a twice finer mesh) than the conventional method, allowing thereby to reduce the mesh size with respect to the non-interlaced version for a given accuracy. In addition, we present similar expressions for the dipolar ik-differentiation interlaced scheme, and we perform a comparison with the AD interlaced scheme. Rough tests for the relative speed of the dipolar P(3)M method using ik-differentiation and the interlaced/non-interlaced AD schemes show that when FFT computing time is the bottleneck, usually when working at high precisions, the interlaced AD-scheme can be several times faster than the other two schemes. For calculations with a low accuracy requirement, the interlaced version can perform worse than the ik and the non-interlaced AD schemes.     

Error analysis in Barker's method: extension to ternary systems

An extension of Barker's method to ternary systems is briefly outlined. Expressions for the standard deviations of the excess molar Gibbs free energy and the equilibrium pressure as functions of composition are obtained. These expressions are applied to accurate experimental data for the cryogenic (liquid) mixture CH₃F+N₂O+Xe recently measured in our laboratory.     

Biomimicry designs for photoelectrochemical systems: Strategies to improve light delivery efficiency

In the past years, photoelectrocatalysis has been developed to offer green and sustainable application to wastewater remediation, water disinfection, H₂ production and CO₂ reduction. The advances of these systems with new semiconductor photoelectrocatalysts that are photoexcited with visible light giving photogenerated charge carriers efficiently, separated in a photoelectrochemical cell, are explained. These studies do not consider the light transport as fundamental aspect of light–matter interaction, although the harvesting of photons at the semiconductor surface limits the quantum yield by the existing semiconductor architectures. This opinion review envisages biomimicry as an alternative natural guide for synthesizing more efficient photoelectrodes. Micro- and nanostructure shapes from nature are identified to prepare new bio-inspired photoelectrodes for photoelectrochemical reactors with the light transport as indispensable element. The implementation of strategies of phototroph organisms to maximize light adsorption and the enhancement of photoelectrocatalytic surface area are analyzed as key factors for such bio-based photoelectrodes.     

Exact and Approximate Expressions for Bubble-Particle Collision

The flotation microprocess of collision is investigated and an exact expression for the probability of collision (Pc) is developed based on the intermediate flow of Yoon and Luttrell (1). This expression for Pc only assumes that the bubble and particle are spherical and that the particle radius is less than the bubble radius (i.e., Rp < RB). In addition to removing the requirement that Rp < RB, the influence of a particle settling velocity is also included in the model development. The expression for Pc is shown to be a function of three dimensionless groups: (i) the magnitude of the dimensionless particle settling velocity, ||G ||; (ii) the bubble Reynolds number, ReB; and (iii) the ratio of particle to bubble radius, Rp/RB. The probability of collision model is compared to available experimental data and good agreement is shown. A parametric study is also completed for 0 1. Copyright 1999 Academic Press.     

Functional materials: from hard to soft porous frameworks

This Review aims to give an overview of recent research in the area of porous, organic-inorganic and purely organic, functional materials. Possibilities for introducing organic groups that exhibit chemical and/or physical functions into porous materials will be described, with a focus on the incorporation of such functional groups as a supporting part of the pore walls. The number of organic groups in the network can be increased such that porous, purely organic materials are obtained.     

Correction to: Combined uncertainty factor for sampling and analysis

Accreditation and Quality Assurance - In the penultimate paragraph of the original publication, a confidence interval of 93&nbsp;mg/kg to 971&nbsp;mg/kg was reported. These values should be...