Short-range Molecular Interactions Research Articles

Zeolite ATN: Topological characterization and predictive analysis on potential energies using entropy measures

Zeolites serve as multifunctional microporous materials and have potential applications as catalysts, ion exchangers, and adsorbents. Researchers are interested in the topological characterization of zeolite frameworks due to their complex 3D arrangement of atoms. ATN is one of the variants of zeolite whose building block is arranged in a non-isometric cyclic permutation. The long-range and short-range molecular interactions of the ATN framework are influenced by the geometric arrangement of molecules. In this paper, we have investigated Shannon's information entropy measures of the ATN framework using bond degree and neighborhood degree sum based indices as weights. Further, a predictive analysis with the aid of entropy measures to determine the long-range and short-range potential energies has been implemented. The model proposed in this study can be incorporated into the fields of molecular physics and theoretical chemistry to determine the energy levels of microporous materials. Therefore, the predictive model will make a substantial contribution to QSAR/QSPR modeling.

Improved Diffusion Interaction Parameter Measurement to Predict the Viscosity of Concentrated mAb Solutions.

During the developability assessment of therapeutic monoclonal antibody (mAb) candidates, utilization of robust high-throughput predictive assays enables rapid selection of top candidates with low risks for late-stage development. Predicting the viscosities of highly concentrated mAbs using limited materials is an important aspect of developability assessment because high viscosity can complicate manufacturability, stability, and administration. Here, we report a high-throughput assay measuring protein-protein interactions to predict mAb viscosity. The diffusion interaction parameter (kD) measures colloidal self-association in dilute solutions and has been reported to be predictive of the mAb viscosity at high concentrations. However, kD of Amgen early stage IgG1 mAb candidates measured in 10 mM acetate at pH 5.2 containing sucrose and polysorbate (denoted A52SuT) shows only weak correlation to their viscosities at 140 mg/mL in A52SuT. We hypothesize that kD measured in A52SuT reflects primarily long-range electrostatic repulsions because most of these mAb candidates carry strong net positive charges in this low ionic strength formulation with pH (5.2) well below pI values of mAb candidates. However, the viscosities of high concentration mAbs depend heavily on short-range molecular interactions. We propose an improved kD method in which salt is added to suppress charge repulsions and to allow for detection of key short-range interactions in dilute solutions. Salt types and salt concentrations were screened, and an optimal salt condition was identified. This optimized method was further validated using two test mAb sets. Overall, the method improves the Pearson R2 between kD and viscosity (6-230 cP) from 0.24 to 0.80 for a data set consisting of 37 mAbs.

Comments on excess molar volumes reported in “Study of short range and long range molecular interactions in binary liquid mixtures of N,N-dimethylformamide (DMF) and 1-propanol”

• V m E values of Prajapati and coworkers compared to published literature data of ten other researchers. • Published V m E values are much smaller in absolute magnitude than values of Prajapati and coworkers. • Published V m E versus mole fraction curves show simple parabolic behavior. • V m E versus mole fraction curves of Prajapati and coworkers show several local minima and maxima. A polemic is given concerning the volumetric properties reported for binary N,N-dimethylformamide + 1-propanol mixtures in the published paper by Prajapati and coworkers. The reported excess molar volumes differ significantly from the published literature values of ten independent research groups, all of which are much smaller in absolute magnitude than the values reported by Prajapati and coworkers.

Study of short range and long range molecular interactions in binary liquid mixtures of N,N-dimethylformamide (DMF) and 1-propanol

In the present study precisely measured properties; static dielectric constant (ε0), refractive index (n) and density (ρ) of binary liquid mixtures of N,N-dimethylformamide (DMF) and 1-propanol (1-PN) have been used to determine linear correlation parameter (grr), mutual linear correlation parameter (gAB), excess Helmholtz free energy functions (ΔF) and excess molar polarization (ΔP). The dipolar contributions to these functions arising from long range electrostatic interaction, short range interaction between identical molecules and short range interaction between dissimilar molecules have been assessed separately. The excess thermodynamic functions calculated from the experimental data supports the formation of clusters with antiparallel or destructive angular correlation (β-clusters). The variation of excess static dielectric constant, excess refractive index and excess molar volume have been used to discuss the type, the strength and the nature of intermolecular interactions betweenconstituent species. Comparison of the predicted values of static dielectric constant and refractive index of the liquid mixtures using various mixing rules with the experimentally determined values have been assessed in terms of Average Percentage Deviation (APD).

Mesoscopic Lattice Boltzmann Modeling of the Liquid-Vapor Phase Transition.

We develop a mesoscopic lattice Boltzmann model for liquid-vapor phase transition by handling the microscopic molecular interaction. The short-range molecular interaction is incorporated by recovering an equation of state for dense gases, and the long-range molecular interaction is mimicked by introducing a pairwise interaction force. Double distribution functions are employed, with the density distribution function for the mass and momentum conservation laws and an innovative total kinetic energy distribution function for the energy conservation law. The recovered mesomacroscopic governing equations are fully consistent with kinetic theory, and thermodynamic consistency is naturally satisfied.

First-principles experimental demonstration of ferroelectricity in a thermotropic nematic liquid crystal: Polar domains and striking electro-optics

We report the experimental determination of the structure and response to applied electric field of the lower-temperature nematic phase of the previously reported calamitic compound 4-[(4-nitrophenoxy)carbonyl]phenyl2,4-dimethoxybenzoate (RM734). We exploit its electro-optics to visualize the appearance, in the absence of applied field, of a permanent electric polarization density, manifested as a spontaneously broken symmetry in distinct domains of opposite polar orientation. Polarization reversal is mediated by field-induced domain wall movement, making this phase ferroelectric, a 3D uniaxial nematic having a spontaneous, reorientable polarization locally parallel to the director. This polarization density saturates at a low temperature value of ∼6 µC/cm2, the largest ever measured for a fluid or glassy material. This polarization is comparable to that of solid state ferroelectrics and is close to the average value obtained by assuming perfect, polar alignment of molecular dipoles in the nematic. We find a host of spectacular optical and hydrodynamic effects driven by ultralow applied field (E ∼ 1 V/cm), produced by the coupling of the large polarization to nematic birefringence and flow. Electrostatic self-interaction of the polarization charge renders the transition from the nematic phase mean field-like and weakly first order and controls the director field structure of the ferroelectric phase. Atomistic molecular dynamics simulation reveals short-range polar molecular interactions that favor ferroelectric ordering, including a tendency for head-to-tail association into polar, chain-like assemblies having polar lateral correlations. These results indicate a significant potential for transformative, new nematic physics, chemistry, and applications based on the enhanced understanding, development, and exploitation of molecular electrostatic interaction.

Characterization of short-range molecular interaction by empirical solvent polarity scale to analyze the Kerr effect of nematic liquid crystals in the isotropic phase

It is well known that a relatively large Kerr effect in the isotropic phase of nematic liquid crystals (NLCs) is related to the existence of short-range ordering (SRO). Thus, the conversion of the long-range ordering (LRO) behavior in the nematic phase to the SRO in the isotropic phase of NLCs can characterize the nonlinear electro-optic Kerr effect. To show conversion from LRO to SRO, we employ an empirical solvent polarity scale (ETN). Interestingly, ETN originates from the solvatochromic polarity (SP) parameters, which demonstrates the quantitative value for describing the molecular interaction in each temperature point, even in the isotropic phase of NLCs. Our results show that the higher ETN value leads to a larger Kerr constant (B) owing to the larger short-range molecular interaction between rigid rod-like NLCs. To demonstrate a linear relationship of the B value with the ETN and SP parameters, a new correlation is introduced for the first time. Our investigations and newly introduced parameters strongly indicate that short-range molecular interactions still exist in the isotropic phase of NLCs, even when the macroscopically observable LRO behaviors disappear.

Lattice Boltzmann model with self-tuning equation of state for multiphase flows.

A lattice Boltzmann (LB) model for multiphase flows is developed that complies with the thermodynamic foundations of kinetic theory. By directly devising the collision term for the LB equation at the discrete level, a self-tuning equation of state is achieved, which can be interpreted as the incorporation of short-range molecular interaction. A pairwise interaction force is introduced to mimic the long-range molecular interaction, which is responsible for interfacial dynamics. The derived pressure tensor is naturally consistent with thermodynamic theory, and surface tension and interface thickness can be independently prescribed. Numerical tests, including static and dynamic cases, are carried out to validate the present model and good results are obtained. As a further application, head-on collision of equal-sized droplets is simulated and the elusive "bouncing" regime is successfully reproduced.

Describing screening in dense ionic fluids with a charge-frustrated Ising model.

Charge correlations in dense ionic fluids give rise to novel effects such as long-range screening and colloidal stabilization which are not predicted by the classic Debye-Hückel theory. We show that a Coulomb or charge-frustrated Ising model, which accounts for both long-range Coulomb and short-range molecular interactions, simply describes some of these ionic correlations. In particular, we obtain, at a mean field level and in simulations, a non-monotonic dependence of the screening length on the temperature. Using a combination of simulations and mean field theories, we study how the correlations in the various regimes are affected by the strength of the short ranged interactions.

Interplay between Long-Range Crystal Order and Short-Range Molecular Interactions Tunes Carrier Mobility in Liquid Crystal Dyes

We investigated the influence of molecular packing on the optical and electrical properties of the liquid crystalline dye 4,7-bis[5-(2-fluoro-4-pentyl-phenyl)-2-thienyl]-2,1,3-benzothiadiazole (FPPTB). FPPTB is crystalline at room temperature, exhibits a nematic phase at temperatures above 149 °C and is in an isotropic melt at temperatures above 230 °C. Solution processed FPPTB films were subject to thermal annealing through these phase transition temperatures and characterized with X-ray diffraction and polarized optical microscopy. Cooling FPPTB films from the nematic and isotropic phases increased crystal domain size, but also induced local structural variations in the molecular packing of crystalline FPPTB. The decrease in long-range order was correlated with an increase in short-range π–π interactions, leading to changes in molecular aggregation which persisted even when the FPPTB films were cooled to room temperature. Annealing-induced changes in molecular aggregation were confirmed with optical spectroscopy. The carrier mobility in FPPTB films increased over 2 orders of magnitude from (2.2 ± 0.4) × 10–5 cm2 V–1 s–1 in as-spun films to μ = (5.0 ± 0.8) × 10–3 cm2 V–1 s–1 in films cooled from the isotropic melt. We discuss the relationship between thermal stability and high carrier mobility values in terms of the interplay between long-range molecular order and increased π–π interactions between molecular pairs in the FPPTB film.

Multifunctional Optical Thin Films Fabricated by the Photopolymerization of Uniaxially Oriented Lyotropic Liquid Crystal Monomers for Electro-Optical Devices.

A multifunctional optical thin film (MOTF) is fabricated by coating the newly synthesized perylene-based reactive mesogen (PBRM) and stabilized by the subsequent photopolymerization. Based on the spectroscopic results combined with morphological observations, it is found that nematic liquid crystal (NLC) is aligned parallel to the molecular long axis of PBRM not only due to the long-range physical anchoring effect but also due to the short-range molecular physical interactions between alignment layer and NLC molecules. From the electro-optical properties of LC test cells fabricated with the PBRM MOTF, it is clearly demonstrated that the PBRM MOTF can work as the planar LC alignment layer as well as the in-cell coatable polarizer. The coatable PBRM MOTF from lyotropic chromonic reactive mesogens can pave a new way for the flexible optoelectronic devices.

Traveling waves and global oscillations triggered by attractive molecular interactions in an excitable system.

During pattern formation in spatially extended systems, different mechanisms with different characteristic length scales, e.g., reaction-diffusion processes or molecular interactions, can be active. Such multiscale effects may generate new phenomena, which are not observed in systems where pattern formation occurs on a single scale. Here, we derive and analyze a reaction-diffusion model of the FitzHugh-Nagumo type with short-range attractive molecular interactions of the activator species. The model exhibits a wave instability. Simulations in one and two dimensions show traveling waves with a wavelength set by the parameters of the molecular interaction in the model. In two dimensions, simulations reveal a labyrinthine arrangement of the waves in systems with isotropic diffusion, whereas parallel bands of counterpropagating waves are formed in simulations of a model with anisotropic diffusion. The latter findings are in good qualitative agreement with experimental observation in the catalytic NO+H_{2} reaction on an anisotropic Rh(110) surface. In addition we have identified a transition regime in the simulations, where a short scale instability triggers global oscillations in an excitable regime.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Structure and properties of acetone solvates in binary mixtures with some nonpolar solvents

Variations of short-range molecular interactions in acetone-nonpolar solvent systems have been evaluated, and the nature of these variations has been determined in terms of a new continual parameter-free approach to modeling the structure and properties of binary liquid nonelectrolyte mixtures. The results have been obtained by comparing the experimental heats of mixing of acetone with nonpolar solvents with the calculated changes in the energy of solvation in analogous model systems. The theoretical and experimental data suggest formation of azeotrope and demonstrate the effect role of short-range intra- and intermolecular interactions on the azeotrope parameters. No symmetry has been found in the differences between the compositions of solvation shells of acetone molecules and nonpolar counterparts as compared to the solvation shell compositions typical of mixtures formed by only polar or only nonpolar solvents.

Calculated line broadening parameters for methane perturbed by diatomic molecules

We report semiclassical line broadening calculations for methane perturbed by diatomic molecules: nitrogen, N2, oxygen, O2 and hydrogen, H2, at room temperature. For this, we have developed a symmetrized version of the Robert and Bonamy theory. The interaction potential was built from electrostatic (octopole and hexadecapole for methane, quadrupole for the diatomic molecules) and atom–atom contributions. The relative (classical) trajectories of the molecules were computed in the frame of the usual parabolic model, through analytical formula. High orders of developments had to be used for the short range molecular interactions in the case of N2 and O2. For H2, a lower order of development was found to be convenient. We have compared our calculations to some of the available experimental data for hydrogen and oxygen. For nitrogen, we have already reported some comparisons to measurements [T. Gabard, V. Boudon, J. Quant. Spectrosc. Radiat. Transfer 111 (2010) 1328–1343]. Thus, we report here new extensive calculations for the dyad (near 1300cm−1) and the pentad (near 3000cm−1) spectral regions.

Acoustical assessment of body water balance

A new medical application of acoustics has recently emerged: assessment of body hydration status by ultrasonic measurement of muscle water content. The need for an easy-to-perform method for the detection of water imbalance is of the utmost clinical importance. Body hypohydration may cause severe health and performance problems, decreasing cognitive and physical work capabilities, while excessive hydration is a common symptom of many other diseases. The speed of longitudinal acoustic waves in muscle, as well as in other soft tissues, is defined by tissue molecular composition because both the density and bulk compressibility of tissue depend mainly on short range molecular interactions. Skeletal muscle is the largest water compartment in the body; it comprises 40% of body mass and 75% of muscle is water. The ultrasound velocity in muscle is a linear function of water content with the slope of about 3.0 m/s per 1% change in water content. We will describe the design, measurement principles, and testing results for new acoustic devices for assessment of hydration status of elderly and infants, two most vulnerable groups of population. Advantages and disadvantages of acoustical method of hydration over currently available methods are discussed.

Ion clustering in aqueous solutions probed with vibrational energy transfer

Despite prolonged scientific efforts to unravel the hydration structures of ions in water, many open questions remain, in particular concerning the existences and structures of ion clusters in 1∶1 strong electrolyte aqueous solutions. A combined ultrafast 2D IR and pump/probe study through vibrational energy transfers directly observes ion clustering in aqueous solutions of LiSCN, NaSCN, KSCN and CsSCN. In a near saturated KSCN aqueous solution (water/KSCN molar ratio = 2.4/1), 95% of the anions form ion clusters. Diluting the solution results in fewer, smaller, and tighter clusters. Cations have significant effects on cluster formation. A small cation results in smaller and fewer clusters. The vibrational energy transfer method holds promise for studying a wide variety of other fast short-range molecular interactions.

Line broadening coefficient calculations for methane perturbed by nitrogen

We report semiclassical line broadening calculations for methane perturbed by nitrogen at room temperature. For this, we have developed a symmetrized version of the Robert and Bonamy theory. The interaction potential was built from electrostatic (octopole and hexadecapole for methane, quadrupole for nitrogen) and atom–atom contributions. The relative (classical) trajectories of the molecules were computed in the frame of the usual parabolic model, through analytical formula. High orders of developments had to be used for the short range molecular interactions. As a consequence, a combination of symbolic computation and source code generation was employed to implement practical calculations. We have compared our calculations to the most recent experimental data available in the ν 4 band, the ν 3 band and the octad spectral region of methane.

Time-resolved x-ray studies of the dynamics of smectic-Alayer realignment by magnetic fields

While the rotation of smectic layers under an applied field may at first appear to be a relatively simple problem, the dynamic processes involved are rather complex. An applied field produces a torque on the liquid crystal director, but has no direct influence on the smectic layers. If the director is reoriented significantly, however, the layers must also reorient in order to accommodate this (the layered structure is produced by short-range molecular interactions). Indeed, if the liquid crystalline order is not maintained during the realignment then matters become even more complex. In this paper we use time-resolved x-ray scattering to investigate the realignment of smectic- A layers in thin-film devices using a magnetic field. No evidence is found for continuous rotation of the smectic layers under any circumstances in such devices, a result that is not found when using bulk samples. No evidence indicating the formation of the nematic phase is observed during realignment. A molecular-dynamics technique is used to model the system which indicates that the sample becomes significantly disorganized during the realignment process when large angular rotations are induced.

Master crossover functions for one-component fluids

By introducing three well-defined dimensionless numbers, we establish the link between the scale dilatation method able to estimate master (i.e., unique) singular behaviors of the one-component fluid subclass and the universal crossover functions recently estimated [Garrabos and Bervillier, Phys. Rev. E 74, 021113 (2006)] from the bounded results of the massive renormalization scheme applied to the Phi(d)(4)(n) model of scalar order parameter (n=1) and three dimensions (d=3), representative of the Ising-like universality class. The master (i.e., rescaled) crossover functions are then able to fit the singular behaviors of any one-component fluid without adjustable parameter, using only one critical energy scale factor, one critical length scale factor, and two dimensionless asymptotic scale factors, which characterize the fluid critical interaction cell at its liquid-gas critical point. An additional adjustable parameter accounts for quantum effects in light fluids at the critical temperature. The effective extension of the thermal field range along the critical isochore where the master crossover functions seems to be valid corresponds to a correlation length greater than three times the effective range of the microscopic short-range molecular interaction.