Orientational ordering, conformation, and polarizability of molecules in the reentrant phase of discoid nematics

This paper presents data on orientational ordering in a reentrant discoid nematic and on changes in the polarizability of discogenic molecules in a homologous series. The phase transition of a nematic to the discotic column phase is accompanied by a jump of the orientational ordering parameter and is characterized by close relationship between the orientational and translational ordering of molecules. The lengthening of the flexible peripheral molecular chains in the reentrant nematic phase considerably changes their conformational state, decreasing the anisotropy of their polarizability. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 1, pp. 89–97, 1997.     

Molecular simulation of the adsorption and structure of benzene confined in mesoporous silicas

Grand Canonical Monte Carlo simulations are used to study the adsorption of benzene at 298 K in an atomistic cylindrical silica nanopore of a diameter 3.6 nm. The adsorption involves a transition from a partially filled pore (a two layers thick film at the pore surface) to a completely filled pore configuration. Strong layering of the benzene molecules at the pore surface is observed. It is found that the layering decays as the distance to the pore surface increases. The position of the peaks for the density of the C, H atoms and the center of mass of the molecules shows that benzene molecules prefer an orientation in which their ring is perpendicular to the pore surface. This result is corroborated by calculating orientational order parameters and examining the distribution of the distances between the H and C atoms of the benzene molecules and the H and O atoms of the silica substrate.     

Statistical mechanics of a two-dimensional lattice model of benzene adsorption in zeolites

In this Letter, we present a mean field calculation of the statistical mechanics of a lattice model of benzene adsorption in the quasi two-dimensional network of pores in zeolites. A lattice fluid model is introduced with monomer states to represent molecules standing perpendicular to the principle axis of the pore, dimer states to represent molecules lying flat against the pore wall, and vacant sites or holes. For a wide range of interaction parameters the model gives steps in adsorption isotherms similar to those observed experimentally for benzene adsorption in silicalite. Our treatment attributes the experimentally observed steps in the level of adsorption with rising pressure, to orientational transitions amongst molecules in the adsorbed phase with two possible ground states arrangements of the benzene molecules in the zeolite pores energetically competing with each other.     

Computer simulation investigation of the water-benzene interface in a broad range of thermodynamic States from ambient to supercritical conditions

The dependence of the properties of the water-benzene system on the thermodynamic conditions in a broad range of temperatures and pressures has been investigated by computer simulation methods. For this purpose, Monte Carlo simulations have been performed at 23 different thermodynamic states, ranging from ambient to supercritical conditions. The density profiles of the water and benzene molecules have been determined at each of the thermodynamic states investigated. Information on the dependence of the mutual solubility of the two components in each other as well as of the width of the interface on the temperature and pressure has been extracted from these profiles. The width of the interface has been found to increase with increasing temperature up to a certain point, where it diverges. The temperature of this divergence corresponds to the mixing of the two phases. The determination of the critical mixing temperature at various pressures allowed us to estimate the upper critical curve, separating the two-phase and one-phase liquid systems, of the phase diagram of the simulated water-benzene system. In analyzing the preferential orientation of the interfacial molecules relative to the interface, it has been found that the main orientational preference of the benzene molecules is to lie parallel with the plane of the interface, and the water molecules penetrated deepest into the benzene phase prefer to stay perpendicular to the interface, pointing by one of their O-H bonds almost straight toward the benzene phase, whereas the waters located at the aqueous side of the interface are preferentially aligned parallel with the interfacial plane. Although the strength of the observed orientational preferences decreases rapidly with increasing temperature, the preferred orientations themselves are found to be independent of the thermodynamic conditions. Remains of the orientational preferences of the molecules are found to be present up to temperatures as high as 650 K. The analysis of the relative orientation of the neighboring water-benzene pairs has revealed that the radius of the first hydration shell of the benzene molecules is independent of the thermodynamic conditions, even if the system consists of one single phase. It has been found that the nearest water neighbors of the benzene molecules are preferentially located above and below the benzene ring, whereas more distant water neighbors, belonging still to the first hydration shell, prefer to stay within the plane of the benzene molecule. In the two-phase systems the dipole vector of the nearest waters has been found to be preferentially perpendicular to the vector pointing from the center of the benzene molecule to the water O atom.     

Confinement Effects on the Benzene Orientational Structure

Liquids under confinement exhibit different properties compared with their corresponding bulk phases, for example, miscibility, phase transitions, and diffusion. The underlying cause is the local ordering of molecules, which is usually only studied using pure simulation methods. Herein, we derive experimentally the structure of benzene confined in MCM‐41 using total neutron scattering measurements. The study reveals a layering of molecules across a pore, and four concentric cylindrical shells can be distinguished for a pore with the radius of 18 Å. The nanoscale confinement of the liquid has a major effect on the spatial and orientational correlations observed between the molecules, when compared with the structure of the bulk liquid. These differences are most marked for molecules in parallel configurations, and this suggests differences in chemical reactivity between the confined and bulk liquids.     

Orientationally ordered layers of saturated hydrocarbons and their derivatives on quartz surfaces

The structure of the adjacent-to-wall layers of aliphatic hydrocarbons on quartz surface was investigated. Measurements of dichroism of the dyestuff molecules, or “guest” in the matrix of the basic substance, allowed establishing the presence of the orientational ordering in liquid layers at distances up to 200 nm. Additional measurements of the optical anisotropy (birefringence) in such layers have substantiated the existence of that ordering and its type. The structural characteristics of the adjacent-to-wall layers, such as thickness, type, and degree of the orientational ordering of molecules depend on the specific hydrocarbon used and the preparation (modification) of the surface of the solid substrate.     

NMR methods of studying orientational order in the liquid crystalline and isotropic phases of mesogenic samples

The understanding of how to describe the orientational order of the molecules in liquid crystalline phases, and in the isotropic phase formed by mesogens, has undergone considerable development in the past 25 years; this progress is reviewed. In parallel with the theoretical developments it has also been shown that NMR spectroscopy plays a unique role in the measurement of the orientational order of the molecules, and it is explained how biaxial ordering can be characterized for rigid molecules, and how the conformationally-dependent order parameters necessary for flexible molecules can be obtained.     

Ultrafast orientational dynamics of nanoconfined benzene

Ultrafast optical Kerr effect spectroscopy has been used to study the orientational dynamics of benzene and benzene-d(6) confined in nanoporous sol-gel glass monoliths with a range of average pore sizes. All of the observed orientational diffusion of confined benzene is found to occur on a slower time scale than in the bulk, even in pores with diameters that are significantly larger than a benzene molecule. The orientational dynamics of benzene-d(6) are found to be inhibited to a lesser extent than those of benzene, which is attributed to the differences in wetting properties of the two liquids on silica. The decays are fit well by a sum of two exponentials, the faster of which depends on pore size. Similar results are found in pores that have been modified with trimethylsilyl groups, although the relaxation is faster than in unmodified pores. Comparison to Raman line width data for confined benzene-d(6) suggests that the liquid exhibits significant structuring at the pore walls, with the benzene molecules lying flat on the surfaces of unmodified pores.     

Structure of the acetone liquid-vapor interface as seen from Monte Carlo simulations

The orientational order of the molecules at the liquid-vapor interface of acetone has been investigated by computer simulation. To fully describe the orientational preferences of the acetone molecules, the bivariate joint distribution of two independent orientational parameters has been determined at different layers of the interface. The strength of the orientational ordering of the interfacial molecules has been found to be liquid-like rather than crystal-like. The obtained results have revealed that the interfacial acetone molecules have dual orientational preferences. The main symmetry axis of the molecules declines by about 50-70 degrees from the interface normal axis, pointing toward the liquid phase in both of the preferred orientations. However, the plane of the molecules in the orientation preferred on the liquid side of the interface is perpendicular to the interfacial plane, whereas the other preferred orientation, which is present on the vapor side of the interface, corresponds to the alignment obtained from this orientation by an almost 90 degrees rotation around the main symmetry axis. Because the population of the liquid side is higher than that of the vapor side of the interface, the first of the two preferred orientations is the dominant alignment over the entire interface, in good agreement with recent experimental findings (Chen, H.; Gan, W.; Wu, B. H.; Wu, D.; Zhang, Z.; Wang, H. F. Chem. Phys. Lett. 2005, 408, 284).     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.     

Structural Effects of Self-Organization of Biaxial Molecules with Internal Rotation in Nematic Liquid Crystals

The effect of correlation between the conformational and orientational degrees of freedom of biaxial molecules with internal rotation on the conformational, orientational, and mixed order parameters of the molecules and on the function of the conformational distribution of molecules in nematic liquid crystals was studied in terms of molecular statistical theory. The correlation has a strong effect on polarizability of molecules with -conjugated fragments. An explanation is offered to the experimental dependences of the mean value and anisotropy of polarizability on the character and degree of orientational ordering of molecules in the nematic phase.     

Orientational phases of classical quadrupoles on a triangular net

The classical Monte Carlo (MC) method is used to study the effect of temperature on the ordering of quadrupoles arranged on a triangular net with toroidal boundary conditions. The results are used to discuss the orientational ordering of nitrogen and hydrogen molecules adsorbed on the basal plane of graphite.     

Enantiomeric interactions between liquid crystals and organized monolayers of tyrosine-containing dipeptides

We have examined the orientational ordering of nematic liquid crystals (LCs) supported on organized monolayers of dipeptides with the goal of understanding how peptide-based interfaces encode intermolecular interactions that are amplified into supramolecular ordering. By characterizing the orientations of nematic LCs (4-cyano-4'-pentylbiphenyl and TL205 (a mixture of mesogens containing cyclohexane-fluorinated biphenyls and fluorinated terphenyls)) on monolayers of l-cysteine-l-tyrosine, l-cysteine-l-phenylalanine, or l-cysteine-l-phosphotyrosine formed on crystallographically textured films of gold, we conclude that patterns of hydrogen bonds generated by the organized monolayers of dipeptides are transduced via macroscopic orientational ordering of the LCs. This conclusion is supported by the observation that the ordering exhibited by the achiral LCs is specific to the enantiomers used to form the dipeptide-based monolayers. The dominant role of the -OH group of tyrosine in dictating the patterns of hydrogen bonds that orient the LCs was also evidenced by the effects of phosphorylation of the tyrosine on the ordering of the LCs. Overall, these results reveal that crystallographic texturing of gold films can direct the formation of monolayers of dipeptides with long-range order, thus unmasking the influence of hydrogen bonding, chirality, and phosphorylation on the macroscopic orientational ordering of LCs supported on these surfaces. These results suggest new approaches based on supramolecular assembly for reporting the chemical functionality and stereochemistry of synthetic and biological peptide-based molecules displayed at surfaces.     

The structure and conformation of a mesogenic compound between almost zero and almost complete orientational order

The conformational distributions in molecules that form liquid crystalline phases are predicted to depend strongly on orientational order. Results are presented here to test this hypothesis. The mesogen 4-hexyloxy-4'-cyanobiphenyl (6OCB) has been studied by NMR spectroscopy in the isotropic phase and in the nematic phase. In the isotropic phase the field-induced orientational ordering produces small dipolar couplings between ¹³C and ¹H nuclei, which were determined from the ¹³C spectra. Couplings between ¹H nuclei were also obtained using 2D selective refocusing experiments. In the nematic phase, both ¹H-¹H dipolar couplings and quadrupolar splittings for deuterium nuclei were measured for partially-deuterated samples. Both proton and deuterium spectra were also obtained for 6OCB in an equimolar mixture with 4-(ethoxybenzylidene)-4'-butylaniline (EBBA). This mixture exhibits SmA and SmB phases. The data obtained from these experiments has been analysed to yield the probability distribution of the conformations in this molecule generated by rotations about bonds. It is found that there is a substantial influence of the orientational order of the molecules on these distributions.     

有序分子系统的线性与非线性光谱学的简化描述

A simplified formulation for treating the linear and nonlinear spectroscopy of ordered molecular systems is presented,in order to help experimentalists to have an explicit physical picture and quantitative tool on using linear and nonlinear spectroscopy to study molecules in ordered molecular systems. This formulation is expended from our recent quantitative orientational and polarization treatment on second-order nonlinear spectroscopic techniques in interface studies,namely,the Second Harmonic Generation（SHG）and Sum Frequency Generation-Vibrational Polarization Spectroscopy（SFG-VPS）. The key to this formulation is to simplify the effective linear or nonlinear molecular susceptibility and construct the general orientational functional with a clear approach to calculate the orientational and intensity parameters from the experimental parameters,which determines the orientational and polarization behavior of the general orientational functional in a particular experimental configuration. Also discussed are the advantages of coherent spectroscopic techniques over incoherent ones for the accurate measurement of orientation and ordering of ordered molecular system.     

Continuum transport model of Ogston sieving in patterned nanofilter arrays for separation of rod-like biomolecules

This article proposes a simple computational transport model of rod-like short dsDNA molecules through a microfabricated nanofilter array. Using a nanochannel consisting of alternate deep wells and shallow slits, it is demonstrated that the complex partitioning of rod-like DNA molecules of different sizes over the nanofilter array can be well described by continuum transport theory with the orientational entropy and anisotropic transport parameters properly quantified. In this model, orientational entropy of the rod-like DNA is calculated from the equilibrium distribution of rigid cylindrical rod near the solid wall. The flux caused by entropic differences is derived from the interaction between the DNA rods and the solid channel wall during rotational diffusion. In addition to its role as an entropic barrier, the confinement of the DNA in the shallow channels also induces large changes in the effective electrophoretic mobility for longer molecules in the presence of EOF. In addition to the partitioning/selectivity of DNA molecules by the nanofilter, this model can also be used to estimate the dispersion of separated peaks. It allows for fast optimization of nanofilter separation devices, without the need of stochastic modeling techniques that are usually required.     

Robust Ordered Bundles of Porous Helical Nanotubes Assembled from Fully Rigid Ionic Benzene‐1,3,5‐tricarboxamides

Size‐controlled and ordered assemblies of artificial nanotubes are promising for practical applications; however, the supramolecular assembly of such systems remains challenging. A novel strategy is proposed that can be used to reinforce intermolecular noncovalent interactions to construct hierarchical supramolecular structures with fixed sizes and long‐range ordering by introducing ionic terminals and fully rigid arms into benzene‐1,3,5‐tricarboxamide (BTA) molecules. A series of similar BTA molecules with distinct terminal groups and arm lengths are synthesized; all form hexagonal bundles of helical rosette nanotubes spontaneously in water. Despite differences in molecular packing, the dimensions and bundling of the supramolecular nanotubes show almost identical concentration dependence for all molecules. The similarities of the hierarchical assemblies, which tolerate certain molecular irregularities, can extend to properties such as the void ratio of the nanotubular wall. This is a rational strategy that can be used to achieve supramolecular nanotubes in aqueous environments with precise size and ordering at the same time as allowing molecular modifications for functionality.     

Effect of molecular structure of a dichroic dye and the ordering of a liquid crystal on the dichroism of the dye-liquid crystal binary mixtures

The orientational ordering of dyes doped into liquid crystals has been investigated. The experimental results show that the ordering of the dyes can be expressed as a function of the order parameter of the liquid crystal host and the molecular structure of the dye. In addition a theory of the ordering of molecules in a binary mixture system has been derived by extending Kimura's theory. The validity of the theory has been confirmed by comparison with the experimental results using various combination of azo dyes and liquid crystals.     

Effect of molecular structure of a dichroic dye and the ordering of a liquid crystal on the dichroism of the dye-liquid crystal binary mixtures

The orientational ordering of dyes doped into liquid crystals has been investigated. The experimental results show that the ordering of the dyes can be expressed as a function of the order parameter of the liquid crystal host and the molecular structure of the dye. In addition a theory of the ordering of molecules in a binary mixture system has been derived by extending Kimura's theory. The validity of the theory has been confirmed by comparison with the experimental results using various combination of azo dyes and liquid crystals.     

Two-particle entropy and structural ordering in liquid water

Entropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of surrounding water molecules (treated as points, represented by the center of mass) around the central one. It has been shown that this term can serve as the metric of the overall orientational ordering in liquid water. Analyzing each of these three terms as a function of intermolecular distance, r, we also find a rational definition of the hydration shell around the water molecule; the estimated radii of the first and second hydration shells are 0.35 nm and 0.58 nm, respectively. We find, moreover, that the first hydration shell around the water molecule participates roughly in 70% of the total orientational entropy of water, and this rate is roughly temperature independent.