Molecular characteristics and surface layer structure of poly(siloxane imides)

The effects of spontaneous ordering of molecular chains of poly(siloxane imide) block copolymers in the surface layers of thin films on glass and gold supports have been studied by the oblique polarized beam and photoelasticity methods. The effective thermodynamic rigidity of molecular chains of the block copolymers (the statistical segment length) has been found to be A = 10.4 × 10^?7 cm. The orientational ordering of molecular chains in poly(siloxane imide) surface layers is characterized by small values of the orientational order parameter (S ₀ ～ 0.007). This finding is explained by the microphase separation of the block copolymers. The evaporated gold layer contributes to the effect of surface birefringence owing to formation of the ordered system composed of islets—clusters of gold atoms.     

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.     

Interfacial polarization phenomena in organic molecular films

Electrostatic phenomena occurring at the interface between metal/organic and organic/organic materials are discussed from the viewpoint of dielectrics physics. Focusing on two important origins of surface polarization phenomena, orientational ordering of polar molecules and displacement of excess charges at the interface, surface polarization phenomena of organic thin films are discussed. To define the orientational order of polar molecules, orientational order parameters are introduced, and surface polarization due to the alignment of dipoles is expressed. The generation of Maxwell displacement current (MDC) and optical second harmonic generation (SHG) that are specific for surface organic monomolecular films are discussed, and some experimental evidence are shown. As an extension of the concept of surface Fermi level introduced to discuss the electrostatic phenomena due to electron transfer at the interface between metal-organic insulators, the surface Fermi level is extended to the discussion on the electrostatic phenomena of organic semiconductor materials on metals. In this paper, some experimental evidence of surface polarization originating from polar molecules and displacement of excess charges are shown. After that, with consideration of these surface phenomena, single electron tunneling of organic films are briefly discussed in association with surface polarization phenomena.     

Molecular surface and order parameters in liquid crystals

The surface model for solute ordering in nematics, which is based on the decomposition of the orientational potential according to the contributions of surface elements, leads to a simple procedure for the calculation of both orientational properties and the cholesteric order induced by a chiral compound. However, a realistic representation of the molecular surface accessible to the solvent is required. The rolling sphere algorithm, applied to the ensemble of atomic van der Waals spheres of a molecule, provides a natural determination of such a surface, sinceit smoothes away the smallscaledetails. Thesurfaceordering model implemented with the rolling sphere smoothing of the surface is described and applied to several molecular systems. It is shown that the orientational order parameters are substantially independent of the rolling sphere radius identified with the average curvature of the solvent molecular surface. On the contrary, a sensible dependence on such a parameter emerges for the chirality order parameter, this behaviour pointing out the role of the shape of solvent molecules in the chirality recognition of solutes. A fair agreement is obtained in the comparison with experimental data.     

The behavior of benzene confined in a single wall carbon nanotube

We present the molecular dynamics study of benzene molecules confined into the single wall carbon nanotube. The local structure and orientational ordering of benzene molecules are investigated. It is found that the molecules mostly group in the middle distance from the axis of the tube to the wall. The molecules located in the vicinity of the wall demonstrate some deviation from planar shape. There is a tilted orientational ordering of the molecules which depends on the location of the molecule. It is shown that the diffusion coefficient of the benzene molecules is very small at the conditions we report here. © 2015 Wiley Periodicals, Inc.     

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).     

The nature of the ordered phase of the confined self-assembled rigid rod model

We investigate the nature of the ordered phase and the orientational correlations between adjacent layers of the confined three-dimensional self-assembled rigid rod model, on the cubic lattice. We find that the ordered phase at finite temperatures becomes uniaxial in the thermodynamic limit, by contrast to the ground state (partial) order where the orientation of the uncorrelated layers is perpendicular to one of the three lattice directions. The increase of the orientational correlation between layers as the number of layers increases suggests that the unconfined model may also exhibit uniaxial ordering at finite temperatures.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

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.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Ordering transitions in nematic liquid crystals induced by vesicles captured through ligand-receptor interactions

We report that phospholipid vesicles incorporating ligands, when captured from solution onto surfaces presenting receptors for these ligands, can trigger surface-induced orientational ordering transitions in nematic phases of 4'-pentyl-4-cyanobiphenyl (5CB). Specifically, whereas avidin-functionalized surfaces incubated against vesicles composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) were observed to cause the liquid crystal (LC) to adopt a parallel orientation at the surface, the same surfaces incubated against biotinylated vesicles (DOPC and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (biotin-DOPE)) caused the homeotropic (perpendicular) ordering of the LC. The use of a combination of atomic force microscopy (AFM), ellipsometry and quantitative fluorimetry, performed as a function of vesicle composition and vesicle concentration in solution, revealed the capture of intact vesicles containing 1% biotin-DOPE from buffer at the avidin-functionalized surfaces. Subsequent exposure to water prior to contact with the LC, however, resulted in the rupture of the majority of vesicles into interfacial multilayer assemblies with a maximum phospholipid loading set by random close packing of the intact vesicles initially captured on the surface (5.1 ± 0.2 phospholipid molecules/nm(2)). At high concentrations of biotinylated lipid (>10% biotin-DOPE) in the vesicles, the limiting lipid loading was measured to be 4.0 ± 0.3 phospholipid molecules/nm(2), consistent with the maximum phospholipid loading set by the spontaneous formation of a bilayer during incubation with the biotinylated vesicles. We measured the homeotropic ordering of the LC on the surfaces independently of the initial morphology of the phospholipid assembly captured on the surface (intact vesicle, planar multilayer). We interpret this result to infer the reorganization of the phospholipid bilayers either prior to or upon contact with the LCs such that interactions of the acyl chains of the phospholipid and the LC dominate the ordering of the LC, a conclusion that is further supported by quantitative measurements of the orientation of the LC as a function of the phospholipid surface density (>1.8 molecules/nm(2) is required to cause the homeotropic ordering of the LC). These results and others presented herein provide fundamental insights into the interactions of phospholipid-decorated interfaces with LCs and thereby provide guidance for the design of surfaces on which phospholipid assemblies captured through ligand-receptor recognition can be reported via ordering transitions in LCs.     

Structural ordering and spectral properties of smectic A with biaxial solute molecules

The influence of (i) orientational-translational ordering of solvent and solute molecules, (ii) anisotropic intermolecular solute-solvent interactions and (iii) the features of the electronic structure of biaxial solute molecules dissolved in a smectic A phase on the spectral position of polarized bands of a solute electronic absorption has been investigated. Equations for the positional-orientational pseudopotential in a pure smectic A doped with biaxial solute molecules have been obtained within the framework of the molecular statistical approach. The question about the correlation of contributions of partial orientational and translational molecular ordering to the spectral properties of a molecular system has been answered.     

Molecular dynamics simulations studies of nanoparticles in an isotropic liquid crystal matrix: Single particle behavior and pairwise interactions

We report results of molecular dynamics simulation studies of the behavior of spherical nanoparticles (NPs) in a dense isotropic nematogen matrix comprised of soft spherocylinders (SSCs). The SSCs exhibit a tendency for frustrated planar anchoring at the NP surface that results in a long-range (compared to the size of the NPs and SSCs) reduction in local orientational ordering and increased fluctuations in local orientational ordering compared to the pure isotropic phase of the SSCs. The potential of mean force between two nanoparticles exhibits a novel long-range repulsive tail separated from short-range molecular packing peaks by a shallow local minimum in free energy. The long-range repulsion is caused by NP-induced ordering fluctuations while the shallow minimum results from increased local ordering within the confinement region in between two NPs. The influence of the NPs on local orientational order in the nematogen matrix and the nematogen-induced interaction between NPs are found to depend strongly on the size of the NPs.     

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.     

A novel mesophase formed by top-shaped molecules in the bulk and unsupported thin films: a molecular dynamics study

We have used molecular dynamics simulations to investigate the ordering of top-shaped molecules in bulk phases and in unsupported thin films. Each rigid anisotropic molecule was composed of 11 Lennard-Jones interaction centers (beads). In an attempt to enhance the nematic stability in preference to smectic, the three central beads were assigned a larger Lennard-Jones diameter than the tail beads, giving the molecule a shape resembling a top. The molecular model was found to exhibit an unusual bulk mesophase with long-range orientational order and with molecular center-of-mass positions arranged in parallel interdigitated layers, with layer spacing smaller than half the length of the long axis of a molecule. However, despite the toplike molecular shape, no nematic phase was observed in the pressure range studied. Unsupported films of the isotropic liquid were cooled in order to locate a triple point between the novel mesophase, vapor, and isotropic liquid. At temperatures slightly above the triple point, enhanced surface ordering of molecules was found to occur in the unsupported film. At temperatures slightly below the triple point, the preferred molecular alignment in the unsupported film was parallel to the interface, in violation of arguments that have been proposed based on the relative enthalpies of various cleavage planes for close-packed structures.     

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.     

The molecular-level relationship between the properties of liquid water molecules and orientational order

The relationship between the orientational (tetrahedral) order (q) of an individual liquid water molecule and its various properties such as Voronoi volume, potential energy, kinetic energy, and nearest neighbors was thoroughly examined using molecular dynamics simulations of TIP5P model at 278, 298, and 318 K. By constructing Voronoi polyhedra (VP), we found that the average volume of water molecules classified according to q decreased monotonically as q increased, while the surface of VP increased in the range of high q. Kinetic energy was almost invariant but potential energy decreased monotonously as q increased. The volumes of molecules having a very large q increased as temperature decreased, implying a possible density maximum phenomena. Using time correlation functions, it was shown that total energy rather than potential energy was a more significant factor in the determination of the orientational order. With varying temperature, the relation between the properties of central molecules and those of nearest neighbor molecules were investigated. It required a very systematic cooperative motion to obtain LDL (low-density liquid) formed by ordering. It was supposed that density maximum phenomena should be accomplished by the growth of LDL and HDL (high-density liquid) of low quality with a consistent population of HDL and a drop of LDL of high quality as temperature lowered.     

Salt effect on molecular orientation at air/liquid methanol interface

The salt effects on molecular orientation at air/liquid methanol interface were investigated by the polarization-dependent sum frequency generation vibrational spectroscopy(SFG-VS). We clarified that the average tilting angle of the methyl group to be u = 308 58 at the air/pure methanol surface assuming a d-function orientational distribution. Upon the addition of 3 mol/L Na I, the methyl group tilts further away from the surface normal with a new u = 418 38. This orientational change does not explain the enhancement of the SFG-VS intensities when adding Na I, implying the number density of the methanol molecules with a net polar ordering in the surface region also changed with the Na I concentrations. These spectroscopic findings shed new light on the salt effects on the surfaces structures of the polar organic solutions. It was also shown that the accurate determination of the bulk refractive indices and Raman depolarization ratios for different salt concentrations is crucial to quantitatively interpret the SFG-VS data.