Liquid-crystalline fork-like dendrons

ABSTRACT

Dendritic molecules having several rigid-rod moieties can be applied to induce liquid crystallinity for a variety of non-mesomorphic functional molecules such as metal complexes, nanoparticles, fullerenes and π-conjugated molecules when these dendritic molecules are covalently bonded to those non-mesomorphic molecules. These complex molecules are called supermolecular liquid crystals. Due to the cooperation of several mesogenic moieties, these dendritic molecules exhibit very stable liquid-crystalline (LC) phases. We have used fork-shaped LC dendrons having two or three rigid-rod moieties to induce liquid crystallinity for functional molecules such as interlocked molecules and π-conjugated molecules. In these fork-like molecules, the rigid-rod cores are attached to the 3,4,5-position of the phenyl moieties through flexible spacer, and these molecules are bonded to functional molecules through the 1-position. They basically form smectic LC phases, which induce the layered arrangement of functional moieties. Here we report on a new family of fork-like mesogens containing a hydrogen bonding moiety or an ionic group. They are designed to build supramolecular materials.     

Molecular dynamics investigation of the effects of a water surface on the aggregation of bent-core molecules

Molecular dynamics simulations are used to determine how the presence of a water surface affects the way that bent-core surfactant molecules interact with one another. The simulations are carried out for isolated pairs of bent-core molecules, and for pairs of bent-core molecules on a water surface. The results show that the water surface fundamentally alters the nature of the interaction between the bent-core molecules: a stable complex is formed when the two molecules are on the water surface, but not for an isolated pair of molecules. This difference occurs because the water surface constrains the internal structure and orientation of the molecules, which makes the packing of the molecules into a stable complex more thermodynamically favorable.     

Orientational order in binary mixtures of hard Gaussian overlap molecules

Based on a standard constant-pressure Monte Carlo molecular simulation, we have studied liquid crystal phases of binary mixtures of nonspherical molecules. The components of the mixtures are two types of hard Gaussian overlap (HGO) molecules. The first type of molecule has a small molecularelongation parameter (short HGO molecules) and cannot form stable liquid crystal phase in the bulk by themselves. The second type of molecule has a large elongation parameter (long HGO molecules) and can form a liquid crystal phase easily. In the mixtures, the short HGO molecules can form an orientationally ordered phase because the long HGO molecules form confining surfaces to induce the alignment of the short molecules. We also study the isotropic-nematic phase transition in different mixtures composed of short and long HGO molecules with different elongations and concentrations. The obtained result implies that small anisotropic molecules can show liquid crystal behavior.     

The effect of the diversity of molecules in sets and similarity of sets on the quality of prediction in QSAR studies

We report here: (a) formulas/procedures for calculating the similarity of molecules, considering their chemical structure, size, shape and hydrophilicity (b) a procedure for clusterization of the sets of molecules, according to similarity (c) formulas/procedures for calculating the diversity of molecules in clusterized sets as well as similarity of clusterized sets, based on Shannon Entropy formalism The paper analyses the influence of the diversity of molecules and similarity of calibration/prediction sets on the quality of prediction for prediction set molecules. The calculated influence of certain molecular feature (chemical structure, size, shape and hydrophilicity) on toxicity depends on the structure of the database, specifically the number of molecules and diversity of molecules having analyzed molecular feature. A QSAR analysis of 49 phenol derivatives revealed the effect of the diversity of molecules in sets and of the similarity of sets on the quality of prediction for prediction set molecules: (a) a direct correlation with the similarity of sets, regardless of analyzed molecular feature (b) an inverse correlation with the diversity of molecules in the calibration set, from the point of view of chemical structure, size and shape (c) a direct correlation with the diversity of molecules in calibration set, from the point of view of hydrophilicity (d) a direct correlation with the diversity of molecules in prediction set, regardless of analyzed feature.     

Self-assembly of α-6T Molecule on Ag(100) and Related STM Induced Luminescence

We have investigated the self-assembly and light emission properties of organic α-sexithiophene (α-6T) molecules on Ag(100) under different coverage by scanning tunneling microscopy (STM). At very low coverage, the α-6T molecules form a unique enantiomer by grouping four molecules into a windmill supermolecular structure. As the coverage is increased, α-6T molecules tend to pack side by side into a denser stripe structure. Fur-ther increase of the coverage will lead to the layer-by-layer growth of molecules on Ag(100) with the lower-layer stripe pattern serving as a template. Molecular fluorescence for α-6T molecules on Ag(100) at a coverage of five monolayers has been detected by light excitations,which indicates a well decoupled electronic states for the top-layer α-6T molecules. How-ever, the STM induced luminescent spectra for the same sample reveal only plasmonic-like emission. The absence of intramolecular fluorescence in this case suggests that the elec-tronic decoupling is not a sufficient condition for generating photon emission from molecules. For intramolecular fluorescence to occur, the orientation of the dynamic dipole moment of molecules and the energy-level alignment at the molecule-metal interface are also important so that molecules can be effectively excited through efficient dipolar coupling with local plasmons and by injecting holes into the molecules.     

The solid-state structure of calix[4]arene dihydroxyphosphonic acid–l-lysine complex

The solid-state structure of calix[4]arene dihydroxyphosphonic acid with l-lysine shows a high degree of complexity. The system presents three independent molecules of amino acid, all in different conformational structures, associated with four molecules of calixarene, in the presence of a relatively high number of solvent molecules. The general topology of the complex is guided by the layer of two dimeric units of calixarene molecules and by the large network of hydrogen bonds generated by the molecules of lysine. The arrangement of lysine molecules in the crystal generates a 1-D ladder network.     

Symmetries and fuzzy symmetries of graphene molecules

In this paper, we will investigate the fuzzy layer group symmetries of two-dimensional (2D) periodic molecules. Here, we select several graphene molecules as typical examples to discuss. For these two-dimensional graphene molecules, their MO energies, symmetries and fuzzy symmetries are preliminarily studied. In addition, we especially make a detailed comparison between the zigzag and armchair graphene molecules. These studies will develop a theoretical framework that will help us to investigate the fuzzy symmetries of various layer group molecules as well as molecules with 3D periodic structure.     

Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes

We have performed a comprehensive analysis of water molecules at the protein-ligand interfaces observed in 392 high-resolution crystal structures. There are a total of 1829 ligand-bound water molecules in these 392 complexes; 18% are surface water molecules, and 72% are interfacial water molecules. The number of ligand-bound water molecules in each complex structure ranges from 0 to 21 and has an average of 4.6. Of these interfacial water molecules, 76% are considered to be bridging water molecules, characterized by having polar interactions with both ligand and protein atoms. Among a number of factors that may influence the number of ligand-bound water molecules, the polar van der Waals (vdw) surface area of ligands has the highest Pearson linear correlation coefficient of 0.63. Our regression analysis predicted that one more ligand-bound water molecule is expected for every additional 24 A2 in the polar vdw surface area of the ligand. In contrast to the observation that the resolution is the primary factor influencing the number of water molecules in crystallographic models of proteins, we found that there is only a weak relationship between the number of ligand-bound water molecules and the resolution of the crystal structures. An analysis of the isotropic B factors of buried ligand-bound water molecules suggested that, when water molecules have fewer than two polar interactions with the protein-ligand complex, they are more mobile than protein atoms in the crystal structures; when they have more than three polar interactions, they are significantly less mobile than protein atoms.     

Molecular Dynamics Simulations of the First Steps of the Formation of Polysiloxane Layers at a Zinc Oxide Surface

Three different dissolved silane molecules adsorbed at a polar ZnO surface (000&1macr;) are studied by means of constant temperature molecular dynamics simulations. The adsorbed single silane molecules exhibit a different behavior depending on the chemical nature of their tail. For octyltrihydroxysilane molecules with their rather unpolar tail an orthogonal orientation at the polar metal oxide surface is statistically favored with all three polar hydroxide groups of the head being in contact with the polar ZnO surface and the unpolar tail remaining in the isopropanol phase. On the contrary, due to their highly polar tail, aminopropyltrihydroxysilane molecules show a more or less parallel orientation at the surface. Apart from some minor fluctuations two hydroxide groups as well as the amino group of the tail are in contact with the surface. The behavior of the thiolpropyltrihydroxysilane molecules is somehow located in between resulting in parallel as well as orthogonal orientations of the molecule at the surface. Though many of the results obtained for single adsorbed silane molecules can also be transferred to adsorbed silane molecules within whole layers a remarkable difference appears: Now even for aminopropyltrihydroxysilane molecules a mixture of parallel and orthogonal alignment of the molecules can be observed whereas some of the octyltrihydroxysilane molecules also show a parallel orientation.     

Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.     

Synthesis of technomimetic molecules: towards rotation control in single-molecular machines and motors

Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with rotary motions, including gears, wheelbarrows and motors. Following the bottom-up approach the synthesis of technomimetic molecules grants access to the study of mechanical properties at the molecular level. These molecules are designed to operate as single molecules on surfaces under the control of the tip of a scanning tunneling microscope or atomic force microscope.     

Cold collisions of complex polyatomic molecules

We introduce a method for classical trajectory calculations to simulate collisions between atoms and large rigid asymmetric-top molecules. We investigate the formation of molecule-helium complexes in buffer-gas cooling experiments at a temperature of 6.5 K for molecules as large as naphthalene. Our calculations show that the mean lifetime of the naphthalene-helium quasi-bound collision complex is not long enough for the formation of stable clusters under the experimental conditions. Our results suggest that it may be possible to improve the efficiency of the production of cold molecules in buffer-gas cooling experiments by increasing the density of helium. In addition, we find that the shape of molecules is important for the collision dynamics when the vibrational motion of molecules is frozen. For some molecules, it is even more crucial than the number of accessible degrees of freedom. This indicates that by selecting molecules with suitable shape for buffer-gas cooling, it may be possible to cool molecules with a very large number of degrees of freedom.     

Molecular dynamics study of spectral characteristics of water-carbon oxide disperse systems

Absorption and reflection IR spectra of aqueous disperse systems that absorbed carbon oxide molecules are calculated. Systems of small and large clusters containing 2 ≤ n ≤ 10 and 11 ≤ n ≤ 20 water molecules, respectively, are studied. Each cluster can absorb one or two carbon oxide molecules. Both real and imaginary parts of dielectric permittivity of disperse systems depend on the number of adsorbed CO molecules to a greater extent than that of water molecules in clusters. The integral intensity of the absorption of IR radiation by cluster systems increases after the absorption of carbon oxide molecules by clusters. However, the ability to absorb and reflect IR radiation decreases with an increase in the concentration of absorbed CO molecules. Upon the growth of heteroclusters due to addition of water molecules, integral intensity of the absorption of thermal radiation can be enhanced or damped. In general, the clusterization and capture of CO molecules by clusters result in an anti-greenhouse effect.     

Molecular weight determination by cationisation

In General cationised molecules are more stable than redical molecular ions or protonated molecules. The fragmentation of the polar molecules resulting from a cationsation by for instance alkali ions, has a higher activation energy than splitting off fuctional groups after a protonation. Cationisation is therefore an intersting tool for the determination of molecular weights. Three different methods for achiving a cationisation are described and discussed: (1) field-indiced cationisation at low anode temperatures using a heterogenous reaction of the molecules in the gas phase with molecules of a salt in the adsorption layer on the field anode; (2) a largely thermally induced catisation at high emitter temperatures and low electric fields; (3) a cationisation, causing less thermal excitation to the molecules, using the field desorption technique.     

Manipulating double-decker molecules at the liquid-solid interface

We have used a scanning tunneling microscope (STM) to manipulate heteroleptic phthalocyaninato, naphthalocyaninato, and porphyrinato double-decker (DD) molecules at the liquid-solid interface between 1-phenyloctane solvent and graphite. We employed nanografting of phthalocyanines with eight octyl chains to place these molecules into a matrix of heteroleptic DD molecules; the overlayer structure is epitaxial on graphite. We have also used nanografting to place DD molecules in matrices of single-layer phthalocyanines with octyl chains. Rectangular scans with a STM at low bias voltage resulted in the removal of the adsorbed DD molecular layer and substituted the DD molecules with bilayer-stacked phthalocyanines from phenyloctane solution. Single heteroleptic DD molecules with lutetium sandwiched between naphthalocyanine and octaethylporphyrin were decomposed with voltage pulses from the probe tip; the top octaethylporphyrin ligand was removed, and the bottom naphthalocyanine ligand remained on the surface. A domain of decomposed molecules was formed within the DD molecular domain, and the boundary of the decomposed molecular domain self-cured to become rectangular. We demonstrated a molecular "sliding block puzzle" with cascades of DD molecules on the graphite surface.     

The hydration of sodium dehydrocholate micelles

The hydration of micellised sodium dehydrocholate molecules was determined by viscosity measurements. It was found that there are 39 water molecules for each micellised surfactant molecule. About ten water molecules may be attributed to the hydration of the sodium carboxylate group. By assignation of two water molecules to each of the three carbonyl groups, the total hydration of a micellised sodium dehydrocholate molecule was estimated as about 16 water molecules. The remaining 23 water molecules per micellised sodium dehydrocholate molecule may be attributed to water trapped in the structure of micelles.     

Energetics of low-molecular-mass products of mechanical fracture of poly(methyl methacrylate)

It is experimentally revealed that monomer and water molecules released during the fracture of PMMA have a bimodal velocity distribution. The first distribution peak for the monomer corresponds to energetic (hot) MMA molecules (0.13–0.70 eV), and the second peak is attributed to MMA molecules bearing a low energy (0.016–0.060 eV). On the basis of the results of earlier theoretical studies of the mechanically induced polymer-chain scission, it was concluded that the energetic monomer molecules are produced immediately in the event of mechanical chain rupture and are nonthermal in nature. In the bimodal velocity distribution of occluded water molecules desorbed from a subsonic crack, the first and the second peaks are attributed to “hot” and “cold” molecules with translational temperatures of 605 ± 180 K and 53 ± 5 K, respectively. A possible mechanism of the mechanically induced desorption of occluded water is discussed. The mechanodesorption of water molecules is due to the portion of vibrational energy transferred to side methyl carboxylate groups that retain water molecules by the unloading-wave front traveling along the main chain from a macromolecule scission site. Along with hot water molecules, a considerable amount of hot free hydroxyls were detected. The mechanism of formation of the latter species is associated with the double-well structure of the hydrogen bond potential and similar to the mechanism of mechanodesorption of hot molecules of water.     

Spontaneous pattern of linear molecules in strongly confined spaces

In this work, we study the tight packing of short linear molecules in confined space by performing molecular dynamic simulations. The short chain-like molecules spontaneously arrange within single-walled carbon nanotubes (SWNTs) and exhibit a variety of chiral and achiral structures, depending on the pore size and molecule length. Simulation results show that the packing structures for these confined short linear molecules are controlled by the competition between positional order and orientational order. For linear molecules with short molecular length, such as the two-site Lennard-Jones molecules, the orientational order gradually decreases as temperature increases, and then the positional order begins to disappear. While for longer molecules, such as four-site Lennard-Jones molecules, the positional order decreases more rapidly than the orientational order as temperature increases. We also investigated the effect of molecular rigidity. For linear molecules with higher rigidity, part of packing structures may slowly rotate as a whole, and the rotation of packing arrangements is found to be induced by the preexisting defects.     

Hydration processes of electrolyte anions and cations on pt(111), Ir(111), Ru(001) and Au(111) surfaces: coadsorption of water molecules with electrolyte ions

Water adsorption on Pt( 111) and Ru(001) treated with oxygen, hydrogen chloride and sodium atom at 20 K has been studied by Fourier transform infrared spectroscopy, scanning tunneling microscopy and surface X-ray diffraction. Water molecules chemisorb predominantly on the sites of the electronegative additives, forming hydrogen bonds. Three types of hydration water molecules coordinate to an adsorbed Na atom through an oxygen lone pair. In contrast, water molecules adsorb on electrode surfaces in a simple way in solution. In 1 mM CuSO4 + 0.5 M H2SO4 solution on an Au(111) electrode surface, water molecules coadsorb not only with sulfuric acid anions through hydrogen bonding but also with copper, over wide potential ranges. In the first stage of underpotential deposition (UPD), each anion is accommodated by six copper hexagon (honeycomb) atoms on which water molecules dominate. At any UPD stage water molecules interact with both the copper atom and sulfuric acid anions on the Au(111) surface. Water molecules also coadsorb with CO molecules on the surface of 2 x 2-2CO-Ru(001). All of the hydration water molecules chemisorb weakly on the surfaces. There appears to be a correlation between the orientation of hydrogen bonding water molecules and the electrode potential.     

Nanostructured columnar and cubic liquid-crystalline assemblies consisting of unconventional rigid mesogens based on triphenylmethanes

Liquid-crystalline (LC) molecules of unconventional shapes that form columnar and micellar cubic structures have been synthesized using triarylmethyl moieties as building blocks. The molecules have bowl- and dumbbell-shape. Despite the rigidity and bulkiness of the triarylmethyl moieties, the molecules form columnar and micellar cubic LC phases. The bowl-shaped molecules containing one triarylmethyl moiety show LC phases. The LC temperature ranges of the dumbbell-shaped molecules containing two triarylmethyl moieties connected by rigid rods are wider than those of bowl-shaped molecules containing one triarylmethyl moiety. The UV-vis spectroscopy of the dumbbell-shaped molecules having a terphenyl moiety reveals that the terphenyl moieties aggregate in the mesophase.