Computer modelling studies of 18-crown-6 with urea and thiourea

Abstract

Computer modelling studies have been carried out on the interaction of 18-crown-6 with a variety of guest molecules, including urea, thiourea and substituted ureas. The five known crystal structures of these host/guest systems were used as models. We were interested to establish whether the arrangement of guest molecules around a host molecule in the crystal was indicative of the lowest energy configuration for a host/guest fragment or was a consequence of packing effects. Two models were therefore considered for each structure and the structures minimised via molecular mechanics. In the first mode, the structure consisted of one unit cell and periodic boundary conditions were used in the calculation. Coulombic effects were calculated using the Ewald summation. In the second model, the structure consisted of an 18-crown-6 molecule surrounded by two hydrogen-bonded guest molecules. Both models were minimised using the CERIUS package using the DreidingII forcefield.

The crystal structure minimisations reproduced the structures very well with an average change in cell volume of 3.6% and a mean r.m.s. positional deviation of 0.20 Å. The fits for the fragment models were significantly larger for all structures (mean 0.30 Å) but even so it can be concluded that the arrangement in the crystal gave a good indication of the lowest energy configuration of the host/guest in vacuo.     

Selective effect of guest molecule length and hydrogen bonding on the supramolecular host structure

A host supramolecular structure consisting of bis-(2,2':6',2' '-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to guest molecules in dramatic ways, as observed by using scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite surface under ambient conditions. It is observed that small linear molecules can be encapsulated within the host supramolecular lattice. The characteristics of the host structure were nearly unaffected by the encapsulated guest molecules of terphthalic acid (TPA) dimers, whereas appreciable changes in cavity dimension can be observed with azobenzene-4,4'-dicarboxylic acid. The STM study and density functional theory (DFT) analysis reveal that intermolecular hydrogen bonding interaction plays an essential role in forming the assembling structures. The difference in guest molecule length is considered the important cause for the different guest-host complexes.     

微凝胶胶体晶体研究进展

Poly(N-isopropylacrylamide)(PNIPAM)微凝胶粒子是一种软的胶体粒子.和单分散的SiO_2、PS、PMMA等硬的胶体粒子一样,单分散的PNIPAM微凝胶粒子也可以自组装成为高度有序的胶体晶体.微凝胶粒子软物质的特性及其对外部刺激的响应性赋予其不同于硬球的组装行为.微凝胶胶体晶体的高度有序结构及其刺激响应性使其在诸多领域有重要用途.本文分别介绍了三维及二维微凝胶胶体晶体组装的研究进展,并对已开发的基于微凝胶胶体晶体的应用进行了总结.     

Orientational control of guest molecules in an organic intercalation system by host polymer tacticity

Four kinds of stereoregular poly(muconic acid)s, which are synthesized by topochemical polymerization and subsequent solid-state hydrolysis, are used as the organic host materials for intercalation. We describe the reaction behavior and layered structure of intercalation compounds using stereoregular poly(muconic acid)s and n-alkylamines as host and guest, respectively. The packing structure of the guest alkylamines was determined by X-ray diffractions as well as IR and Raman spectroscopies. We have found that the orientation of the guest molecules is controlled by the host polymer tacticity, depending on the structure of the two-dimensional hydrogen-bonding network formed in the polymer sheets of the crystals.     

Lyotropic liquid crystal guest–host material and anisotropic thin films for optical applications

We propose a new approach for the production of thin film optical functional materials. The method is based on molecular design whereby two different types of lyotropic liquid crystals (LC), lyotropic LC based on columnar supramolecules and water-soluble rod-like polymer molecules are mixed. The resulting lyotropic guest–host system allows production of optical retardation films with tunable optical anisotropy controlled by composition of the guest–host system. Coatable retarders can be used in modern liquid crystal displays and TVs for optical compensation and enhancement of the LCD's performance.     

FABRICATION OF PHOTONIC CRYSTAL WITH SUPERLATTICES

A novel technique was used to fabricate three-dimensional photonic crystals with superlattices. The super structure was fabricated by assembling monodispersed microspheres in the grooves of the scales of morpho butterfly, which makes the photonic crystal being composed of two kinds of different photonic structures (natural groove structure of butterfly wing and artificial microspherical colloids arrangement). The superstructural photonic crystal exhibits some unique optical properties different from both the butterfly wing and the colloidal crystal. The approach exhibited here provides a new way for fabricate photonic crystals with superlattices.     

Guest controlled aggregation of amphiphilic sulfonatomethylated calix[4]resorcinarenes in aqueous solutions

Supramolecular nanoaggregates formed through the association of amphiphilic sulfonatomethylated calix[4]resorcinarenes with different substituents on the lower rim (methyl, pentyl, heptyl) and number of aromatic, aliphatic, and cationic guests differing in their shapes and sizes were investigated in aqueous solution by various NMR techniques ((1)H, 2D NOESY, FT-PGSE). It was shown that slight variations of the alkyl chain length on the lower rim of calixresorcinarenes dramatically change their aggregation behavior. Unlike the other calixresorcinarenes studied, the "head-to-tail" packing mode is observed for calixresorcinarene with pentyl moieties on the lower rim, which is unusual for amphiphilic calixarene aggregates. This calixresorcinarene demonstrates the stronger binding capacity toward the guest molecules due to their encapsulation into the capsule-like aggregate subunits. The guest-host complexation modifies the properties of both components, with the size of the resulted colloid particles being controlled by the guest nature.     

FABRICATION OF PHOTONIC CRYSTAL WITH SUPERLATTICES

1. INTRODUCTION The very latest subject of physics to surface in biology is the photonic crystal, which is ordered, subwavelength structured material capable of controlling the propagation of light in the similar manner as which atomic crystal control electrons [1,2]. Due to the application of the photonic crystal in laser, integrated optical circuit, it attracted great attention in the past decade. Photonic crystals can be fabricated by microfabrication methods, holographic methods, and c…     

Dynamics of p-terphenyl crystals at the phase transition temperature: a zero-field EPR study of the photoexcited triplet state of pentacene in p-terphenyl crystals

Pulsed zero-field electron paramagnetic resonance free induction decay (ZF EPR FID) techniques are employed to study the phase transition of p-terphenyl crystals (Tc = 193 K) by measuring selectively populated photoexcited triplet ZF transitions of dilute pentacene molecules in p-terphenyl single crystals. The sensitivity of ZF spectroscopy to small shifts in local magnetic fields enables the studies of guest-host configuration changes over a wide temperature range. Here we report the observation of guest pentacene (-h(14) and -d(14)) triplet ZF EPR FID spectra that disappear abruptly at Tc and of spectral broadening and shift below Tc. We interpret these spectral changes as evidence for guest couplings to host phenyl rings. Further, these data allow assignments of spectroscopic sites to crystallographic sites that occur in the phase transition.     

Hydrolysis of glutaric anhydride to glutaric acid in the presence of β-cyclodextrin. Crystallographic and NMR study

Crystallization of glutaric anhydride in the presence of β-cyclodextrin (βCD) from aqueous solution resulted in crystals of the glutaric acid/βCD inclusion complex. The result was verified by NMR spectroscopic experiments, which moreover showed that βCD does not protect glutaric anhydride from hydrolysis. The structure determination by X-ray crystallography revealed a host:guest ratio of 1:1 and crystal packing identical to that of natural βCD, i.e., herring bone packing, as is common for guest molecules of small size. Glutaric acid has partial occupancy in the complex and it is disordered in three positions and conformations inside the cavity. All three conformations are stabilised by: (a) Interactions among its carboxyl groups and the host’s primary side hydroxyls pointing towards the cavity, thus justifying the conformations of the latter and (b) by two water molecules located on either side of the cavity, as well as hydroxyl groups of neighbouring hosts. In all conformations the guest is not extended, oxygen atoms between the two carboxyl groups being within H-bond distance.     

Dihalobenzene Shape Sorting by Nonporous Adaptive Crystals of Perbromoethylated Pillararenes

The separation of dihalobenzene isomers, such as dichlorobenzene isomers and difluorobenzene isomers, has a high practical value in both synthetic chemistry and industrial production. Herein we provide a simple to operate and energy‐efficient adsorptive separation method using nonporous adaptive crystals of perbromoethylated pillar[5]arene ( BrP5 ) and pillar[6]arene ( BrP6 ). BrP6 crystals show a preference towards the ortho isomer of dichlorobenzene in isomer mixtures, but cannot discriminate difluorobenzene isomers. Single‐crystal structures reveal that this selectivity is derived from the stability of the new host–guest crystal structure of BrP6 after uptake of the preferred guest and the binding strength of the host–guest interactions. Furthermore, because of the reversible transition between guest‐free and guest‐loaded structures, BrP6 crystals are recyclable.     

Re-entrant melting and freezing in a model system of charged colloids

We studied the phase behavior of charged and sterically stabilized colloids using confocal microscopy in a low polarity solvent (dielectric constant 5.4). Upon increasing the colloid volume fraction we found a transition from a fluid to a body centered cubic crystal at 0.0415+/-0.0005, followed by reentrant melting at 0.1165+/-0.0015. A second crystal of different symmetry, random hexagonal close packed, was formed at a volume fraction around 0.5, similar to that of hard spheres. We attribute the intriguing phase behavior to the particle interactions that depend strongly on volume fraction, mainly due to the changes in the colloid charge. In this low polarity system the colloids acquire charge through ion adsorption. The low ionic strength leads to fewer ions per colloid at elevated volume fractions and consequently a density-dependent colloid charge.     

Alignment modulation of azobenzene-containing liquid crystal systems by photochemical reactions

Recent progress in alignment modulation of azobenzene-containing liquid crystal systems by photochemical reactions has been reviewed by dividing the modulation methods into two types: phase transitions (order–disorder change) and change of liquid crystal directors (order–order change). First, photochemical phase transitions and alignment changes of liquid crystals in guest/host mixtures and polymers are summarized. Then, alignment control of liquid crystals by linearly polarized light and photoactive surface layers is discussed. Finally, recent applications of alignment change and photochemical phase transitions of liquid crystals in holographic technology and photomechanical effects are introduced. In addition, future possible applications for a variety of practical devices, such as display devices, optical switching and reversible optical image storage, are mentioned.     

Importance of packing coefficients of host cavities in the isomerization of open host frameworks: guest-size-dependent isomerization in cholic acid inclusion crystals with monosubstituted benzenes

The crystal structures of inclusion compounds of cholic acid (CA) with 28 monosubstituted benzenes have been systematically investigated. All of the crystals belong to the monoclinic space group P2(1) and have bilayer structures with one-dimensional molecular channels that can include guest compounds. They are classified into four types of host frameworks that depend on the conformations and stacking modes of the host compound. The host frameworks and the host-guest ratios depend primarily on the molecular volumes of the guest compounds. The packing coefficient of the host cavity (PCcavity), which is the volume ratio of the guest compound to the host cavity, is used to clarify the relationship between the guest volume and isomerization of the host frameworks. The value of PCcavity, for stable inclusion compounds lies in the range of 55-70%. Compounds out of this range induce isomerization of the host frameworks. The packing coefficients of other host-guest compounds, in which the guest components are included in the host cavities through steric dimensions and van der Waals forces, are also in this range. These results indicate that PCcavity is a useful parameter correlation for guest recognition and isomerization of the host frameworks.     

Detecting the adsorption of dye molecules in homogeneous poly(propylene imine) dendrimer monolayers by surface plasmon resonance sensor

In this work, we studied guest-host interactions between various dye molecules and the fifth-generation poly(propylene imine) (PPI-5) dendrimers in aqueous solutions using a surface plasmon resonance (SPR) sensor. The effect of the properties of guest and host molecules (e.g., charge and shape) and media (e.g., pH and ion strength) on affinity between guest and host molecules was investigated. Based on an immobilized homogeneous monolayer of PPI-5 dendrimer tethered to carboxyl-terminal self-assembled monolayers, the adsorption behavior of a group of dye molecules in PPI-5 was obtained. Results show that the strong affinity of PPI-5 to Rose Bengal and erythrosine B is attributed to the good match in charge and shape between the cavities of the dendrimer and the dye molecules. Maximum adsorption around a pH value of 7 was observed. The kinetic behaviors of different dye molecules in dendrimers were also studied. A fundamental understanding of guest-host interactions in dendrimers will guide the design of new-generation sensors and drug delivery carriers.     

Computer simulation of chiral liquid crystal phases. IV. Intermolecular chirality transfer to rotamers in a cholesteric phase

Intermolecular chirality transfer was studied by investigating the conformational distribution of rotamers in a cholesteric guest-host phase using Monte Carlo (MC) simulations in the NVT ensemble. The guest-host system under investigation was given by N_c = 238 rigid, chiral Gay-Berne atropisomers as host molecules and N_a = 18 flexible Gay-Berne rotamers as guest molecules. The rigid, chiral Gay-Berne atropisomers of point symmetry group D₂ were defined by joining two Gay-Berne particles through a bond with a suitable fixed dihedral angle. The possibility of internal rotation about the bond axis without a rotational barrier was introduced as an internal degree of freedom for the guest molecules, for convenience denoted as Gay-Berne rotamers. Starting from an isotropic configuration, cholesteric phases were obtained on equilibrating the guest-host systems, whereby left-handed and right-handed cholesterics were formed depending on the M- and P-helicity of the atropisomers, respectively. Analysing the conformational distribution of the guest molecules in the cholesteric phase, we found an enantiomeric excess of rotamers of the guest molecules with the same helicity as the host molecules which is favoured on account of the intermolecular interactions in the cholesteric phase.     

Host—guest Complementarity and Crystal Packing of Intercalated Layered Structures

Intercalated layered structures are analyzed in order to estimate the rules governing their crystal packing. An overview is given on structural types of layered intercalates based on various types of host structures and guest species. The factors describing the host–guest complementarity in intercalated layered structures like: the character of active sites, the host–guest and guest–guest interactions, the size of guests and topology of layers are investigated and their effect on crystal packing is illustrated on examples. Special attention will be paid to the conditions for the regular ordering of guests in the interlayer space, as the requirement of structure ordering is of great importance in design of intercalates for special applications, where one has to control the interlayer porosity or electronic properties of guest molecules etc. A method of structure analysis based on a combination of molecular modeling and experiments has been worked out for intercalates. Molecular modeling (force field calculations) in conjunction with experiments (diffraction methods and vibration spectroscopy) enables us to analyze the disordered intercalated structures, where the conventional diffraction analysis fails.     

Structural characterization of organosiloxane liquid crystals with a transverse or longitudinal dipole

In this work we report the characterization of two organosiloxane liquid crystalline compounds by means of DSC, polarizing optical microscopy and X-ray diffraction. These compounds can be used for dye guest-host ferroelectric displays. We focus this investigation on the molecular organization of the SmC phases of the two pure compounds to help elucidate the physical behaviour of mixtures with different concentrations of the dye and the guest host. The existence of longitudinal and transverse dipoles in the molecules of the dye and the chiral guest-host respectively are responsible for the different molecular organizations in the SmC mesophases of each compound. Taking into account the experimental results and the complexity of the molecules, we present coherent models to explain the molecular arrangements in the mesophases of both compounds.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 1. Crystallographic studies of beta-cyclodextrin complexes with N-acetyl-L-phenylalanine methyl ester and N-acetyl-L-phenylalanine amide pseudopeptides

Cyclodextrins (CDs) are widely utilized in studies of chiral and molecular recognition. By changing the functionality of the guest molecule, the effect of such changes on recognition by the host CD molecule can be examined. We report crystal structure determinations for two nearly isomorphous complexes of phenylalanine derivatives: beta-CD/N-acetyl-L-phenylalanine methyl ester and beta-CD/N-acetyl-L-phenylalanine amide. The complexes crystallize as hydrated head-to-head host dimers with two included guest molecules in space group P1. The crystal packing is such that it presents a nonconstraining hydrophobic pocket adjacent to a hydrophilic region, where potential hydrogen-bonding interactions with hydroxyl groups of neighboring cyclodextrin molecules and waters of hydration can occur. The two host molecules display very similar conformations; only a few of the primary hydroxyl groups are conformationally disordered. There are a number of changes in the location of water of hydration molecules, some of which are the result of different hydrogen-bonding interactions. For the different guest molecules, similar modes of penetration are observed in the CD torus; however, there is a 0.985-A shift in the position of the guest molecules in the host torus, which takes place without changing the hydrophobic interactions displayed by the phenyl side chains. This observation and the thermal motion of the guest molecules in the ester complex are taken as evidence that complex binding forces are weak. The pseudopeptides experience a significant degree of flexibility in the crystalline environment provided by CD dimers. Conformational differences of the pseudopeptide backbones and the presence of disordered water molecules in the host-guest interface provide examples of different hydrogen-bonding schemes of similar potential energy. The crystal system presents an opportunity to establish a database of molecular interactions for small peptides and peptide analogues with waters of hydration and functional groups in nonconstraining binding environments.     

Self-association of rhodamine dyes in different host materials

The aggregation of rhodamine 6G in liquid crystalline solution (anisotropic host) was studied using polarised spectroscopy and in a guest-host system. The self-association of rhodamine B was investigated in molecular sieves of type AlPO(4)-5 (microporous host) using diffuse reflectance spectroscopy. Also, the molecular interaction of rhodamines in normal solvents (isotropic hosts) was studied using visible spectroscopy for comparison. Therefore, the role of the host nature in the different phases on the self-association of the guest molecules has been investigated and compared. The absorption spectrum of the rhodamine dye in liquid crystalline host is affected by a specific interaction related to the alignment by the liquid crystal property as well as solvent polarity. Due to the existence of a large amount of water molecules absorbed into channels and cavities of aluminophosphate molecular sieve, the maximum absorption wavelengths of the dye loaded AlPO(4)-5 is affected by aqueous environment of the aluminophosphate pores.