A molecular simulation study of a cyclic siloxane with attached biphehylyl 4-allyloxybenzoate mesogens

Abstract

A molecular simulation study of a cyclic siloxane macromolecule based on a pentamethylcyclosiloxane core and biphenylyl 4-allyloxybenzoate mesogenic units is reported. Molecular dynamics and semi-empirical calculations were used to provide insight into the conformation and the dielectric properties of the material. Out of three proposed conformations of the molecules, a cylindrical conformation was found to be the most probable. The intermolecular interactions were found to be optimized for the case where the mesogenic groups were planar and parallel to each other. The calculated mesogen length and inter-mesogen distances were consistent with available X-ray data. Electrostatic interactions were found to make a very significant contribution to the total energy. For the cylindrical model, the major component of the dipole was calculated to be along the long axis of the molecules. This is consistent with the alignment of the molecules parallel to a low frequency applied electric field as found experimentally.     

Static and dynamic molecular mechanics modelling and X-ray scattering calculations for a cyclic siloxane macromolecule

A liquid crystalline system consisting of cyclic penta(methylsiloxane) cores with biphenylyl 4-propoxybenzoate mesogens is studied with respect to its molecular conformation and the intermolecular ordering of pendant groups by employing molecular mechaincs calculations, while a molecular dynamics simulation indicates the degree of conformational flexibility. The calculated X-ray scattering patterns for these structures provide insight into the origin of the experimentally observed results. A good agreement is found between the calculated and experimental reflections data, supporting the ‘cylinder’ global topology as the basis for forming a ‘columnar’ structure. Further, a comparison of the calculated and experimental meriodional sections shows a strong similarity of both the meridional intensities and d-spacings.     

DSC study of transformation kinetics of liquid-crystallines based on 1,4-phenylene 4-n-methoxybenzoate-4-allyloxybenzoate

The transformation kinetics of liquid-crystalline 1,4-phenylene 4-n-methoxybenzoate-4-allyl-oxybenzoate (PMOBAOB) and a liquid-crystalline poly(mesogen/methyl) siloxane (PMMS) was studied by means of a non-isothermal method using differential scanning calorimetry. This determination led to an apparent activation energy of transformation of 639.0 and 306.5 kJ mol^–1, respectively. The values of the Avrami exponentn were 1.8 and 1.1. The results show that the process of transformation of PMOBAOB involves a constant number of nuclei growing in two dimensions at a constant rate, while the process of transformation of PMMS-PMOBAOB involves a constant number of nuclei growing in one dimension at a constant rate.     

Synthesis and characterization of twin mesogens containing siloxane units as central spacers

A mesogenic ester, 4-hexyloxyphenyl 4-vinyl benzoate was synthesized and studied. The synthesis and characterization of bimesogenic molecules employing this ester with oligosiloxane spacers of different lengths are described. The compounds were characterized by IR ¹H NMR, elemental and thermal analysis, and polarized light microscopy.     

Understanding diffusion in confined systems: methane in a ZK4 molecular sieve. A molecular dynamics simulation study

The equilibrium probability distribution of N methane molecules adsorbed in the interior of n alpha cages of the ZK4 zeolite, the all-silica analogue of zeolite A, is modeled by a modified hypergeometric distribution where the effects of mutual exclusion between particles are extracted from long molecular dynamics simulations. The trajectories are then analyzed in terms of time-correlation functions for the fluctuations in the occupation number of the alpha cages. The analysis digs out the correlations induced by the spatial distribution of the adsorbed molecules coupled with a migration mechanism where a molecule can pass from one alpha cage to another, one-by-one. These correlations lead to cooperative motion, which manifests itself as a nonexponential decay of the correlators. Our results suggest ways of developing improved lattice approaches that may be useful for studying diffusion in much larger systems and for a much longer observation time.     

Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study

Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle.     

Detecting DNA mismatches with metallo-insertors: a molecular simulation study

Molecules that selectively recognize DNA mismatches (MMs) play a key role as nucleic acids probes and as chemotherapeutic agents. Metallo-insertors bind to the minor groove (mG) of double strand (ds) DNA, expelling the mismatched base pairs and acting as their π-stacking replacement. In contrast, metallo-intercalators bind to the major groove (MG) of ds DNA and π-stack to adjacent base pairs. In this study we focused on structural and energetic properties of Δ-[Rh(bpy)(2)(chrysi)](3+) (1), Δ-[Ru(bpy)(2)(ddpz)](2+) (2), and Δ-[Ru(bpy)(2)(eilatin)](2+) (3) as prototypical examples of metallo-insertors and intercalators. For all molecules we characterized both insertion and intercalation into a DNA dodecamer via force field based molecular dynamics (MD) and hybrid quantum-classical (QM/MM) MD simulations. A structural analysis of the 1-3/DNA noncovalent adducts reveals that the insertion provokes an untwist of the DNA, an opening of the mG and of the phosphate backbone in proximity of the mismatch, while the intercalation induces smaller changes of these structural parameters. This behavior appears to be correlated with the size of the inserting/intercalating ligand in proximity of the metal coordination site. Moreover, our simulations show that the different selectivity of 1 toward distinct MM types may be correlated with the thermodynamic stability of the MMs in the free DNA and with that of the corresponding insertion adduct. Understanding the factors which tune a specific insertion is of crucial importance for designing specific luminescent probes that selectively recognize MMs, as well as for developing more effective anticancer drugs active in MM repair of deficient cells lines.     

Ortho-selectivity in aluminophosphate molecular sieves: A molecular simulation study

Monte Carlo adsorption simulations of xylenes have been performed in aluminophosphate molecular sieve structures. A new force field fitted for o-xylene in AlPO₄-5 was used. It is shown that force fields have good transferability among the aluminophosphate sieves series and the new force field adequately describes the experimentally observed adsorption isotherms for xylene/AlPO₄-5. A previous investigation of adsorption isotherms and structural analysis has been extended to AlPO₄-8 and VPI-5 sieves. In AlPO₄-8, like in AlPO₄-5, the variations in the channels diameters and the corresponding interaction energy of the molecule-crystal lattice drive all molecular positioning. In VPI-5, the modulation between wide and narrow regions becomes negligible due to the larger pore diameter, so no ortho-selectivity was observed. The simulations confirm the ortho-selectivity mechanism proposed to aluminophosphates.     

A generalized model for the molecular arrangement in the columnar mesophases of polycatenar mesogens. Crystal and molecular structure of two hexacatenar mesogens

The columnar mesophases of two series of hexacatenar palladium(II) mesogens have been studied in detail by a combination of X-ray diffraction on aligned and unaligned samples and dilatometry. The results of these studies, combined with the results of two single crystal structure determinations, have allowed a model of the molecular arrangement in the columnar phases to be proposed. This model differs in detail from that generally accepted for the arrangement of polycatenar mesogens in columnar phases, and a new model is proposed which accounts for both new and existing data.     

Thermal decomposition of a honeycomb-network sheet: A molecular dynamics simulation study

The thermal degradation of a graphene-like two-dimensional honeycomb membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that at lower temperature the probability distribution of breaking bonds is highly peaked at the rim of the membrane sheet whereas at higher temperature bonds break at random everywhere in the hexagonal flake. The mean breakage time τ is found to decrease with the total number of network nodes N by a power law τ ∝ N(-0.5) and reveals an Arrhenian dependence on temperature T. Scission times are themselves exponentially distributed. The fragmentation kinetics of the average number of clusters can be described by first-order chemical reactions between network nodes n(i) of different coordination. The distribution of fragments sizes evolves with time elapsed from initially a δ-function through a bimodal one into a single-peaked again at late times. Our simulation results are complemented by a set of 1st-order kinetic differential equations for n(i) which can be solved exactly and compared to data derived from the computer experiment, providing deeper insight into the thermolysis mechanism.     

微乳胶粒的形成与表面活性剂的作用——粗粒化力场分子动力学模拟研究

从微观机理上研究表面活性剂对微乳胶粒形成的影响有利于推动微乳状液在各个领域的应用研究．本文采用分子动力学模拟方法研究了微乳胶粒的形成过程及表面活性剂对微乳胶粒形成的影响．正十二烷（C12H26）和十二烷基硫酸钠（SDS）作为油分子和表面活性剂分子的模型,Martini粗粒化（coarse．grained,CG）力场描述分子间和分子内的相互作用,对含有不同浓度的正十二烷和表面活性剂的12个模型分别进行了100ns的分子动力学模拟．模拟结果显示,不含表面活性剂的体系迅速发生水油相分离,且分离过程伴随着势能的明显下降;含有表面活性剂的体系中,在相同时间内通过模拟得到了稳定的、表面活性剂分子包裹油分子的胶粒．对不同温度下模拟得到的数据分析发现,胶粒形成初期的动力学特征可以近似地表达为二级反应,聚集活化能为14．6kJ／mol．     

The effect of molecular structure on the thermal properties of ferroelectric liquid crystalline cyclic siloxane tetramers

A series of liquid crystalline cyclic siloxane tetramers was prepared to investigate, in a systematic manner, the role of molecular structure of (a) the spacer group, (b) the mesogenic side group and (c) the chiral end group, on the liquid crystalline behaviour of these novel tetramers. The results from this systematic structure/property correlation study clearly showed the effects of the structure of the chiral end group and the mesogenic side group on the thermal stability and temperature range of the SmC* phase (ferroelectric) exhibited by these materials. For a given chiral end group, the effect of the length of the spacer group on the thermal stability and temperature range of the SmC* phases depended greatly on the structure of the mesogenic side group. By appropriate choice of spacer group, mesogenic side group and chiral end group, a number of tetramers exhibiting wide SmC* ranges (ferroelectricity) from below room temperature were synthesized.     

W-shaped mesogens and variations of their molecular structure

New bent-core liquid crystalline dimers with W-shaped molecular geometry have been prepared and studied. We have modified the dimer shape by variation of the connecting part between two bent-core units and changing the terminal chains (perfluoroalkyl, siloxanealkyl). Additionally, we have altered the inner bend angle value (120°, 60° and 148°) by utilization of different aromatic units. Mesomorphic properties of new dimers were established based on the texture observation in the polarizing microscope and DSC measurements. Moreover, x-ray structural analysis has been performed for selected dimers to confirm phase identification. For most of the studied dimers, nematic or columnar phases have been detected, for several compounds appearing in a nematic-columnar phase sequence on cooling from the isotropic phase. The studied dimers showed richer polymorphism than their monomeric counterparts.     

Protein nanopores with covalently attached molecular adapters

Molecular adapters are crucial for the stochastic sensing of organic analytes with alpha-hemolysin (alphaHL) protein nanopores when direct interactions between analytes and the pore cannot readily be arranged by conventional protein engineering. In our earlier studies, cyclodextrin adapters were lodged noncovalently within the lumen of the alphaHL pore. In the present work, we have realized the controlled covalent attachment of a beta-cyclodextrin (betaCD) adapter in the two possible molecular orientations inside alphaHL pores prepared by genetic engineering. There are two advantages to such a covalent system. First, the adapter cannot dissociate, which means there are no gaps during stochastic detection, a crucial advance for single-molecule exonuclease DNA sequencing where the continuous presence of a molecular adapter will be essential for reading individual nucleotides. Second, the ability to orient the adapter allows analytes to bind through only one of the two entrances to the betaCD cavity. We demonstrate that the covalently attached adapters can be used to alter the ion selectivity of the alphaHL pore, examine binding events at elevated temperatures, and detect analytes with prolonged dwell times.     

Interactions of lipid bilayers with supports: a coarse-grained molecular simulation study

The study of lipid structure and phase behavior at the nanoscale is of utmost importance due to implications in understanding the role of the lipids in biochemical membrane processes. Supported lipid bilayers play a key role in understanding real biological systems, but they are vastly underrepresented in computational studies. In this paper, we discuss molecular dynamics simulations of supported lipid bilayers using a coarse-grained model. We first focus on the technical implications of modeling solid supports for biomembrane simulations. We then describe noticeable influences of the support on the systems. We are able to demonstrate that the bilayer system behavior changes when supported by a hydrophilic surface. We find that the thickness of the water layer between the support and the bilayer (the inner-water region in the latter part of this paper) adapts through water permeation on the microsecond time scale. Additionally, we discuss how different surface topologies affect the bilayer. Finally, we point out the differences between the two leaflets induced by the support.     

The birth of a bubble: a molecular simulation study

We study the nucleation of a bubble in a metastable Lennard-Jones (LJ) fluid, confined to a spherical pore with wetting walls, by a combination of grand canonical, canonical ensemble, and gauge cell Monte Carlo simulation methods complemented by the Voronoi-Delaunay tessellation analysis of statistical geometry of intermolecular cavities. We construct the isotherm of confined fluid in the form of a continuous van der Waals' loop, in which the unstable backward trajectory between the spinodals corresponds to bubble states. We show that as the degree of metastability increases and the fluid becomes progressively stretched, the decrease of fluid density is associated with the evolution of a population of interstitial intermolecular cavities. At the spinodal, the fluid becomes mechanically unstable: Interstitial cavities partly coalesce into a larger cavity located due to the system symmetry around the pore center. This cavity represents a bubble embryo, which grows at the expense of interstitial cavities. The nucleation barrier is calculated by direct thermodynamic integration along the isotherm. We compare our simulation results to the predictions of the classical nucleation theory and experiments on capillary condensation-evaporation of nitrogen in pores of hybrid organic-inorganic mesoporous molecular sieve HMM-3.     

Transformation kinetics of liquid-crystallines based on 1,4-phenylene 4-n-alkylbenzoate-4-allyloxybenzoate by DSC

The transformation kinetics of a series of liquid-crystallines based on 1,4-phenylene 4-n-alkybenzoate-4-allyloxybenzoate (PABAOB) was studied by nonisothermal methods using differential scanning calorimetry. These determinations led to the values of activation energy of transformation from 691.3 to 628.3 kJ/mol, respectively. The values of the Avrami exponent n were from 3.0 to 2.6. The values of transformation activation energy decreased with the ascending of alkyl. The result shows that the process of transformation of PABAOB is a constant number of nuclei growing in three dimensions at constant rate and the crystal growth being controlled probably by a diffusion process. © 1997 John Wiley & Sons, Inc. Int J Chem Kinet 29: 317–321, 1997     

Molecular dynamics simulation of an electric field driven dipolar molecular rotor attached to a quartz glass surface

Molecular dynamics simulations of the response of a dipolar azimuthal 3-chloroprop-1-ynyl rotor mounted on the surface of quartz glass to a rotating electric field were performed. The rotor motion was classified as synchronous, asynchronous, random, or hindered, based on the value of the average lag of the rotor behind the field and a comparison of the intrinsic rotational barrier V(b) with kT. A phase diagram of rotor behavior was deduced at 10, 300, and 500 K as a function of field strength and frequency. A simple model for the rotor motion was developed, containing the driving force, the temperature, the height of the torsional barrier, and the friction constant of the rotor. Defining E(bo) to be the electric field strength necessary to get rotational response from the rotor ("breakoff field") and mu to be the rotor dipole moment component in the plane of rotation, we find that E(bo) is frequency independent when 2 microE(bo) is less than either V(b) or kT (the driving force needs to overcome the more important of the two, the intrinsic barrier or random thermal motion). At higher frequencies, E(bo) is a quadratic function of the frequency and the driving force fights friction, which is dictated by intramolecular vibrational redistribution (IVR) from the pumped rotational mode to all others. Fitting the simple model to simulation data, we derived a friction constant of 0.26 ps eV x (nu - 0.5)/THz between 500 and 1000 GHz.     

A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study

We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes as well as the simulated GILs. The proposed diffusion model facilitates the qualitative a priori prediction of the impact of ion modifications on the diffusive characteristics of new ionic liquids.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.