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.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

二原子分子和三原子分子的周期表

门捷列夫元素周期表是自然科学中最重要的原则之一．然而,对于分子而言,却缺乏类似的表格．本文提出两个分别对应于二原子分子和三原子分子的周期表．这些分子周期表的格式和门捷列夫原子周期表相似．在这些表格中,分子依照它们各自的族数G和周期数P分类排列,G是价电子的数目而P则表示分子的尺寸．分子的基本性质,包括键长、结合能、力常数、电离势、自旋多重度、化学反应活性以及键角等等,都随着表中的G和P作周期性的变化．二原子分子和三原子分子的周期性因而被揭示开来．本文还进一步指出这种周期性是源出于分子的壳状电子构型．周期表中不仅包含了游离的分子,还包含了多原子分子中的“赝”分子．这些周期表可用来从本质上分类分子,广泛地预言分子的未知性质,了解在多原子分子中赝分子的作用,以及开拓新的研究领域,如芳香族、团簇或纳米微粒的周期性等．因此这些表格不仅能够引起多学科领域中科学工作者的关注,而且还能引起理科学生们的兴趣．     

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.     

Periodic tables of diatomic and triatomic molecules

The Mendeleev periodic table of atoms is one of the most important principles in natural science. However, there is shortage of analog for molecules. Here we propose two periodic tables, one for diatomic molecules and one for triatomic molecules. The form of the molecular periodic tables is analogous to that of Mendeleev periodic table of atoms. In the table, molecules are classified and arranged by their group number G, which is the number of valence electrons, and the periodic number P, which represents the size of the molecules. The basic molecular properties, including bond length, binding energy, force constant, ionization potential, spin multiplicity, chemical reactivity, and bond angle, change periodically within the tables. The periodicities of diatomic and triatomic molecules are thus revealed. We also demonstrate that the periodicity originates from the shell-like electronic configurations of the molecules. The periodic tables not only contain free molecules, but also the "virtual" molecules present in polyatomic molecules. The periodic tables can be used to classify molecules, to predict unknown molecular properties, to understand the role of virtual molecules in polyatomic molecules, and to initiate new research fields, such as the periodicities of aromatic species, clusters, or nanoparticles. The tables should be of interest not only to scientists in a variety of disciplines, but also to undergraduates studying natural sciences.     

When things are not as they seem: quantum interference turns molecular electron transfer "rules" upside down

We present an interesting consequence of the differences between cross-conjugated and linearly conjugated molecules: the breakdown of conventional understanding of trends in molecular electron transfer. Interference effects are dominant in cross-conjugated molecules with unusual results: long molecules may have faster rates of electron transfer than short molecules, saturated molecules may have faster rates of electron transfer than conjugated molecules of the same length, and the rate of electron transfer cannot be correlated with energy gaps between the donor and acceptor states and the energy levels of the bridging molecule.     

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.     

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.     

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.     

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.     

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.     

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.     

Dielectric relaxation studies of dipolar aromatics in polyethylene. II. Oriented low-density polyethylene

Stretched polyethylene has been used for several years by organic spectroscopists as a means of orienting isolated aromatic molecules. Dielectric relaxation studies are reported which consider dipolar aromatic molecules dissolved in stretched polyethylene in order to learn more about the environment of these oriented molecules. The research builds on earlier studies of the dielectric relaxation behavior of dipolar aromatic molecules dissolved in unoriented low density polyethylene. Studies demonstrate that molecules in the amorphous phase are oriented at temperatures below the glass transition, both the β and γ relaxations being orientation dependent. It is shown through studies of oriented rods that large numbers of the orientable molecules are immobilized by the oriented polyethylene and cannot relax. An essential criterion for immobilization to occur is that molecules exhibit geometrical symmetry.     

Dielectric properties of water clusters containing CO and NO molecules. Computational experiment

The absorption of CO and NO molecules by (H₂O)₂₀ clusters was studied by the method of molecular dynamics. In general, the clusters containing CO molecules are more stable mechanically, while the clusters with NO molecules are more stable against heating. The mobility of NO molecules in such clusters is higher than that of CO molecules. The total dipole moment, the static dielectric permeability, the number of active electrons in the clusters, and the specific number of hydrogen bonds between water molecules possess peak values when the number of doping molecules i = 6. IR absorption spectra mostly acquire a smooth shape at i > 6. Capture of CO and NO molecules by water cluster operates as anti-greenhouse effect.     

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.     

Control of alkanethiolate monolayer structure using vapor-phase annealing

We describe an annealing procedure for self-assembled monolayers (SAMs) that uses vapor-phase molecules to modify the local domain structure. Existing SAMs of decanethiolate on Au{111} were annealed using vapor-phase dodecanethiol molecules, so that the original and newly introduced molecules could be distinguished using scanning tunneling microscopy (STM). Molecules deposited from the vapor phase inserted at existing monolayer defect sites and domain boundaries, and at substrate step edges forming discrete network-like domains. The SAM molecular lattice can be preserved across molecular terrace boundaries between the decanethiolate and dodecanethiolate domains. Candidate molecular electronic component molecules were inserted from solution in the decanethiolate matrix as isolated molecules. These inserted molecules could then be surrounded by dodecanethiolate molecules introduced from the vapor phase, thus demonstrating a method for controlling the local environment of inserted molecules.     

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.     

Synthesis and application of quantum dots FRET-based protease sensors

Preparation of FRET-based quantum dots as protease sensors-RGDC peptide molecules are bound to the surface of CdSe/ZnS quantum dots. The peptide molecules are then labeled with rhodamine dye molecules. The emission color of the quantum dots change from green to orange due to fluorescence resonance energy transfer (FRET) between the quantum dots and the bound rhodamine molecules. Cleavage of the peptide by selective proteases releases the rhodamine molecules from the quantum dots surface, which results in decreasing FRET efficiency between the quantum dots and the rhodamine molecules. The emission color of the quantum dots changes back to green.     

Analytical laser ionization spectrometry in flame: Choice of the analytical form for the determination of rare earth elements

Based on the ionization potentials and dissociation energies of rare earth monoxides, these molecules are classified into two groups. For the molecules of the first type, the ionization potential is lower than the dissociation energy. Laser excitation of these molecules leads to their predominant ionization. For the molecules of the second type, the ionization potential is higher than the dissociation energy. Depending on the absolute values of the latter, atomic lines can be observed in the ionization spectrum. The elements that form molecules of the first type in flame should be determined as monoxide molecules. For the elements forming molecules of the second type, determination in the atomic form gives better results.