Superstructures of Functional Colloids: Chemistry on the Nanometer Scale

Chemistry is classically concerned with the connection of atoms and molecules into new functional units. The rules of connection are yet to be extended to the generation and connection of larger objects, whose dimensions are measured in nanometers. However, linking objects of this size through molecules approaching each other randomly is inefficient, instead the principle of self-assembly is decisive, in which lyotropic structure formation or amphiphilic interaction play a significant role. As a result of the nature of the energetic driving forces, the objects generated in this way are often well-defined aggregate structures or highly symmetric volume phases. In contrast to “molecular chemistry”, the linking of larger objects also disregards the inherent borders of classical fields of chemistry: for example, the nanoscale association of inorganic colloids with polymers affords hybrid materials that combine the physical properties of both partners. In such a way, catalytic, optical, and electronic features of inorganic colloids might be combined with the mechanical characteristics of polymers such as film formation, elasticity, and melt processibility.     

Interfaces between Molecular and Polymeric “Metals”: Electrically Conductive,Structure-Enforced Assemblies of Metallomacrocycles

The design, synthesis, characterization, and understanding of new molecular and macro-molecular substances with “metal-like” electrical properties represents an active research area at the interface of chemistry, physics, and materials science. An important, long-range goal in this field of “materials by design” is to construct supermolecular assemblies which exhibit preordained collective phenomena by virtue of “engineered” interactions between molecular building blocks. In this review, such a class of designed materials is discussed which, in addition, bridges the gap between molecular and polymeric conductors: assemblies of electrically conductive metallomacrocycles. It is seen that efforts to rationally construct stacked metal-like molecular arrays lead logically to structure-enforced macromolecular assemblies of covalently linked molecular subunits. Typical building blocks are robust, chemically versatile metallophthalocyanines. The electrical optical, and magnetic properties of these metallomacrocyclic assemblies and the fragments thereof, provide fundamental information on the connections between local atomic-scale architecture, electronic structure, and the macroscopic collective properties of the bulk solid.     

Does Topology Dictate the Incidence of the Twist‐Bend Phase? Insights Gained from Novel Unsymmetrical Bimesogens

We prepared a significant number of unsymmetrical liquid‐crystalline dimers that exhibit the twist‐bend nematic phase; a state of matter that exhibits spontaneous breaking of mirror symmetry and, for some materials, a microsecond electrooptic response. A number of novel unsymmetrical bimesogens were synthesized and in comparing their thermal behaviour to previous literature examples, we have uncovered an unexpected relationship between the thermal stability of the nematic and N_TB phases. This relationship demonstrates that molecular shape dictates the incidence of this fascinating phase of matter and leads us to speculate as to the existence of “twist‐bend nematic phases” on length scales beyond those of the molecule.     

Symmetry Breaking and Non-Born-Oppenheimer Effects in Radical Cations

The various electronic states in which molecules can exist are often considered to be independent. In this article we turn our attention to the limitations of this assumption, namely the interaction between different electronic states through the nuclear motion. This interaction can have several important consequences, two of which are discussed in some detail. One is a distortion of the molecular framework, leading to a lowering of the symmetry of a molecule in excited or ionic states compared to the neutral ground state. General aspects of this symmetry lowering are outlined and interpreted with the aid of typical examples. The other consequence considered is the ability of the nuclei to “jump” between different molecular potential energy surfaces (non-Born-Oppenheimer effects). The nature of this behavior is analyzed and it is argued that the “jumping” can be very fast and efficient, dominating completely the nuclear motion. To exemplify our general ideas we refer to the photoelectron spectra of ethylene and related compounds and demonstrate that they are governed by strong non-Born-Oppenheimer effects. It emerges that the Franck-Condon principle fails in the analysis of their vibronic structure.     

Symmetrizer: Algorithmic determination of point groups in nearly symmetric molecules

Symmetry is an extremely useful and powerful tool in computational chemistry, both for predicting the properties of molecules and for simplifying calculations. Although methods for determining the point groups of perfectly symmetric molecules are well‐known, finding the closest point group for a “nearly” symmetric molecule is far less studied, although it presents many useful applications. For this reason, we introduce Symmetrizer, an algorithm designed to determine a molecule's symmetry elements and closest matching point groups based on a user‐adjustable tolerance, and then to symmetrize that molecule to a given point group geometry. In contrast to conventional methods, Symmetrizer takes a bottom‐up approach to symmetry detection by locating all possible symmetry elements and uses this set to deduce the most probable point groups. We explain this approach in detail, and assess the flexibility, robustness, and efficiency of the algorithm with respect to various input parameters on several test molecules. We also demonstrate an application of Symmetrizer by interfacing it with the WebMO web‐based interface to computational chemistry packages as a showcase of its ease of integration. © 2012 Wiley Periodicals, Inc.     

Symmetry operation measures

We introduce a new mathematical tool for quantifying the symmetry contents of molecular structures: the Symmetry Operation Measures. In this approach, we measure the minimal distance between a given structure and the structure which is obtained after applying a selected symmetry operation on it. If the given operation is a true symmetry operation for the structure, this distance is zero; otherwise it gives an indication of how different the transformed structure is from the original one. Specifically, we provide analytical solutions for measures of all the improper rotations, S n p, including mirror symmetry and inversion, as well as for all pure rotations, C n p. These measures provide information complementary to the Continuous Symmetry Measures (CSM) that evaluate the distance between a given structure and the nearest structure which belongs to a selected symmetry point-group.     

Macroscopic Self-Evolution of Dynamic Hydrogels to Create Hollow Interiors

A solid-to-hollow evolution in macroscopic structures is challenging in synthetic materials. A fundamentally new strategy is reported for guiding macroscopic, unidirectional shape evolution of materials without compromising the material's integrity. This strategy is based on the creation of a field with a “swelling pole” and a “shrinking pole” to drive polymers to disassemble, migrate, and resettle in the targeted region. This concept is demonstrated using dynamic hydrogels containing anchored acrylic ligands and hydrophobic long alkyl chains. Adding water molecules and ferric ions (Fe³⁺) to induce a swelling–shrinking field transforms the hydrogels from solid to hollow. The strategy is versatile in the generation of various closed hollow objects (for example, spheres, helix tubes, and cubes with different diameters) for different applications.     

Macroscopic Self‐Evolution of Dynamic Hydrogels to Create Hollow Interiors

A solid‐to‐hollow evolution in macroscopic structures is challenging in synthetic materials. A fundamentally new strategy is reported for guiding macroscopic, unidirectional shape evolution of materials without compromising the material's integrity. This strategy is based on the creation of a field with a “swelling pole” and a “shrinking pole” to drive polymers to disassemble, migrate, and resettle in the targeted region. This concept is demonstrated using dynamic hydrogels containing anchored acrylic ligands and hydrophobic long alkyl chains. Adding water molecules and ferric ions (Fe³⁺) to induce a swelling–shrinking field transforms the hydrogels from solid to hollow. The strategy is versatile in the generation of various closed hollow objects (for example, spheres, helix tubes, and cubes with different diameters) for different applications.     

Shape and symmetry of heptacoordinate transition-metal complexes: structural trends

The stereochemistries of heptacoordinate transition-metal complexes are analyzed by using continuous symmetry and shape measures of their coordination spheres. The distribution of heptacoordination through the transition-metal series is presented based on structural database searches including organometallic and Werner-type molecular complexes, metalloproteins, and extended solids. The most common polyhedron seems to be the pentagonal bipyramid, while different preferences are found for specific families of compounds, as in the complexes with three or four carbonyl or phosphine ligands, which prefer the capped octahedron or the capped trigonal prism rather than the pentagonal bipyramid. The symmetry maps for heptacoordination are presented and shown to be helpful for detecting stereochemical trends. The maximal symmetry interconversion pathways between the three most common polyhedra are defined in terms of symmetry constants and a large number of experimental structures are seen to fall along those paths.     

Jahn–Teller Effects in Molecular Cations Studied by Photoelectron Spectroscopy and Group Theory

The traditional “ball‐and‐stick” concept of molecular structure fails when the motion of the electrons is coupled to that of the nuclei. Such a situation arises in the Jahn–Teller (JT) effect which is very common in open‐shell molecular systems, such as radicals or ions. The JT effect is well known to chemists as a mechanism that causes the distortion of an otherwise symmetric system. Its implications on the dynamics of molecules still represent unsolved problems in many cases. Herein we review recent progress in understanding the dynamic structure of molecular cations that have a high permutational symmetry by using rotationally resolved photoelectron spectroscopy and group theory. Specifically, we show how the pseudo‐Jahn–Teller effect in the cyclopentadienyl cation causes electronic localization and nuclear delocalization. The fundamental physical mechanisms underlying the vaguely defined concept of “antiaromaticity” are thereby elucidated. Our investigation of the methane cation represents the first experimental characterization of the JT effect in a threefold degenerate electronic state. A special kind of isomerism resulting from the JT effect has been discovered and is predicted to exist in all JT systems in which the minima on the potential‐energy surface are separated by substantial barriers.     

Electric fields for generating unconventional motion of small objects

Electric fields can be used in several ways to generate motion of objects. In this article, we focus on some more or less unconventional approaches, allowing in a direct or indirect way to design systems which show controlled motion, eventually combined with other functionalities such as light emission. We review some of the most recent results in this context with a special focus on bipolar electrochemistry as a straightforward approach for breaking symmetry, which is a necessary ingredient for any type of motion.     

An Approach for Visualization of the Active Site of Enzymes with Unknown Three-Dimensional Structures

Abstract

A new approach for virtual characterization of the active site structure of enzymes with unknown three-dimensional (3D) structure has been proposed. It includes analysis of data on enzyme interaction with reversible competitive inhibitors, their 3D structures and moulding of the substrate-binding region. The superposition of ligands in biologically active conformations allows to determine the shape and dimension of the active site cavity accommodating these compounds. Monoamine oxidase A (MAO-A), a “typical” enzyme with unknown spatial organisation, was used to test this method. The correctness of such approach was validated by the analysis of HIV protease interaction with its inhibitors using 3D structures of their complexes. Mould of the substrate/inhibitor binding site can be used for the visualization of this binding site and for searching new ligands in molecular databases.     

Polymer 4D printing: Advanced shape-change and beyond

4D printing is an exciting branch of additive manufacturing. It relies on established 3D printing techniques to fabricate objects in much the same way. However, structures which fall into the 4D printed category have the ability to change with time, hence the “extra dimension.” The common perception of 4D printed objects is that of macroscopic single-material structures limited to point-to-point shape change only, in response to either heat or water. However, in the area of polymer 4D printing, recent advancements challenge this understanding. A host of new polymeric materials have been designed which display a variety of wonderful effects brought about by unconventional stimuli, and advanced additive manufacturing techniques have been developed to accommodate them. As a result, the horizons of polymer 4D printing have been broadened beyond what was initially thought possible. In this review, we showcase the many studies which evolve the very definition of polymer 4D printing, and reveal emerging areas of research integral to its advancement.     

Starburst Dendrimers: Molecular-Level Control of Size,Shape, Surface Chemistry,Topology, and Flexibility from Atoms to Macroscopic Matter

Starburst dendrimers are three-dimensional, highly ordered oligomeric and polymeric compounds formed by reiterative reaction sequences starting from smaller molecules—“initiator cores” such as ammonia or pentaerythritol. Protecting group strategies are crucial in these syntheses, which proceed via discrete “Aufbau” stages referred to as generations. Critical molecular design parameters (CMDPs) such as size, shape, and surface chemistry may be controlled by the reactions and synthetic building blocks used. Starburst dendrimers can mimic certain properties of micelles and liposomes and even those of biomolecules and the still more complicated, but highly organized, building blocks of biological systems. Numerous applications of these compounds are conceivable, particularly in mimicking the functions of large biomolecules as drug carriers and immunogens. This new branch of “supramolecular chemistry” should spark new developments in both organic and macromolecular chemistry.     

Fundamentals of Silicon Chemistry: Molecular States of Silicon-Containing Compounds

Silicon and its compounds have made possible the design of new materials, which, from computers to space travel, have helped to shape the technology of our 20th century. Conversely, the demands of new technology have stimulated the fast development of silicon chemistry as part of the “renaissance” of inorganic chemistry. This article uses selected examples of predominantly organosilicon compounds to discuss in simplified terms the measurement and assignment of suitable spectroscopic “molecular fingerprints” as well as the resulting benefit for the preparative chemist. The comparison of “equivalent” states of “chemically related” molecules is emphasized, based on perturbation arguments and supporting quantum-chemical models. Special attention is given to the relation between structure and energy, which allows us to understand and to predict the connectivity between and the spatial arrangement of silicon “building blocks”, the energy-dependent electron distribution over the effective nuclear potentials of a molecular framework, and, especially, the partly considerable effects of “silicon substituents” on molecular properties. Future-directed extensions and applications include polysilane band structures, Rydberg states of chromophores containing silicon centers, redox reactions and ion-pair formation of silicon-substituted π systems, and molecular dynamic phenomena in solution or on thermal fragmentation in the gas phase. The main objective is a set of clear and practical rules for interpreting measurements and planning experiments.     

“Non-muffin tin” corrections of the SCF Xα-SW Method. I

The recently developed crystalline cluster method within the framework of the Johnson multiple scattering technique was successfully used in calculations of ionic cubic crystals and the defects with a cubic symmetry. In this paper a simple way of extension of the method to noncubic systems by a partial elimination of “muffin-tin” approximation (MTA ) is proposed. The procedure suggested does reduce the intermediate integrals to the one-dimensional ones, and they are calculated analytically. It is supposed that an approach of taking into account the nonspherical shape of the potential inside the “muffin-tin” (MT ) spheres will be effective in crystals with an ionic type of chemical bond.     

POV-Ray软件在分子对称性中的应用

以交错式乙烷为例,详细地介绍了如何使用POV-Ray软件制作展示分子对称元素的精美视频动画,可以帮助学生直观形象地分析分子结构,很好地掌握分子对称性的相关教学内容,切实提高课程的教学效果。     

Quantitative symmetry and chirality--a fast computational algorithm for large structures: proteins, macromolecules, nanotubes, and unit cells

Symmetry is one of the most fundamental properties of nature and is used to understand and investigate physical properties. Classically, symmetry is treated as a binary qualitative property, although other physical properties are quantitative. Using the continuous symmetry measure (CSM) methodology one can quantify symmetry and correlate it quantitatively to physical, chemical, and biological properties. The exact analytical procedures for calculating the CSM are computationally expensive and the calculation time grows rapidly as the structure contains more atoms. In this article, we present a new method for calculating the CSM and the related continuous chirality measure (CCM) for large systems. The new method is much faster than the full analytical procedures and it reduces the calculation time dependency from N! to N(2), where N is the number of atoms in the structure. We evaluate the cost of the applied approximations, estimate the error of the method, and show that deviations from the analytical solutions are within an error of 2%, and in many cases even less. The method is applicable at the moment for the cyclic symmetry point groups- C(i), C(s), C(n), and S(n), and therefore it can be used also for chirality measures, which are the minimal of the S(n) measures. We demonstrate the application of the method for large structures across chemistry: proteins, macromolecules, nanotubes, and large unit cells of crystals.