Molecules common structures/geometries

What are some common structures/geometries for molecules ... 

Crystalline solids have atoms, ions, or molecules packed in regular geometric arrays, with the structural unit called the unit cell. Some of the common crystal geometries are described in this section. In addition, we will consider the role of the relative sizes of the components in determining the structure. Use of a model kit, such as the one available from ICE, makes the study of these structures much easier. 

Tetrachloride and tetrabromide complexes are known for thorium, protactinium, uranium, neptunium, and plutonium. These are similarly produced by halide-based oxidation of metals or hydrides, or by halogenation of oxides. A common structural type is reported for most compounds. The reported structure of thorium tetrachloride reveals that the coordination geometry about the metal is dodecahedral.The compounds are generally volatile and can be sublimed. The gas-phase electron diffraction structure of suggests that the molecule is... 

Surfactant molecules commonly self-assemble in water (or in oil). Even single-surfactant systems can display a quite remarkably rich variety of structures when parameters such as water content or temperature are varied. In dilute solution they form an isotropic solution phase consisting of micellar aggregates. At more concentrated surfactant-solvent systems, several isotropic and anisotropic liquid crystalline phases will be formed [2]. The phase behavior becomes even more intricate if an oil (such as an alkane or fluorinated hydrocarbon) is added to a water-surfactant binary system and the more so if other components (such as another surfactant or an alcohol) are also included [3], In such systems, emulsions, microemulsions, and lyotropic mesophases with different geometries may be formed. Indeed, the ability to form such association colloids is the feature that singles out surfactants within the broader group of amphiphiles [4]. No wonder surfactants phase behavior and microstructures have been the subject of intense and profound investigation over the course of recent decades. 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

Chapter 3, Geometry Optimizations, describes how to locate equilibrium structures of molecules, or, more technically, stationary points on the potential energy surface. It includes an overview of the various commonly used optimization techniques and a consideration of optimizing transition strucmres as well as minimizations. 

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