Molecular modeling three-dimensional atomic

For molecules of molecular weight above 20,000 g/mol, X-ray diffraction remains the only experimental approach available to obtain detailed and reliable three-dimensional atomic models. The major steps of the method include the obtention of large and well-ordered crystals, their exposure to X-rays and collection of diffraction data and the phasing of these data to obtain by Fourier analysis a three-dimensional view (or map) of the electron density of the molecule. Finally a three-dimensional atomic model of the protein is fitted like a hand in a glove within this map, using a kit containing all the available biochemical and spectroscopic information (Table 6.2). The reliability of the final atomic model is of course dependent on the qnality of the electron density map. This qnality depends on the number of X-ray data per atom and on the resolution and accnracy of these data, which in turn are highly dependent on the size and quality of the crystals. 

The ball and wire display is used for model building Although it is convenient for this purpose other model displays show three dimensional molecular structure more clearly and may be preferred The space filling display is unique m that it portrays a molecule as a set of atom centered spheres The individual sphere radii are taken from experi mental data and roughly correspond to the size of atomic electron clouds Thus the space filling display attempts to show how much space a molecule takes up... 

Molecular modeling helps students understand physical and chemical properties by providing a way to visualize the three-dimensional arrangement of atoms. This model set uses polyhedra to represent atoms, and plastic connectors to represent bonds (scaled to correct bond length). Plastic plates representing orbital lobes are included for indicating lone pairs of electrons, radicals, and multiple bonds—a feature unique to this set. 

In chemistry, perhaps because of the significance in visualizing molecular strac-ture, there has been a focus on how students perceive three-dimensional objects from a two-dimensional representation and how students mentally manipulate rotated, reflected and inverted objects (Stieff, 2007 Tuckey Selvaratnam, 1993). Although these visualization skills are very important in chemistry, it is evident that they are not the only ones needed in school chemistry (Mathewson, 1999). For example, conceptual understanding of nature of different types of chemical bonding, atomic theory in terms of the Democritus particle model and the Bohr model, and... 

A molecule is a three-dimensional array of atoms. In fact, many of a molecule s properties, such as its odor and chemical reactivity, depend on its three-dimensional shape. Although molecular and structural formulas describe the composition of a molecule, they do not represent the molecule s shape. To provide information about shapes, chemists frequently use ball-and-stick models or space-filling models. 

We have designed PBUILD, a new CHEMLAB module, for easy construction of random copolymers. A library of monomers has been developed from which the chemists can select a particular sequence to generate a polymeric model. PBUILD takes care of all the atom numbering, three dimensional coordinates, and knows about stereochemistry (tacticity) as well as positional isomerism (head to tail versus head to head attachment). The result is a model of the selected polymer (or more likely a polymer fragment) in an all trans conformation, inserted into the CHEMLAB molecular workspace in literally a few minutes. 

The electronic wave function of an n-electron molecule is defined in 3n-dimensional configuration space, consistent with any conceivable molecular geometry. If the only aim is to characterize a molecule of fixed Born-Oppenheimer geometry the amount of information contained in the molecular wave function is therefore quite excessive. It turns out that the three-dimensional electron density function contains adequate information to uniquely determine the ground-state electronic properties of the molecule, as first demonstrated by Hohenberg and Kohn [104]. The approach is equivalent to the Thomas-Fermi model of an atom applied to molecules. 

Within this historical setting, the actual birth of stereochemistry can be dated to independent publications by J. H. van t Hoff and J. A. Le Bel within a few months of each other in 1874. Both scientists suggested a three-dimensional orientation of atoms based on two central assumptions. They assumed that the four bonds attached to a carbon atom were oriented tetrahedrally and that there was a correlation between the spatial arrangement of the four bonds and the properties of molecules, van t Hoff and Le Bell proposed that the tetrahedral model for carbon was the cause of molecular dissymmetry and optical rotation. By arguing that optical activity in a substance was an indication of molecular chirality, they laid the foundation for the study of intramolecular and intermolecular chirality. 

Molecular modeling techniques are a powerful tool to obtain a very detailed insight in the three-dimensional structure of dendrimer molecules at the atomic level. They have been applied to calculate sizes of the polypropylene imine) dendrimers and radial density profiles in order to estimate the free volume inside the dendrimers, as well as to make predictions about de Gennes dense-packed generations. The molecular modeling work by Coussens and co-workers [20] was focused on the generations 1-5 of the DAB-dendr-(CN)n and DAB-dendr-(NH2)n (n = 4, 8, 16,32, 64). 

Figure 3. Three-dimensional modeling of cardiolipin tetralinoleoyl created by Chem3D Pro, ver 4.0 with running of MM2, a software of molecular mechanics, to minimize steric energy in vacuo. Each atom is displayed in colour, H (blue), C (black), O (red), and P (purple) (see separate colour tip).

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