Three-dimensional molecule

The three-dimensional structure of ethane, C2H6, has the shape of two tetrahedra joined together. Each carbon atom is sp3 hybridized, with four sigma bonds formed by the four sp3 hybrid orbitals. Dashed lines represent bonds that go away from the viewer, wedges represent bonds that come out toward the viewer, and other bond lines are in the plane of the page. All the bond angles are close to 109.5°. 

Several views of methane. Methane has tetrahedral geometry, using four sp hybrid orbitals to form sigma bonds to the four hydrogen atoms. 

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CO—C H,—CO—0—CHj—CHOH—CHj—OOC—CgH,—CO— These are comparatively soft materials and they are soluble in a number of organic solvents. Under more drastic conditions (200-220°) and with a larger proportion of phthahc anhydride, the secondary alcohol groups are esterified and the simple chains become cross-hnked three dimensional molecules of much higher molecular weight are formed ... 

The commonly used resins in the manufacture of decorative and industrial laminates ate thermosetting materials. Thermosets ate polymers that form cross-linked networks during processing. These three-dimensional molecules ate of essentially infinite size. Theoretically, the entire cured piece could be one giant molecule. The types of thermosets commonly used in laminates ate phenoHcs, amino resins (melamines), polyesters, and epoxies. 

Three-Dimensional Modeling of Chemical Structures. The two-dimensional representations of chemical stmctures are necessary to depict chemical species, but have limited utiHty in providing tme understanding of the effects of the three-dimensional molecule on properties and reactive behavior. To better describe chemical behavior, molecular modeling tools that reflect the spatial nature of a given compound are required. 

For this study, p-xylene and triisopropylcyclohexane (TIPcyC6) were the two molecular probes chosen, using toluene as a solvent. Their molecular dimensions were obtained from the shadow of the three-dimensional molecule projected onto a plane according to the method of Rohrbaurgh et al. [5] (Table 2). A molecular probe is considered not to penetrate into a cylindrical pore if two of its dimensions are greater than the pore diameter [6], As the free diameter of the window of the supercage of the Y zeolite is equal to 0.74 nm, it is considered that only TIPCyC6 cannot penetrate into the zeolite microporosity. 

Figure 11.10 Lewis structures of water (H20). (a) shows two possible configurations of water, but only H-O-H satisfies the electronic requirements of the oxygen atom, (b) shows three possible bond distributions for this structure, but only one (with a single bond to each of the hydrogens and two lone pairs on the oxygen) meets the requirements of all three atoms, (c) shows the bent structure of H-O-H which follows from the need to separate the two lone pairs and two single bonds as far as possible in the three-dimensional molecule, (d) shows a space-filling version of this arrangement, where the oxygen is black and the two hydrogens white.

Lignin is a polymer built up of phenylpropane units substituted with hydroxy and methoxy groups, see Figure 48. Lignin is a three-dimensional molecule like a 3-D matrix, see Figure 48 [65]. 

It is not always easy to look at stereostructures - two-dimensional representations of three-dimensional molecules - and decide whether two separate representations are the same or different. To compare structures, it is usually necessary to manipulate one or both so that they can be compared directly. Here are a few demonstrations of how to approach the problem on paper. Of course, constructing models for comparison is the easiest method, but there will always be occasions when we have to figure it out on paper. 

Projections are used, particularly in organic chemistry, to represent three-dimensional molecules in two dimensions. In a Fischer projection, the atoms or groups of atoms attached to a tetrahedral centre are projected onto the plane of the paper from such an orientation that atoms or groups appearing above or below the... 

F.R. Parker, JChemPhys 27, 720-33(1957) [Use of Monte Carlo calculations for three-dimensional molecules interacting in pairs according to Lennard-Jones (LJ) potential. The program... 

In this contribution, we would like to show how such an approach allowed us to synthesize both soft and very hard molecule-based magnets. This contribution is organized as follows first, we define briefly the field of molecular magnetism, then we indicate the successive steps which led us to three-dimensional molecule-based magnets with fully interlocked structures. We describe these original structures in detail. Finally, we focus on the physical properties of these objects, with special emphasis on the huge coercivity of one of the compounds, which confers a memory effect on this compound. 

The three tartaric acids may be used to illustrate the method employed in depicting three-dimensional molecules in two-dimension projections. 

FIGURE 24.10 According to the lock-and-key model, an enzyme is a large, three-dimensional molecule containing a crevice with an active site. Only a substrate whose shape and structure are complementary to those of the active site can fit into the enzyme. The active site of the enzyme hex-ose kinase is visible as the cleft on the left in this computergenerated structure, as is the fit of the substrate (yellow) in the active site. 

By means of chemical reactions thermosetting plastics form three-dimensional structures. In the example above the nitrogen compound urea reacts with formaldehyde (methanal), in which process three molecules combine and a molecule of water is formed. In this example two H atoms react, but all other H atoms ( ) enter into the same reaction. Since urea is a three-dimensional molecule, the network will also be three-dimensional. For instance switches and sockets are made of UF. Other thermosetting plastics are polyurethane PU (insulation) and melamine-formaldehyde MF (panels). 

An antigen is a highly complex, three-dimensional molecule, and the precise location of epitopes on or within the antigen in most cases is not known. Furthermore, antigen retrieval methods may unfold the antigen molecule, exposing hidden (buried) epitopes. 

A key challenge is figuring out how to get less exotic polymers to self-assemble. Physical scientists are a long way from being able to control polymer syntheses so that the self-assembly of complicated, three-dimensional molecules is possible. This is a very active area of research, one that promises eventually to result in interesting new scientific understanding, new technological tools, and new materials with unique properties. 

These structures, when written as shown below (left), are called Fischer projection formulas, which are attempts to represent three-dimensional molecules in two dimensions. For example, the two molecules would appear in three-dimensional space as shown below (right)... 

Thermosetting cure produces highly cross-linked three-dimensional molecules of infinite size. 

Cross-Linking. Thermoplastics are stable linear molecules which are softened by heat and soluble in solvents of similar polarity this makes for easy processability. Primary covalent cross-linking in thermosets converts them into three-dimensional molecules of infinite... 

Atomic bonding is not restricted to the bonding of atoms into separate molecules but also gives rise to the formation of lattices, of giant three-dimensional molecules so to speak. 

Rotaxanes are three-dimensional molecules made from two mechanically linked components a ring (macrocycle) and a dumbbell subunit. In this section... 

The authors of a biochemistry text face the problem of trying to present three-dimensional molecules in the two dimensions available on the printed page. The interplay between the three-dimensional structures of hiomolecules and their biological functions will be discussed extensively throughout this hook. Toward this end, we will frequently use representations that, although of necessity are rendered in two dimensions, emphasize the three-dimensional structures of molecules. 

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