Complicated Molecules

Minimal input lilcs fur cyclupentciie and cyclopciitanc can be constructed from a pentag(.)n drawn un grapli paper the way minimal ethylene was drawn (Fig. 4-4). F(.)r more complicated molecules, however, the draw function of PCMODEL or some similar file constnicting program becomes less a convenience and more a necessity,... 

The term resonance energy has been used in several w ays in the literature, but it is generally used to mean the difference between an experimentally determined energy of some relatively complicated molecule and the experimental energy... 

Synthesis Amazingly, this complicated molecule is made in just two steps ... 

When in the late 1940 s the remarkable therapeutic effects of the glucocorticoids cortisone and hydrocortisone were discovered, new raw materials had to be developed to produce these complicated molecules, and new synthetic methods devised to convert either a 20-ketopregnane or 21-acetoxy-20-ketopregnane to the dihydroxyacetone side-chain characteristic of these corticoids. This latter challenge produced some extremely useful new organic chemical reactions, many of which have wider application outside of steroids. 

More complicated molecules, with two or more chemical bonds, have more complicated absorption spectra. However, each molecule has such a characteristic spectrum that the spectrum can be used to detect the presence of that particular molecular substance. Figure 14-17, for example, shows the absorptions shown by liquid carbon tetrachloride, CCfi, and by liquid carbon disulfide, CS2. The bottom spectrum is that displayed by liquid CC14 containing a small amount of C. The absorptions of CS2 are evident in the spectrum of the mixture, so the infrared spectrum can be used to detect the impurity and to measure its concentration. 

If R2 contains an a-hydrogen the method cannot be applied as enaminc formation occurs. Bisamides (or -carbamates) are often used in amidoalkylations of aryl and reactive methylene compounds, but the rather harsh reaction conditions severely limit application in the synthesis of more complicated molecules with other functional groups. 

Equation (4.18) applies only to a diatomic or linear polyatomic molecule. Similar kinds of rotational energy levels are present in more complicated molecules. We will describe the various kinds in more detail in Chapter 10. 

This procedure assumes that the translational, rotational, vibrational, and electronic energy levels are independent. This is not completely so. In the instance of diatomic molecules, we will see how to correct for the interaction. For more complicated molecules we will ignore the correction since it is usually a small effect. 

Alkanes keep going up in size. When they get up to C18H 8 they become solids. The familiar white solid paraffin, which is commonly used for making candles, is made up of solid alkanes. Paraffin is not really a wax, as waxes are made up of more complicated molecules. 

As we have seen by comparing C02 and H20, the shape of a polyatomic molecule affects whether or not it is polar. The same is true of more complicated molecules. For instance, the atoms and bonds are the same in c/s-dichloroethene (28) and frans-dichloroethene (29) but, in the latter, the C—Cl bonds point in opposite directions and the dipoles (which point along the C—Cl bonds) cancel. Thus, whereas c/s-dichloroethene is polar, traws-dichloroethene is nonpolar. Because dipole momenrs are directional, we can treat each bond dipole moment as a vector. The molecule as a whole will be nonpolar if the vector sum of the dipole moments of the bonds is zero. 

The Structures of Simple Molecules.—The foregoing considerations throw some light on the structure of very simple molecules in the normal and lower excited states, but they do not permit such a complete and accurate discussion of these questions as for more complicated molecules, because of the difficulty of taking into consideration the effect of several unshared and sometimes unpaired electrons. Often the bond energy is not great enough to destroy s-p quantization, and the interaction between a bond and unshared electrons is more important than between a bond and other shared electrons because of the absence of the effect of concentration of the eigenfunctions. 

It is probable that the errors introduced by the neglect of all except unexcited and first-excited structures and by equating /3 and /S to a cancel each other to a considerable extent, especially for more complicated molecules than the dihydro-... 

In the case of glasses made from complicated molecules, it would seem probable that such shifts would be possible. On the other hand, in the case of a liquid made from a simple monatomic substance, it might be impossible to obtain any condensed phase at the absolute zero having greater... 

Heats of combustion are very accurately known for hydrocarbons. For methane the value at 25°C is 212.8 kcal mol (890.4 kJ mol ), which leads to a heat of atomization of 398.0 kcal mol (1665 kJ mol ) or a value of for the C—H bond at 25°C of 99.5 kcal mol (416 kJ mol ). This method is fine for molecules like methane in which all the bonds are equivalent, but for more complicated molecules assumptions must be made. Thus for ethane, the heat of atomization at 25°C is 676.1 kcal mol or 2829 kJ mol (Fig. 1.11), and we must decide how much of this energy is due to the C—C bond and how much to the six C—H bonds. Any assumption must be artificial, since there is no way of actually obtaining this information, and indeed the question has no real meaning. If we make the... 

Figure 3.4. Pentane. The diagram shows the four minimum-energy conformations of pentane. The global minimum is on the far left. Reflection and rotation of some of these geometries worrld generate more structures, but nothing with a different energy. Pentane is a simple molecule. More complicated molecules have many more conformations. Bryostatin 2 and PM-toxin A have so many mirrimtrm-energy conformations that to list them all would be a major undertaking and would require a large library to store the result.

This relatively small catalog of molecular shapes accounts for a remarkable number of molecules. Even complicated molecules such as proteins and other polymers have shapes that can be traced back to these relatively simple templates. The overall shape of a large molecule is a composite of the shapes associated with its inner atoms. The shape around each inner atom is determined by steric numbers and the number of lone pairs. 

Chlorophyll, plastoquinone, and cytochrome are complicated molecules, but each has an extended pattern of single bonds alternating with double bonds. Molecules that contain such networks are particularly good at absorbing light and at undergoing reversible oxidation-reduction reactions. These properties are at the heart of photosynthesis. 

A biochemical catalyst is called an enzyme. Enzymes are specialized proteins that catalyze specific biochemical reactions. Some enzymes are found in extracellular fluids such as saliva and gastric juices, but most are found inside cells. Each type of cell has a different array of enzymes that act together to determine what role the cell plays in the overall biochemistry of the organism. Enzymes are complicated molecules. Biochemists have determined the molecular structures of some enzymes, but the structures of many enzymes are not yet known. 

Assuming that a reasonable force field is known, the solution of the above equations to obtain the vibrational frequencies of water is not difficult However, in more complicated molecules it becomes very rapidly a formidable one. If there are N atoms in the molecule, there are 3N total degrees of freedom and 3N-6 for the vibrational frequencies. The molecular symmetry can often aid in simplifying the calculations, although in large molecules there may be no true symmetry. In some cases the notion of local symmetry can be introduced to simplify the calculation of vibrational frequencies and the corresponding forms of the normal modes of vibration. 

As for more complicated molecules, the exo-addition 106> in the 2-norbonyl radical was explained from the point of view of SO extension 105>. The 2-carbon is not exactly sp2 hybridized but extends more in the exo direction than in the endo direction15. The nonplanarity of almost-s 2 carbon in radicals is also expected in 2-chloroethyl and 4-t-butylcyclo-hexyl in which stereoselective recombinations are known. A rather exaggerated illustration of the mode of extension of SO MO is given below... 

Therefore, it seems worthwhile to examine this idea by studying the interaction of some more complicated molecules (e.g., unsaturated hydrocarbons, such as ethylene, propylene, cyclopropane) with the metal surfaces. This type of study might also be of some practical importance. 

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