Twisted molecules

The linking difference can be considered in terms of changes in the twist, Tiv, and writh, Wr, of the molecule. Twist describes how the DNA strands are coHed around each other writh describes the coiling of the hehcal axis. The change in linking number is related to changes in twist and writh ... 

The first several chapters of any organic chemistry textbook focus on the structure of molecules how atoms connect to form bonds, how we draw those connections, the problems with our drawing methods, how we name molecules, what molecules look like in 3D, how molecules twist and bend in space, and so on. Only after gaining a clear understanding of stracture do we move on to reactions. But there seems to be one exception acid-base chemistry. 

This explains something we saw in the previous chapter when drawing chair conformations, we saw that up is always up regardless of which chair you draw. That is because up and down are issues of configuration, which does not change when the molecule twists into another conformation. 

An enzyme consists of a polypeptide chain with a particular spatial configuration specific to that sequence of amino acids. The molecule twists and turns, forming structural features that are catalytically active, these being known as active sites. There may be more than one active site per enzyme molecule. Sometimes an auxiliary catalyst, known as a coenzyme, is also needed. Apparently, only the relevant active site of the enzyme comes into contact with the substrate and is directly involved in the catalysed reaction. The active site consists of only a few amino acid residues. These are not necessarily adjacent to one another in the peptide chain but may be brought into proximity by the characteristic folding of the enzyme structure. The active site may also include the coenzyme. The remainder of the enzyme molecule fulfils the essential function of holding the components of the active site in their appropriate relative positions and orientation. 

Sometimes transformation of aromatic componnds into ion-radicals leads to stereochemically unusual forms. Octamethylnaphthalene is a nonplanar molecule twisted around the bond that is common for the two six-membered rings. The nitrosonium oxidation results in the formation of the cation-radical with the centrosymmetric flatten chairlike geometry (Rosokha and Kochi 2006). According to the authors, such a skeletal transformation improves the overall planarity of octamethylnaphthalene. For example, the mean deviation of the carbon atoms in the naphthalene core for the flatten chairlike cation-radical (0.007 nm) is less than half of the corresponding value for the neutral twisted parent (0.016 nm). Within this flatten carcass of the anion-radical, the spin density can be delocalized more effectively. 

In the first place, DNA molecules are quite large, sufficiently so to permit them to be seen individually in photographs taken with electron microscopes. The molecular weights vary considerably, but values of 1,000,000 to 4,000,000,000 are typical. X-ray diffraction indicates that DNA is made up of two long-chain molecules twisted around each other to form a double-stranded... 

More complicated molecules twist and bend to make sure that all the atoms take up positions that allow them maximum free space and non-interference with each other. The very complicated DNA molecules with hundreds of atoms in them twist in a characteristic spiral manner (Figure 2.10). The characteristic shape of each molecule influences its effect on how it behaves in our body and within cells. 

Interpretation of the WAXS patterns of native starch is often difficult because of the low crystallinity, small size, defects and the multiple orientations of the amylopectin crystallites (Waigh et al, 1997). Two main types of X-ray scattering patterns have been commonly observed (A and B). Potato starch has been shown to crystallize in a hexagonal unit cell in which the amylopectin molecules twist in a double helix (the B structure) (Lin Jana Shen, 1993). Between adjacent helices a channel is formed in which 36 water molecules can be located within the crystal unit cell. By means of heat treatment this structure can be transformed into a more compact monoclinic unit cell (the A structure) (Shogren, 1992). Amylose (the linear and minor component of starch) can be crystallized from solution in the A and B structures (Buledn etal, 1984), yielding X-ray diffraction patterns similar to those of amylopectin but with higher orientation. 

Molecules have to colUde to react. Most reactions are run in solution, so as a solution gets more concentrated, collisions increase and so does the rate. But there is an upper limit, often determined by solubility, on how concentrated the solution can get. A concentration landmark is that pure water is 55.5 mol/liter pure benzene, QH, is 11.1 mol/liter. Often chemists must run reactions at 1 mol/liter or less. In addition, not all collisions are effective because usually certain parts of the reactant molecules must hit to react otherwise they just bounce off each other. This orientation requirement is part of the AS portion of the barrier, AG = iStfi — TAS. If the reactive partners are part of the same molecule (intramolecular reactions), they collide as the molecule twists and turns much more frequently than if they were separate. In fact, intramolecular reactions can get effective concentrations of well over a milhon mol/liter ... 

Chemical catalysis. In the molecule shown, the R group can exchange between the two carbons shown. In the upper molecule, free rotation, shown by the arrows, means that the two carbons are rarely close together as the molecule twists around. In the lower molecule, the structure holds the two carbons in a fixed position favorable to the exchange reaction. 

Molecules twisting out from the centre to form heiical structures... 

Note that there are two forms of starch amylase and amylopectin. In amylase, the glucose residues are joined end to end by 1—>4 glycosidic bonds between a-anomers of glucose. This produces a linear, unbranched polysaccharide. Hydrogen bonds between amylose molecules twist the chains into large hehcal rodhke stractures that stack to form sheets. These sheets impede digestion by amylase. 

Deoxyribonucleic acid (DNA) stores the genetic information present in living cells. It allows the cell to make proteins according to a definite sequence of atoms. The DNA molecule consists of two long chains molecules twisted around each other and held together by hydrogen bonds This structure is called a double helix (Fig. 5.20). For this discovery, F. Crick, M. Wilkins and J. Watson gained the Nobel Prize for Medicine in 1962. 

A defect theory for blue phases was introduced by Meiboom, Sethna, Anderson, et al. [22-27]. In this theory, the liquid crystal is assumed to form double-twist cylinders where the liquid crystal molecules twist about any radius of the cylinder, as shown in Figure 13.6. The cylinder cannot, however, cover the whole 3-D space without topological defects. Instead of a single cylinder, the blue phases consist of packed double-twist cylinders. There are defects in the regions not occupied by the cylinders. 

The height of the barrier can be estimated from the spectroscopic value of the frequency of the torsional vibration of the molecule (twisting vibration of one end relative to the other end), and from the activation energy (Chapter 10) of the cis-trans isomerization reaction. 

The polarity of the alignment layer surface does not have much influence on alignment phenomena for nematic liquid crj talline materials. However, in the case of FLC materials, the polarity of the alignment layer surface shows an important effect. This is because the interaction between the spontaneous polarization and the polarity of the surface becomes important. This matter has been approached theoretically [27]. The stable director orientation in the SSFLC device was determined by minimizing the total free energy of the surfaces and the bulk elastic distortion as functions of cell thickness, cone angle, helical pitch, elastic constant and surface interaction coefficient. Because of the tendency of the direction of the spontaneous polarization to point either into or out of the substrate surface due to polar surface interaction, the director of the molecules twists from the top to the bottom surface. Therefore, the uniform state can only be stabilized in the case of a small surface interaction coefficient. 

Fig. 2.3. (a) Illustration of a vinyl molecule laid out in a polyethylene-type planar zig-zag. It is not drawn to scale. If the large substituted atoms numbered (1, 2, 3, etc.) exceed 254 pm in diameter, then this structure cannot occur since the substituted atoms would touch. In real vinyl polymers the substituted atoms (or groups of atoms) always exceed 254 pm in diameter and the molecule twists into a heli. as illustrated in (b). This is the 3/1 helix which occurs in polypropylene. The groups, 1,1, and 1" then lie in a line and similarly for 2, 2, and 2" and 3. 3, etc. Hydrogen atoms are not shown in (b). 

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