These specific motifs or patterns are called secondary structure. Two of the most common secondary structural features include alpha helix and beta-pleated sheet (Figure 2.18). Within these structures, intramolecular interactions, especially hydrogen bonding between the backbone amine and carbonyl functional groups are critical to maintain 3-dimensional shape. Molecules belonging to this class of stereoisomers include biphenyls, allenes, spiranes, helicenes, cyclophanes, and molecular propellers. Unlike molecules possessing chiral centers , the above examples possess chiral axes and can also be viewed as helices, where chirality is due to molecular overcrowding.
The highly ordered arrangement of the pigments in LHCI and II illustrates one of several basic concepts used for light harvesting in nature. Here, a circular arrangement of chromophores results in rapid business analyst internship summer 2018 delocalization of the excitation energy which is then transferred between the various spectral species and funneled to P870. Here the redox active clusters are involved in the electron transfer .
Cahn–Ingold–Prelog priority rules, which can be reviewed by following the link and in Figure 2.5. All of the chiral amino acids, except for cysteine, are also in the S-conformation. Cysteine, contains the sulfur atom causing the R-group to have higher priority than the carboxylic acid functional group, leading to the R-conformation for the absolute stereochemistry. However, cysteine does rotate plain polarized light in the levorotary or left-handed direction. Thus, the R- and S-designations do not always correspond with the D- and L- conformation. No one really knows, but it is known that radiation can also exist in left and right handed forms.
Even in the gas phase, some compounds like acetic acid will exist mostly in the form of dimers or larger groups of molecules, whose configurations may be different from those of the isolated molecule. The proton transfer in the second step produces an OH2 group with a positive formal charge on the oxygen. Electron density moves out onto the oxygen with positive formal charge to produce a water molecule. The water molecule is lost and the C–O pi bond reforms, resulting in a molecule with no formal charge. Loss of small molecules such as water is common in condensation reactions. For example, 1-pentene is a five-carbon alkene with a double bond between carbon atoms 1 and 2, and 2-hexyne is a six-carbon alkyne with a triple bond between carbons 2 and 3.
The existence of these molecules is determined by concept known as chirality. The word “chiral” was derived from the Greek word for hand, because our hands are good example of chirality since they are non-superimposable mirror images of each other. Folding is a spontaneous process that is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, van der Waals forces, and it is opposed by conformational entropy.
Can a chiral center be something other than a tetrahedral carbon with four different substituents? The answer to this question is ‘yes’ – however, these alternative chiral centers are very rare in the context of biological organic chemistry, and outside the scope of our discussion here. The substance 2-propanol, unlike 2-butanol, is not a chiral molecule. Carbon #2 is bonded to two identical substituents , not 4 different groups, and so it is not a chiral center.