Stereochemical Terminology

The asymmetric carbon concept has played an important role in the development of organic chemistry. Indeed, it provided the focus for the revolutionary structural theory introduced by Jacobus van't Hoff and Joseph A. Le Bel. However, in recent years the nuance of distinguishing between the purely structural definition of an asymmetric carbon and the operational definition of a stereogenic element (e.g. a chiral center) has become increasingly important. For example, consider the tetrasubstituted adamantane molecule shown on the left. Although four asymmetric carbon atoms (colored light blue) are present in this compound, it exists in the form of only two stereoisomers (enantiomers) rather than the sixteen predicted by the 2n rule. There is, in fact, only one stereogenic center, shown by the red dot at the center of the molecule, and the configuration shown here is (R). The asymmetric carbon atoms are not stereogenic centers, because any two substituents on any of these bridgehead carbons cannot be exchanged without destroying the constitutional integrity of this rigid, highly bridged molecule.
The configurations of the asymmetric bridgehead carbon units in this structure are (R), (S), (R) and (R) respectively, for the Br, Cl, CO2H and CH3 substituents. Its enantiomer would. of course, have the opposite configurations.

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Oxygen Molecular Orbital Diagram

Simple covalent bond models involving electron pair sharing have proven to be a valuable tool for describing the structures of simple molecules, such as methane, water, fluorene and nitrogen. However, this model fails to explain the paramagnetic nature of oxygen. The electrons in most non-metallic compounds are paired (opposite spins) in bonding and non-bonding orbitals, resulting in a zero spin diamagnetic molecule. However, oxygen has a net electron spin of 1, indicating there are two unpaired electrons having the same spin (1/2). One of the triumphs of molecular orbital theory has been its success in rationalizing this fact, as shown in the following correlation diagram.
Each oxygen atom contributes eight electrons to the molecule. Half of these occupy sigma bonding and antibonding orbitals, formed by overlap of 1s and 2s orbitals, that do not contribute to the final bonding picture. Of the remaining eight electrons, six occupy 2σ and 2π bonding orbitals in accord with the aufbau principle. This leaves two electrons which must be placed in the two 2π* antibonding orbitals. By Hund's Rule, these electrons will each occupy one of these degenerate (same energy) orbitals, and have identical spins. The resulting antibonding character cancels one of the three bonding interactions, leaving a total bond order of 2.

Correlation diagrams for fluorine and nitrogen will be displayed above by clicking the appropriate button.

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Unusual Fatty Acids

A wide array of unusual fatty acids is found in seed oils and microorganisms such as bacteria. Among these are fatty acids containing cis-cyclopropane fatty acids (e.g. lactobacillic acid), omega-cycloalkyl fatty acids (e.g. 2-hydroxy-11-cycloheptylundecanoic acid) and cyclopropene fatty acids (e.g. malvalic and sterculic acid).

Lactobacillic acid has been found in a wide range of bacterial species, both gram-negative and gram-positive, ranging from strict anaerobes to aerobes. It is often accompanied by cis-9,10-methylene-hexadecanoic acid, and other homologues (C14 to C20 in chain-length). Some organisms contain cis-9,10-methylene-octadecanoic acid (dihydrosterculic acid), the cyclopropane analogue of oleic acid, together with homologous fatty acids (C16 or C20 in chain-length). In the bacterium Alicyclobacillus cycloheptanicus, 11-Cycloheptylundecanoic, the 2-hydroxy analogue, and 13-cycloheptyltridecanoic acids, together with three minor homologues, comprise nearly 80% of the fatty acids of this species. In Litchi chinensis seed oil, dihydrosterculic acid is the major carbocyclic fatty acid, whereas Sterculia foetida seed oil contains 65-78% cyclopropene lipids, principally sterculic acid.

Two novel polycyclopropane fatty acid derivatives, FR-900848 and U-106305, were isolated from Streptoverticillium fervens by Japanese microbiologists in the early 1990's. Structural formulas for these remarkable compounds are drawn on the right. FR-900848 shows potent, selective activity against filamentous fungi such as Aspergillus niger, Mucor rouxianus, Aureobasidium pullulans, and various Trichophyton sp. U-106305 is an inhibitor of cholesteryl ester transfer protein (CETP).
A few years after their discovery, these compounds were synthesized by British and American chemists. Biosynthetic studies indicate that the carbon backbone is derived from acetate via the polyketide pathway typical of fatty acid biosynthesis. The methylene carbon of each cyclopropane then originates from the methyl group of methionine. Thus, a polyunsaturated fatty acid, produced by the usual polyketide pathway, appears to be cyclopropanated through the sequential addition of methylene groups by a separate methyltransferase enzyme.

Ladderane Fatty Acids from Anammox bacteria

In the late 1980's microbiologists in the Netherlands discovered a remarkable red-colored bacterium that anaerobically oxidized ammonia to elemental nitrogen. Although a simple overall conversion can be written as:
NH4+ + NO2 N2 + 2H2O
The mechanism by which this is accomplished is complex, involving hydrazine and nitric oxide as intermediates. In order to contain hydrazine, a toxic and reactive compound used as a rocket fuel, the anammox reaction takes place inside an internal, membrane-bound compartment or organelle called an anammoxosome. The lipids that make up the anammoxosome's relatively dense and impermeable membrane are unique, consisting in large part of a ladder-like array of fused cyclobutane rings attached to glycerol or other alcohols by ester and ether bonds, as shown here.

The nitrogen cycle converts elemental nitrogen into more usable forms (such as ammonia and nitrate ions) and back again, maintaining a global balance, as shown on the right. First, nitrogen gas is converted directly to ammonia by nitrogen-fixing microbes. Plants and animals consume ammonia, and then release it when they die and decompose. The next step in the cycle is carried out by nitrifying bacteria and archaea, which transform ammonia to nitrites and nitrates. The cycle is completed as denitrifying microorganisms convert nitrates into nitrogen gas, replenishing the atmosphere. Anammox bacteria, such as Brocadia anammoxidans, Kuenenia stuttgartiensis and Scalindua sorokinii, take a short cut through the cycle, creating a path from ammonia and nitrite directly to nitrogen gas. Indeed, anammox bacteria in marine ecosystems actively contribute to biological nitrogen cycling, being responsible for at least 50% of total nitrogen production in the oceans.
A practical use of anammox bacteria lies in wastewater treatment. Sewage plants and industrial processes, such as fertilizer manufacture and petroleum refining, generate millions of liters of ammonia-rich waste, all of which needs to be broken down. Conventional methods use nitrifying bacteria to convert ammonia into nitrite and nitrate, and then denitrifying bacteria to yield nitrogen gas. The nitrifying microbes need oxygen, so machines are needed to aerate the sludge. Also, the denitrifying bacteria need an energy source, which they "burn" to produce carbon dioxide. This fuel is often supplied in the form of methanol. The process is costly, takes up a lot of space and produces a greenhouse gas. Anammox bacteria use ammonia as their fuel, hence there's no need for carbon fuels such as methanol. They do not need oxygen, so the process uses less electricity, and instead of producing carbon dioxide, anammox bacteria consume it, so the method is environmentally friendly. Altogether, this leads to a 90% reduction in operational costs and a 50% reduction in space, compared with conventional methods.

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These pages are provided to the IOCD to assist in capacity building in chemical education. 05/05/2013

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