We call these different spatial orientations of the atoms of a molecule that result from rotations or twisting about single bonds conformations. We know this is not strictly true, since the carbon atoms all have a tetrahedral configuration. The actual shape of the extended chain is therefore zig-zag in nature. However, there is facile rotation about the carbon-carbon bonds, and the six-carbon chain easily coils up to assume a rather different shape.
Many conformations of hexane are possible and two are illustrated below. Extended Chain Coiled Chain. For an animation of conformational motion in hexane. Ethane Conformers.
The simple alkane ethane provides a good introduction to conformational analysis. Here there is only one carbon-carbon bond, and the rotational structures rotamers that it may assume fall between two extremes, staggered and eclipsed. In the following description of these conformers, several structural notations are used.
The first views the ethane molecule from the side, with the carbon-carbon bond being horizontal to the viewer. The hydrogens are then located in the surrounding space by wedge in front of the plane and hatched behind the plane bonds. If this structure is rotated so that carbon 1 is canted down and brought closer to the viewer, the "sawhorse" projection is presented.
Finally, if the viewer looks down the carbon-carbon bond with carbon 1 in front of 2, the Newman projection is seen. To see an eclipsed conformer of ethane orient itself as a Newman projection, and then interconvert with the staggered conformer and intermediate conformers. The most severe repulsions in the eclipsed conformation are depicted by the red arrows. There are six other less strong repulsions that are not shown. In the staggered conformation there are six equal bond repulsions, four of which are shown by the blue arrows, and these are all substantially less severe than the three strongest eclipsed repulsions.
Consequently, the potential energy associated with the various conformations of ethane varies with the dihedral angle of the bonds, as shown below. For a discussion of this feature. The above animation illustrates the relationship between ethane's potential energy and its dihedral angle.
Butane Conformers. The hydrocarbon butane has a larger and more complex set of conformations associated with its constitution than does ethane. Of particular interest and importance are the conformations produced by rotation about the central carbon-carbon bond. As in the case of ethane, the staggered conformers are more stable than the eclipsed conformers by 2. The four circles indicate the four unique groups attached to the central carbon atom, which is chiral.
Another type of optical isomer are diastereomers , which are non-mirror image optical isomers. Diastereomers have a different arrangement around one or more atoms while some of the atoms have the same arrangement.
As shown in the figure below, note that the orientation of groups on the first and third carbons are different but the second one remains the same so they are not the same molecule.
Epimers are a sub-group of diastereomers that differ at only one location. All epimers are diastereomers but not all diastereomers are epimers. Allison Soult , Ph. Department of Chemistry, University of Kentucky. Learning Outcomes Define isomer. Determine the isomeric relationship between a pair of molecules. Identify the chiral centers in a molecule.
Describe different types of isomers. Conformational Isomers Conformational isomers , also known as conformers, differ from one another by their rotation around a single bond. Structural Isomers A structural isomer , also known as a constitutional isomer, is one in which two or more organic compounds have the same molecular formulas but different structures. Stereoisomers Stereoisomers have the same connectivity in their atoms but a different arrangement in three-dimensional space. Geometric Isomers With a molecule such as 2-butene, a different type of isomerism called geometric isomerism can be observed.
Alkenes consist of six different varieties, some of which exhibit structural isomerism. A diagram of the different types of alkenes is shown in Figure 1.
In a vinylidine molecule the two hydrogens are attached to one carbon while the R-groups are on the other carbon. Vinylidene molecules are not common industrially and will not be discussed further.
As illustrated in Figure 1, cis isomers have their hydrogens on the same side of the double bond, while trans isomers have their hydrogens diagonally across from each other. Many food labels these days contain statements about how much cis and trans fats a product contains. As we will see below, cis and trans isomers have different IR spectra, which is why IR spectroscopy can be used to distinguish and quantitate these fats in samples.
When an alkene contains three R-groups and one hydrogen it is called a trisubstituted alkene. These have no structural isomers. In my opinion, the most industrially important alkenes are the vinyl, cis-, trans-, and trisubstituted varieties. As a result, our discussion below focuses on these types of molecules. We shall discover that we can distinguish all six types of alkenes from each other using IR spectroscopy. In a previous column 6 , we saw that the saturated carbon containing functional groups methyl CH 3 and methylene CH 2 both have C-H stretches below Another type of saturated carbon, the methine group, which consists of a carbon atom with three C-C bonds and one C-H bond, also has a C-H stretching peak below methine groups will be discussed in a future column on branched alkanes.
In general, saturated carbons have C-H stretching peaks below From our discussion of aromatic rings we found that these unsaturated molecules have C-H stretches above 2. Alkenes and alkynes , unsaturated molecules with carbon—carbon triple bonds, also have C-H stretches above So, in general, we can say that molecules with saturated carbons have C-H stretches below , while molecules with unsaturated carbons have C-H stretches above These ideas are summarized in Table I.
I have stated in previous columns that all of the peak ranges I present have exceptions, and that there are no absolute rules when it comes to interpreting IR spectra. Although the rules in Table I have known exceptions, they are few and Table I is an excellent tool to use when interpreting IR spectra.
Determining whether the C-H stretches in a spectrum are above or below is quick and easy, and it should be one of the first pieces of information you extract from a spectrum. Instead, the natural precursor is isopentenyl pyrophosphate 3-methylbutenyl pyrophosphate. Two isopentenyl pyrophosphate units combine enzymatically to form geranyl pyrophosphate , which is the precursor for the monoterpenes; reaction with a third isopentenyl pyrophosphate molecule produces farnesyl pyrophosphate , the precursor for the sesquiterpenes.
Isopentenyl pyrophosphate Geranyl pyrophosphate Farnesyl pyrophosphate. Myrcene is found in bay leaves and oil of bay. Geraniol 3D Download 3D Geraniol is found in roses with 2-phenylethanol , citronella oil, pomerosa oil, geraniums, and other flowers. Citral Geranial 3D Download 3D Citral , or geranial , is found in oil of lemon; it is also secreted by some insects to repel predators. It is used commercially in lemon-smelling perfumes and in the synthesis of Vitamin A.
The structure shown here is citral-a; there is also a citral-b isomer, in which the aldehyde and methyl group on the bottom double bond are in a trans relationship. The difference in orientation around the chiral carbon atoms gives these molecules a slightly different overall shape, resulting in slightly different odors when they interact with the olfactory receptors in the nasal passages.
Thujene 3D Download 3D Thujene is found in oil of thuja, sage, tansy, and wormwood. Thujone 3D Download 3D Thujone is found in oil of thuja, sage, tansy, and wormwood. Menthol 3D Download 3D Menthol is found in peppermint and other mint oils.
It is used in cough drops, shaving lotion, and mentholated tobacco. Menthone is the oxidized form of menthol, and has a similar taste and physiological effect. It is the active component of medicinal eucalyptus oils. Camphene 3D Download 3D Camphene is found in turpentine oil, rosemary, cypress oil, and oil of citronella. It is used medicinally as a counter-irritant a substance which produces a superficial inflammation to reduce deeper inflammation and an anti-itching agent.
It produces a cooling sensation, because it stimulates cold receptors see menthol. Its strong odor inspires deep breathing, but in large doses can lead to respiratory collapse. Caryophyllene 3D Download 3D Caryophyllene is found in oil of cloves. Vitamin A also known as retinol is a fat-soluble vitamin, which is produced by the breakdown of the carotenes especially b -carotene. It is found in liver, egg yolks, butter, and milk.
It is a precursor to retinal see below , the primary dye involved in vertebrate vision. It is also involved in cell growth and maintenance of healthy skin tissue, bones, and teeth. Download 3D Squalene is found in shark liver oil, and is also a major component of the lipids on the surface of human skin. Although it is not obvious from the way the structure above is drawn, squalene is a precursor for the biosynthesis of cholesterol. Through a complex series of enzymatically controlled reactions, squalene is converted into an intermediate called lanosterol, which undergoes a number of subsequent reactions to become cholesterol.
In addition to essential oils, terpenes and terpenoids are also found in naturally occurring dyes. Molecules which contain large numbers of carbon-carbon double bonds adjacent to each other a conjugated double bond system absorb light at lower frequencies than molecules with no double bonds or just a few double bonds; some of these compounds absorb light in the visible region of the electromagnetic spectrum, and produce colors which we can see.
Compare the structures of the molecules below with the ones in the section on the Chemistry of Vision. Download 3D Lycopene is a red pigment found in tomatoes, watermelon, guava, papaya, pink grapefruit, apricots, and rosehips. Unripe tomatoes are green in color because of their chlorophyll, but as they ripen, the chlorophyll breaks down, unmasking the red color of the lycopene. Lycopene is a good antioxidant, and is more readily absorbed from cooked tomatoes and tomato paste, especially if the foods contain fat.
This molecule, and the ones below, are structurally similar to that of carotene , and are referred to as carotenoids. Zeaxanthin Download 3D Zeaxanthin is a yellow pigment found in corn, egg yolk, orange juice, mangoes; also contributes to the yellowish color of animal fats.
Carotenoids containing hydroxyl groups are sometimes referred to as xanthophylls. Download 3D Astaxanthin is a pink pigment found in salmon, trout, red seabream and the carapaces of lobster and shrimp.
In live shellfish, the astaxanthin forms a complex with a protein which gives it a blackish color; when the shellfish are boiled, the protein breaks down, unmasking the pink astaxanthin. Canthaxanthin Download 3D Canthaxanthin is a pink pigment found in the feathers of American flamingos. It is obtained from shrimp in their diet; flamingos in captivity turn into plain white birds unless they are fed adequate amounts of shrimp. See entry above. The yellow color of butter and animal fats comes from carotene and related molecules.
Carotene is found along with chlorophyll in photosynthetic organisms; it protects cells by reacting with O 2 molecules. The yellow color of autumn leaves is due to the carotene, which is unmasked as the chlorophyll in the leaves breaks down.
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