Experiment 6. Stereochemistry

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1 Experiment 6. Stereochemistry Introduction Organic molecules with the same molecular formula but different arrangements of atoms are called isomers. Structural isomers are different because the location of a functional group (Figure 5.1c), a modification of the carbon skeleton (Figure 5.1b), or even a different functional group (Figure 5.1d) are easily seen when the various structures are drawn. Other molecular variants, stereoisomers, possess more subtle structural changes based on the spatial orientation of the component atoms. Stereochemistry is the study of the effect of molecular shape on properties. The tetrahedral shape of a singly bonded carbon atom creates molecules that are three-dimensional. When four different atoms or groups are attached to the tetrahedral carbon atom (chiral atom) (Figure 5.2), the resultant molecule can exist in two isomeric forms that are nonsuperimposable mirror images of each other, or enantiomers. Structural Conventions Although molecular model kits enable us to construct accurate and/or representative models of actual molecules, we still use flat drawings to depict structures. The drawings may give no indication as to a molecules stereochemistry or, conversely, may convey which of several isomers is actually being shown. In the latter case, one of several conventions may be used to designate specific configurational forms. These include the following: 1. Wedge Notation (Figure 5.3a): This is a more modern version of Fischer projections. Solid lines are in the plane, dotted lines are behind the plane, and the wedge comes out of the plane. 2. Fischer Projections (Figure 5.3b): In this convention the structure is drawn with vertical and horizontal lines to show the carbon skeleton. The convention specifies that all horizontal lines come out of the plane of the paper toward the viewer. Vertical lines are assumed to be oriented behind the plane.

2 3. Newman Projections (Figure 5.3c): These usually show two atoms (as in a substituted ethane), one sited directly behind the other. The three bonds that converge on the center of the circular atom are attached to the forward carbon atom, while the lines that end at the circles circumference are bonded to the rearmost atom. This type of structural representation is particularly useful for showing the different conformations that a molecule can assume. 4. Sawhorse Projections (Figure 5.3d): These structures can be used instead of Newman Projections. They are perspective drawings, which happen to resemble wooden sawhorses, and because of their pseudo three-dimensionality they are the easiest to relate to actual structures. They are useful for illustrating the stereochemical course of a chemical reaction. Enantiomers These isomers exhibit identical physical and chemical properties, with two exceptions. Separately, these isomers have the ability to rotate plane-polarized light in equal but opposite directions as measured in an instrument called a polarimeter: Their chemical reactivity towards another optically active molecule may also be different. The right-rotating isomer is called dextro-rotatory and is assigned a (+) or (d) prefix. The left- rotating isomer is levo, (-) or (1). When corrected for concentration and instrumental parameters, the degrees rotated in the polarimeter is defined as the specific rotation. Modern stereochemical conventions allow the assignment of configurations to a threedimensional model or any of the two-dimensional representations (Wedge, Fischer, etc.) that are used to depict these isomers (Figures 5.4a and 5.4b). Additional rules make the assignment a completely unambiguous process. Any of the structure conventions discussed above can be used to depict stereoisomers. The large (L), medium (M), and small (S) refer to the atomic number of the atoms attached to the chiral atom as defined by the set of rules known as the Cahn- Ingold-Prelog convention. The handle

3 (H) usually refers to hydrogen, the smallest group. If the other groups are arranged L, M, and S in a clockwise direction, the configuration is an R. If the sequence is L, M, and S in a counter-clockwise manner, the molecule is termed S. When using the Fischer Notation, the handle must occupy either of the vertical positions. Diastereomers If two or more molecules have the same empirical formula and have all of their atoms attached in the same sequence but have a different spatial orientation, then they are called stereoisomers. If two of the isomers are nonsuperimposable mirror images of each other they are optical isomers, or enantiomers. However, if the molecules are not mirror images of each other but meet the requirements of stereoisomers then they are called diastereomers. There are two basic types of diastereomers. 1. The first type arise from restricted rotation around either a double bond or from groups attached to ring atoms. These isomers are described as cis/trans or by the sequence rule convention as E/Z (entgegen, zusammen) (Figure 5.5a-5.5c). The Z-prefix indicates that the two groups of highest priority are attached to the C=C on the same side of the double bond. If on opposite sides, the prefix (E) is used. 2. The second type, and the most difficult to recognize and describe, is created when a molecule has more than one chiral center. For example, if a molecule has two chiral atoms, four isomers can be identified by their atom chiralities (e.g., 1R,2R (Figure 5.6a); 1S,2S (Figure 5.6b); 1R,2S (Figure 5.6c); and 1S,2R (Figure 5.6d). The first and second compounds are enantiomers (mirror images), while the first and third or first and fourth are diastereomers. One important class of diastereomers has its origin in molecules that have an internal plane of symmetry. In the case of a molecule that has two chiral centers, each of which has the same attached groups, the isomers designated 1R,2S and 1S,2R (Figure 5.7a and 5 7b) are in fact identical, and this molecule is optically inactive. This is because the upper half of the molecule is the mirror image of the lower half. The molecule having a plane of symmetry is optically inactive. Molecules of this type are defined as meso. The remaining mirror image pair [1R,2R (Figure 5.7c) and 1S,2S (Figure 5.7d)], when found in equal amounts, are collectively known as a racemic pair.

4 Diastereomers possess different physical properties (mp s, bp s, solubilities, etc.) and although they generally undergo the same chemical reactions, they may do so at very different rates. Since enantiomers possess identical properties (e.g., solubility), they cannot be separated by the methods usually employed for other chemical mixtures. Although newer chromatographic methods have been developed, the classic resolution technique involves the conversion of the racemic pair to diastereomers. This is accomplished by reacting the racemic mixture with some optically active reagent. Thus, the reactions of an R and S pair with an S compound would produce a pair of diastereomers, R,S and S,S (Figure 5.8). When separated, the diastereomers are converted back into their individual optically pure forms. The Wrong Isomer A Modern Tragedy Virtually all of the naturally occurring compounds that possess chiral centers are isolated in only one enantiomeric form (e.g., quinine, morphine, emetine, reserpine, et. al.). Frequently when these compounds were synthesized, it was found that only one of the enantiomers (or diastereomers) possessed the desired pharmacologic activity. The other isomers had either no activity, diminished activity, or a different activity. Synthetic drugs that exist in isomeric forms also exhibit great differences in their physiological actions. Currently, many drugs are sold as racemic mixtures even though only one of the enantiomers produces the desired effect. Chlorphenerimine maleate (Chlortrimeton), an antihistamine, is one such example. In this case the dextrorotary (+) isomer is the most active. The FDA is now considering a regulation that would require all drugs to be sold as the pure, active enantiomeric form. In the 1960 s, a hypnotic and sedative drug, Thalidomide, was prescribed in Europe and used by many pregnant women to relieve morning sickness. Even though the drug had been tested for toxicity and found to be safe, no one knew that it was a potent teratogen. Teratogens induce the development of abnormal fetuses, and in this case many babies with missing or abnormal limbs were born. Since the drug had not been approved in this country,

5 women here were spared this tragic experience. It has since been shown that Thalidomide, which exists in enantiomeric forms, is safe and effective as the R-isomer. It was the S-form that was both teratogenic and antiabortive. Thus, the wrong isomer caused not only malformed fetuses but prevented them from being spontaneously aborted. Interestingly, Thalidomide has also been shown to be useful for treating leprosy and very recent research indicates that it may be useful against the AIDS virus. About the experiment STEREOISOMERS: ENANTIOMERS AND DIASTEREOMERS Organic compounds can exhibit a variety of isomeric forms, many of which are easily distinguished by simple inspection of their structural representations. As the differences become more subtle, normal drawings become inadequate and the best method for seeing isomer differences involves the construction of three- dimensional models of the compounds. Stereoisomers fall into this category. A drawing, no matter how skillful, can never truly impart the shape of a molecule. In addition, models permit one to change the viewing perspective by simply rotating the model in space. Once it has been visualized in three dimensions, a student can learn to recognize isomer types as depicted by flat representations. This is facilitated by several drawing conventions that have been developed for illustrating these isomer types. These conventions are designated Fischer projections, Sawhorse structures, Newman projections, and Wedge notation. This experiment is designed to give the student experience in constructing a variety of stereoisomer models and teach him or her how to relate these models to the twodimensional drawings used by the various conventions mentioned previously. This includes mastering the technique of assigning the Absolute configurations (the three-dimensional arrangement of atoms about a chiral center) to the various chiral atoms depicted in both the models and the structural drawings. A clear understanding of the differences between enantiomers and diastereomers should also be developed. In addition, the concept of conformational isomers as nonisolable forms of the same molecule will be illustrated for substituted cyclohexanes. The student should be acquainted with stereochemical terminology prior to carrying out this experiment. This experiment may be conducted during a recitation period and need not necessarily be conducted during the laboratory.

6 Materials Part A Question 1 Molecular Model Kit (any kind ) Acyclic Molecules Enantiomers Construct a model of 1,2-dibromoethane. Use it as a guide to draw an equivalent Fischer projection. Hold the model so that the two carbon atoms are vertical and rotate the atoms around the upper carbon atom until two new atoms are facing you. Draw this Fischer Projection. Note: Make sure both sets of horizontal atoms are coming out of the plane toward you. Are the two Fischer projections equivalent? Question: Do the descriptions opposite" or side-by-side correspond to the actual molecular structure? Question 2 Construct an asymmetric methane and its mirror image. Question: Are your models superimposable? Question 3 Using each model in number 2 in turn, draw its equivalent Fischer Projection. Assign the absolute configuration (R or S) to the drawings. Check your assignments! Note: Make certain that the horizontal and vertical bonds are oriented correctly! Question 4 Take either of the two models and switch any two groups on the central carbon atom. Compare the modified molecule with the unchanged model. Assign the configuration of the changed molecule. Note: This involves a partial disassembly of your model! Question: Are the two models still mirror images?

7 Question 5 Start with a pair of mirror images and, using one model, switch any pair of groups. Now switch any pair of groups in that same model again! Compare this double switched model with the other unmodified molecule. Assign the configurations of the changed molecule. Note: This double switch is equivalent to that used for converting drawn structures! Part B Question 6 Acyclic Molecules Diastereomers Construct a model of 2-bromo- 3-chlorobutane. Make a mirror-image model. Draw Fischer Projections for both models and assign the absolute configuration to all of the asymmetric atoms. Note: For each drawn structure write the configuration beside the atom (e.g., 2S). Question 7 Make duplicates of the above models. With the carbon atoms in a vertical position, do a single switch on carbon number 2 of one duplicate. Do a single atom switch on the second carbon atom on the other duplicate. Draw Fischer Projections and assign configurations. Note: Arrange the model such that the bromine atom is above the chlorine atom. Question: Are any of the molecules the same?

8 Question 8 Using the models, attempt to find nonsuperimposable mirror-image isomers. For each pair that you find, compare your configurational assignments. Use Fischer projections for comparison. Questions: How many enantiomeric (racemic) pairs did you find? What relationship is there between mirror-image pairs and their R,S-assignments? Question 9 Compare the models, structures, and assignments of any two isomers that are not enantiomers. Question: What kinds of isomers are these? Part C Question 10 Acyclic Molecules Meso isomers Construct a model of 2,3- dibromobutane. As before, build its mirror image and duplicate each model. On the duplicates, switch the configurations around the second carbon atom. Note: Make sure the inner (2,3) carbon atoms are oriented vertically! Question 11 Draw Fischer Projections of the four models and assign configurations to each asymmetric atom. Separate into racemic pairs where possible. Check each model for a plane of symmetry. Question: Are all four molecules unique? What do you call an isomer of this type? What new features does it possess? Part D Question 12 Cyclic Molecules Ring Strain Construct models of 3-, 4-, 5-, and 6-membered rings. Use the long, flexible bonds between the ring atoms. Question: Which rings require the most flexing of the bonds to construct? Which requires the least? Question: Which rings are essentially planar? Which are not?

9 Part E Question 13 Cyclic Molecules Cyclopentanes Assemble cis-l,2-dibromocy-clopentane and its mirror image. Assign the configurations to the chiral atoms. Try to draw Fischer Projections for these molecules. Question: Are the structures superimposable? What kind of isomers are these? Question 14 Note: Have the instructor show you how to draw Fischer Projections for rings! Change the above model to the 1,3-isomer and compare the mirror images Assign configurations. Question: Describe the isomer type. Question 15 Construct trans-l,2-dibromocyclopentane and its mirror image. Assign configurations and draw Fischer Projections Question: Are the structures superimposable? What kind of isomers are these? Question 16 Change the structures from the 1,2 to the 1,3 isomer and compare the mirror images. Question: Describe the isomer type. Part F Question 17 Cyclic Molecules Cyclohexanes Assemble a model of cyclohexane in the chair form. Place marker spheres at each equatorial position of the ring. Note: The instructor will show you chair and boat forms and define axial and equatorial.

10 Question 18 Practice flipping the ring to convert one chair form into the other. Question: In what position do the marker atoms end up? Question 19 Flip the ring to the boat conformation. Identify the flag-pole atoms. Question: How many flag-pole atoms are there? Question 20 Convert the ring model to cis- 1,2-dibromocyclohexane and assemble its mirror image. Assign configurations to the chiral atoms. Question: Are the mirror images superimposable?: Question 21 Flip one of the two-ring models to the other chair form. Check again for superimposability. Question: Are the mirror images superimposable? Is the term meso applicable here?

11 Question 22 Convert your rings to the trans isomeric pair. Assign configurations. Question: Are the images superimposable? Question 23 Flip one ring to the other chair form and compare the two models. Question: Are the isomers the same? Question 24 Question 25 Construct cis-l-bromo-2- chlorocyclohexane and its mirror image. Follow the procedures as in steps Question: Are the isomers unique? Follow the same procedure (steps 20-23) for trans-1- bromo-2-chlorocyclohexane. Question 26 Follow the same procedures for the following: a) cis-1,3-dibromocyclo- hexane b) trans-l,3-dibromocyclo- hexane c) cis-l,4-dibromocyclo- hexane d) trans-l,4-dibromocyclo- hexane Note: You don t have to do the experiment if you can properly predict the outcome. Question 27 Question 28 Questions Disubstituted cyclohexanes (1,2; 1,3; and 1,4) can be described as either being racemic (a d,l pair), meso, or achiral. Construct a chart for the dibromo isomers. It should have 1,2; 1,3; and 1,4 columns and cis and trans rows. For each position, the student should indicate whether the isomer described is racemic, meso, or achiral. Make a chart similar to the one described above for 1-bromo- 2-chlorocyclopentane. Please answer the following questions: The questions below are restated versions of those asked in the notes portion of the experiment. 1. In step 1, are the two Fischer structures of 1,2-dibromoethane the same or different? 2. Do the designations side-by-side and opposite have any meaning when drawing Fischer Projections? 3. What is meant by an asymmetric methane? Are mirror-image, asymmetric methanes superimposable? 4. What atom will usually be designated the handle when assigning absolute configuration? 5. If you single-switch a pair of atoms on a molecule of a specific configuration, what configuration do you get? 6. What happens to the configuration if you do a double switch? Does the sequence of atom swapping, or the actual atoms switched, alter the result? 7. In step 6, what are the configurational assignments for the pair of isomers? 8. Are any of the structures in step 7 identical?

12 9. In step 8, how many racemic (mirror image) pairs do you find? 10. For a racemic pair, what are the configurational assignments? 11. What do you call stereoisomers that are not enantiomers? 12. How many unique isomers are found in step 11? What new type of isomer do you observe? 13. In step 12, which ring is most strained? Which is least strained (most stable)? 14. Which ring deviates the most from planar conformation? Which other ring can be deformed from a planar conformation? 15. How many isomers can exist for cis-l,2-dibromocyclopentane? What type of isomerism does this compound exhibit (step 13)? What are the configurations around the chiral atoms. 16. For cis-l,3-dibromocyclopentane (step 14), answer question For trans-l,2-dibromocyclopentane (step 15), answer question Answer question 15 for trans-l,3-dibromocyclopentane (step 16). 19. When the ring is flipped from one chair to the other in step 18, in what position do the original equatorial atoms end up? 20. In the boat form (step 19), how many flagpole atoms are there? 21. In step 20, how many cis-l,2-dibromocyclohexanes do you observe? 22. After you flip the other conformation (step 21), are the isomers different? Have you broken any bonds during flipping? 23. How many trans-l,2-dibromocyclohexanes are there? Does altering the conformation (flipping) change your answer (steps 22 and 23)? Suggested Readings Atkins, R.C. and F.A. Carey. Organic Chemistry A Brief Course, 1st ed. New York: McGraw-Hill, 1990: Boxer, R. Essentials of Organic Chemistry, 1st ed. Dubuque, Iowa: W. C. Brown, 1997: Fessenden, R.J. and J.S. Fessenden. Fundamentals of Organic Chemistry, 1st ed. New York: Harper and Row, 1990: Hart, H. Organic Chemistry A Short Course, 8th ed. Boston: Houghton Mifflin, 1991: McMurry, J. Fundamentals of Organic Chemistry, 3rd ed. Pacific Grove, California: Brooks/Cole, 1994:

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