CHAPTER 3: Question 2

 

2D explanations

a) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagrams below. The geometry around this carbon atom is tetrahedral, and the four substituents (H, CH3, CO2H, NH2) are all different.
To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rules states that the atoms directly attached to the stereocentre should be considered first, and the higher the atomic number of the atom, the higher its priority. These four atoms are shown in blue below, and are N, C, C, H. This immediately allows the NH2 group to be ranked 1, and the hydrogen atom to be ranked 4. However, the other two substituents both start with a carbon atom and so cannot be distinguished by CIP rule 1. Hence, CIP rule 2 which states that if the first atoms are identical then compare the next ranked atoms is invoked. In this case, it is also necessary to use CIP rule 3 to replace the C=O with two carbon oxygen single bonds. The next atoms to be compared are then the three hydrogen atoms and the three oxygen atoms shown in magenta below. These are compared one at a time, starting with the atoms of highest atomic number on each of the substituents. Thus one of the oxygen atoms of the acid group is compared with one of the hydrogen atoms of the methyl group, and since oxygen has a higher atomic number than hydrogen, the acid substituent is ranked 2 and the methyl group is ranked 3.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S.

To assign the absolute configuration using the L / D nomenclature, the structure must first be converted into a Fischer projection. To do this, the structure is redrawn with the main carbon chain vertical, and the carbon which would be numbered 1 in standard organic nomenclature at the top as shown in step 1 below. Next, the structure is rotated until all the horizontal bonds are pointing towards the viewer (ie drawn with wedges) as shown in step 2. Finally, the wedges and hashes are replaced by normal bonds, and bonds to hydrogen atoms are deleted. Since this process leaves the amino substituent on the left of the vertical line, this is the L-isomer of the compound.


b) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagrams below. The geometry around this carbon atom is tetrahedral, and the four substituents (H, CH3, CO2H, NH2) are all different. The ranking of the four substituents (1 = highest to 4 = lowest) is exactly as described in part a) and is shown on the diagram below.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S. Note that this is identical to part a), illustrating that just because the structures are drawn differently does not mean that they have different configurations.

To assign the absolute configuration using the L / D nomenclature, the structure must first be converted into a Fischer projection. To do this, the structure is redrawn with the main carbon chain vertical, and the carbon which would be numbered 1 in standard organic nomenclature at the top as shown in step 1 below. Next, the structure is rotated until all the horizontal bonds are pointing towards the viewer (ie drawn with wedges) as shown in step 2. Finally, the wedges and hashes are replaced by normal bonds, and bonds to hydrogen atoms are deleted. Since this process leaves the amino substituent on the left of the vertical line, this is again the L-isomer of the compound.


c) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagrams below. The ranking of the four substituents (1 = highest to 4 = lowest) is exactly as described in part a) and is shown on the diagram below.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S. Note that this is identical to parts a) and b), again illustrating that just because the structures are drawn differently does not mean that they have different configurations.

To assign the absolute configuration using the L / D nomenclature, the structure must first be converted into a Fischer projection. To do this, the structure is redrawn with the main carbon chain vertical, and the carbon which would be numbered 1 in standard organic nomenclature at the top as shown in step 1 below. Next, the structure is rotated until all the horizontal bonds are pointing towards the viewer (ie drawn with wedges) as shown in step 2. Finally, the wedges and hashes are replaced by normal bonds, and bonds to hydrogen atoms are deleted. Since this process leaves the amino substituent on the left of the vertical line, this is again the L-isomer of the compound.


d) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagrams below. The geometry around this carbon atom is tetrahedral, and the four substituents (H, F, Cl, Br) are all different.

To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rules states that the atoms directly attached to the stereocentre should be considered first, and the higher the atomic number of the atom, the higher its priority. These four atoms are shown in blue in the diagram above, and are Br, Cl, F, and H. Since these atoms all have different atomic numbers, the four substituents can be ranked as Br=1, Cl=2, F=3, H=4. Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S.


e) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagrams below. The geometry around this carbon atom is tetrahedral, and the four substituents (CH3, T, D, H) are all different.

To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rules states that the atoms directly attached to the stereocentre should be considered first, and the higher the atomic number of the atom, the higher its priority. These four atoms are shown in blue in the diagram above, and are carbon and three isotopes of hydrogen. Hence, the methyl group can be ranked 1. To rank the other three substituents, CIP rule 5 must be used and this states that the heavier the isotope, the higher the priority. Thus tritium (atomic mass 3) is ranked 2, deuterium (atomic mass 2) is ranked 3, and hydrogen (atomic mass 1) is ranked 4. Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S.


f) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagram below. The geometry around this carbon atom is tetrahedral, and the four substituents are all different.

To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rule does not help in this case, since the four atoms attached to the stereocentre are all carbon atoms in this case. Hence, CIP rule 3 is first used to convert each C=O into two C-O bonds as shown below, and then CIP rule 2 is used to compare the atoms attached to the atoms attached to the stereocentre. These twelve atoms are shown in blue in the diagram below. For each substituent, the atom of highest atomic number shown in blue is an oxygen atom, thus comparison of these four atoms does not help decide the ranking of the four substituents. However, for the two substituents at the top of the molecule as drawn above, there is a second oxygen atom shown in blue, whilst for the two substituents at the bottom of the molecule the remaining blue atoms are hydrogen atoms. Thus, the top two substituents will be ranked 1 and 2, and the bottom two substituents will be ranked 3 and 4. It is not possible to further determine the ranking at this stage, since for both top substituents the three blue atoms are oxygens, and for both bottom substituents the three blue atoms are an oxygen and two hydrogen atoms. Thus CIP rule 2 is used again, and the next atoms along each chain are considered, these being shown in magenta in the diagram below. Considering first the two substituents at the top of the molecule, these two atoms are carbon and hydrogen and since carbon has a higher atomic number than hydrogen, the methyl ester substituent will be ranked 1 and the acid 2. Similarly, for the two substituents at the bottom of the molecule, the atoms shown in magenta are again carbon and hydrogen, so the methyl ether is ranked 3 and the alcohol 4.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in a clockwise direction, the absolute configuration is R.


g) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagram below. The geometry around this carbon atom is tetrahedral, and the four substituents are all different.

To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rule does not help in this case, since the four atoms attached to the stereocentre are all sulfur atoms. It is best to consider the S=O bonds in their zwitterionic form (S+-O-) rather than as double bonds, though it is possible to get the same answer by treating them as double bonds and applying CIP rule 3 to convert each S=O into two S-O bonds. CIP rule 2 is used to compare the atoms attached to the atoms attached to the stereocentre. These atoms are shown in blue in the diagram below. For the SPh substituent, the blue atom of highest atomic number is a carbon atom, whilst for each of the other substituents, an oxygen atom is present. Thus the SPh group will have the lowest priority. The other three substituents all have two oxygen atoms, comparison of which does not help determine the ranking, however when the third of the blue atoms on the substituents are compared, these are an oxygen and two carbon atoms. Thus the sulfonic acid substituent will have the highest priority. To distinguish between the remaining two substituents, it is necessary to repeatedly use CIP rules 2 and 3 around the aromatic rings. No difference between the two substituents is apparent until the para-position is reached, when the atoms shown in magenta (S,C,C and C,C, H) must be compared. Since sulfur has a higher atomic number than carbon, the para-thiophenyl- phenylsulfone substituent has a higher priority than the phenylsulfone substituent and is ranked 2.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in a clockwise direction, the absolute configuration is R.


h) The first task is to identify the stereocentre(s). In this case, the only stereocentre is the carbon atom shown in red in the diagram below. The geometry around this carbon atom is tetrahedral, and the four substituents are all different, though two of the substituents differ only in the stereochemistry (E or Z) of the alkene as shown below. Refer to Chapter 2 if you are not clear on how the E / Z nomenclature is used to assign the stereochemistry of alkenes.

To assign the absolute configuration as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rule does not help in this case, since the four atoms attached to the stereocentre are all carbon atoms. Hence, CIP rule 3 is first used to convert each of the C=C into two C-C bonds as shown below. CIP rule 2 is then used to proceed along each chain until a difference between the substituents is found. In this case, the first atoms (C) are all identical, as are the atoms (C,C,H) attached to the first atoms in each chain. Only at the next position along each chain is any difference found, these atoms are shown in blue below. For each substituent, the blue atom of highest atomic number is a carbon atom, so the atoms of next highest atomic number are compared. For three of the substituents these are again carbon atoms, but for the fourth (the vinyl group), the second atom is a hydrogen atom. Thus the vinyl group is ranked fourth. Finally, the third blue atoms in the substituents are compared. This is a carbon atom in the case of the dimethylvinyl group, and a hydrogen atom in the case of the remaining substituents. Thus the dimethylvinyl group is ranked 1. The remaining two substituents (the E and Z methylvinyl groups) cannot be distinguished by CIP rule 2 since at each position, they contain identical atoms. Therefore, CIP rule 6 must be used and since this states that Z has precedence over E, the four substituents can be ranked as shown below.

Finally, the molecule is viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S.


i) The first task is to identify the stereocentre(s). In this case, there are five stereocentres shown in red in the diagram below. Each of these is considered in turn, starting at the left end of the molecule.

To assign the absolute configuration at stereocentre 1 as R or S, the four groups attached to the stereocentre must be ranked in order of priority according to the CIP rules. The first of the CIP rules allows the hydrogen atom to be ranked 4, but since the other three substituents all start with a carbon atom (shown in blue in the diagram below), CIP rules 2 and 3 must be used. Once CIP rule 3 has been applied to the phenyl group, the next atoms along each of the three remaining substituents can be compared. These atoms are shown in magenta and are: H,H,H for the methyl group, C,C,C for the phenyl group and C,C,H for the main carbon chain. Comparing the atoms of highest atomic number in each substituent, the methyl group can then be ranked 3. No difference is found between the remaining two substituents, until the third magenta atoms are compared (C for the phenyl group and H for the main chain). Thus the phenyl group is ranked 1 and the main chain 2. The molecule is then viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in an anti-clockwise direction, the absolute configuration is S.

Consider next stereocentre 2. The first of the CIP rules allows the hydrogen atom to be ranked 4, but since the other three substituents all start with a carbon atom (shown in blue in the diagram below), CIP rule 2 must be used. The next atoms in each of the three remaining substituents are O,H,H (for the CH2OH group), C,C,O (for the right side of the molecule) and C,C,H (for the left side of the molecule), these are shown in magenta below. Comparison of the atom of highest atomic number in each substituent (O,O,C respectively) allows the left side of the molecule to be ranked 3. Comparison of the atoms of second highest atomic number in the remaining two substituents (H and C respectively) allows the right side of the molecule to be ranked 1 and the CH2OH group to be ranked 2. The molecule is then viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in a clockwise direction, the absolute configuration is R.

Consider next stereocentre 3. The first of the CIP rules allows the oxygen atom to be ranked 1, but since the other three substituents all start with a carbon atom (shown in blue in the diagram below), CIP rule 2 must be used. The next atoms in each of the three remaining substituents are H,H,H (for the CH3 group), C,C,H (for the right side of the molecule) and C,C,H (for the left side of the molecule), these are shown in magenta below. Comparison of the atom of highest atomic number in each substituent (H,C,C respectively) allows the methyl group to be ranked 3. To distinguish between the remaining two substituents however, it is necessary to look at the next atoms along the chains, and for both substituents, a decision needs to be made as to which of the magenta carbon atoms to examine further. The rule which is used in this situation is that the magenta atom with the atom of highest atomic number attached to it is used. This is the CH2OH group on the left side of the molecule (since there is an oxygen atom in this substituent) and the CH(NH2)CO2H group on the right side of the molecule (since there is a nitrogen atom in this substituent). The set of atoms to be compared next are then shown in green below, and these are O,H,H and N,C,H. Comparison of the atoms of highest atomic number (O and N) allows the left side of the molecule to be ranked 2 and the right side to be ranked 3. The molecule is then viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three
substituents decreases in an anti-clockwise direction, the absolute configuration is S.

Consider next stereocentre 4. The first of the CIP rules allows the hydrogen atom to be ranked 4, but since the other three substituents all start with a carbon atom (shown in blue in the diagram below), CIP rule 2 must be used. The next atoms in each of the three remaining substituents are H,H,H (for the CH3 group), N,C,H (for the right side of the molecule) and O,C,H (for the left side of the molecule), these are shown in magenta below. Comparison of the atom of highest atomic number in each substituent (H,N,O respectively) allows the methyl group to be ranked 3, the right side of the molecule to be ranked 2, and the left side of the molecule to be ranked 1. The molecule is then viewed with the substituent ranked 4 at the rear as shown below, and since the
priority of the other three substituents decreases in a clockwise direction, the absolute configuration is R.

Consider next stereocentre 5. The first of the CIP rules allows the hydrogen atom to be ranked 4, and the nitrogen atom of the amino group to be ranked 1, but since the other two substituents both start with a carbon atom (shown in blue in the diagram below), CIP rules 2 and 3 must be used. CIP rule 3 is first used to convert the C=O into two C-O bonds, then the next atoms in the two substituents are O,O,O (for the acid group) and C,C,H (for the left side of the molecule), these are shown in magenta below. Comparing the atoms of highest atomic number then allows the acid group to be ranked 2 and the left side of the molecule to be ranked 3. The molecule is then viewed with the substituent ranked 4 at the rear as shown below, and since the priority of the other three substituents decreases in a clockwise direction, the absolute configuration is R.

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