ASSIGNMENT IN ANALYTICAL CHEMISTTY

Janine Stephanie H. Dela

BMLS I-A

ISOMERS
An isomer is a chemical species with the same number and types of atoms as another chemical
species but with distinct properties because the atoms are arranged into different chemical
structures. When atoms can assume different configurations, the phenomenon is termed
isomerism. There are several categories of isomers, including structural isomers, geometric
isomers, optical isomers, and stereoisomers. Isomerization can occur spontaneously or not,
depending on whether the bond energy of the configurations is comparable.
There are other possibilities as well for this same molecular formula - for example, you could
have a carbon-carbon double bond (an alkene) and an -OH group (an alcohol) in the same
molecule.

Another common example is illustrated by the molecular formula C3H6O2C3H6O2. Amongst

the several structural isomers of this are propanoic acid (a carboxylic acid) and methyl ethanoate
(an ester).

CHIRAL COMPOUND
A compound that contains an asymmetric center (chiral atom or chiral center) and thus can occur
in two nonsuperimposable enantiomers.
EXAMPLE
Tartaric acid
STEREOCENTER
In a molecule, a stereocenter is a particular instance of a stereogenic element that is
geometrically a point. A stereocenter or stereogenic center is any point in a molecule, though not
necessarily an atom, bearing different substituents, such that interchanging any two substituents
leads to a stereoisomer.

CHIRALITY CENTERS
Chiral centers are tetrahedral atoms (usually carbons) that have four different substituents.  Each
chiral center in a molecule will be either R or S.  As noted above, molecules with a single chiral
center are chiral.  Molecules with more than one chiral center are usually chiral.  The exception
are meso-compounds.
How to:
Step 1: Eliminate the atoms that cannot be chiral centers.  These include CH2 groups,
CH3 groups, oxygens, halogens, and any atom that is part of a double or triple bond.
For molecule 1, we can eliminate every atom as a possible chiral centers except for one (which is
highlighted with a red arrow).

Step 2: For the remaining atoms, list out the groups (substituents) attached to that atom.  If there
are four different groups, then it is a chiral center.  (Note that two substituents can appear to be
the same if you look only at the first attached atom but you have to keep going to check if they
are really the same or are different.)
The four groups attached to this carbon are: 
-Br, -H, -CH2, -C=.  These are all different.
Therefore, this is a chiral center.
The four groups attached to this carbon are: 
-H, -methyl, -ethyl, -propyl.  These are all different.  Therefore, this is a chiral center. 
(Note that if you stopped at just the first attached atom then it would look like that the two
CH2 groups were the same.  However, if you keep going down the chain, you find that they are
different.)
Groups attached to this carbon are:  -H, -NH2,
-CH2CH2CHOH, -CH2CH2CHOH.  The last two are the same.  Therefore, this is NOT a chiral
center.   (Note, that we had to go all the way to the other side of the molecule to convince
ourselves that they really are the same.)
Groups attached to this carbon are:  -H, -NH2,
-CH2CH2, -CH2CHOH.  There are four different groups attached to this carbon so this is a
chiral center.  (Note that we had to go around the ring to see if the two CH2's were the same or
different.  We can stop at the first point where we find that they are different.
ENANTIOMER
Enantiomer is one of two stereoisomers that are mirror images of each other that are non-
superposable (not identical), much as one's left and right hands are mirror images of each other
that cannot appear identical simply by reorientation
RACEMIC MIXTURE
In chemistry, a racemic mixture, or racemate, is one that has equal amounts of left- and right-
handed enantiomers of a chiral molecule. The first known racemic mixture was racemic acid,
which Louis Pasteur found to be a mixture of the two enantiomeric isomers of tartaric acid. 

DIASTEREOMERS
Diastereomers are a type of a stereoisomer. Diasteoreomers are defined as non-mirror image
non-identical stereoisomers. Hence, they occur when two or more stereoisomers of a compound
have different configurations at one or more of the equivalent stereocenters and are not mirror
images of each other.

MESO COMPOUND
Meso compounds are achiral compounds that has multiple chiral centers. It is superimposed on
its mirror image and is optically inactive despite its stereocenters.
FISCHER PROJECTION
A Fischer projection or Fischer projection formula is a convention used to depict a stereo
formula in two dimensions without destroying the stereochemical information, i.e., absolute
configuration, at chiral centers.

a Fischer projection may be rotated by 180 degrees without changing its meaning. A Fischer
projection may not be rotated by 90 degrees. Such a rotation typically changes the configuration
to the enantiomer.
A prochiral molecule is an achiral molecule containing at least one pair of enantiotropy
ligands. ... In a prochiral molecule, an atom bearing a pair of enantiotropy ligands is called a
prochiral center or prochirality center. If a prochirality center is a carbon atom, it can also be
called a prochiral carbon.
ROTATING FISCHER PROJECTIONS

Rules for Handling Fischer Projections

The Fischer projection of 2-butanol (Abb. 1)  shows one of several possible Fischer projections of
the same enantiomer. Only specific manipulations of Fischer projections are allowed, otherwise
not a projection of the same but of the opposite enantiomer would be obtained. The allowed
manipulations are expressed as follows:

RULE 1

A Fischer projection may be rotated 180° in the illustration plane. 90° and 270° rotations
are not allowed.
Explanation:
A 180° rotation of the Fischer projection means that substituents that initially pointed towards or
away from the viewer continue to point in these same directions. In addition, substituents that
initially lie directly opposite from each other are interchanged. The overall result is basically the
same as that of a 180° rotation of the whole molecule on an axis that is perpendicular to the
illustration plane and passes through the asymmetric carbon (run the animation). Therefore, the
new Fischer projection represents the same enantiomer.
In contrast, a 90° or 270° rotation of the Fischer projection is actually not equivalent to a 90° or
270° rotation of the whole molecule on the axis mentioned above. As a result of a 90° or 270°
rotation of the Fischer projection, the substituents that initially pointed towards or away from the
viewer now point in the opposite directions. In exchange, a 90° or 270° rotation of the whole
molecule on the formerly mentioned axis does not alter the orientation of the substituents in
relation to the illustration plane (run the animation of 90° and 270° rotation of the whole
molecule).
CYCLIC STEREOISOMERS
In the case of cyclic compounds, the free single bond rotation is restricted. It is therefore
important to note whether substituents are on the same side or on opposite sides of the ring.
Different stereoisomers arise from different substituent arrangements relative to the ring side,
because they are incapable of becoming superimposable through conformational changes. As a
result, cyclic compounds contain several specific characteristics.
DEFINITION
If the substituents are on the same side of the ring, they are called cis. If they are on opposite
sides, they are called trans.
1,2-Dimethylcyclopentane, for instance, consists of three stereoisomers:
NAMING CYCLIC STEREOISOMERS
Configurational Stereoisomers of Cycloalkanes

Stereoisomers are also observed

in certain disubstituted (and
higher substituted) cyclic
compounds. Unlike the relatively
flat molecules of alkenes,
substituted cycloalkanes must be
viewed as three-dimensional
configurations in order to
appreciate the spatial orientations
of the substituents. By agreement,
chemists use heavy, wedge-
shaped bonds to indicate a substituent located above the average plane of the ring (note that
cycloalkanes larger than three carbons are not planar), and a hatched line for bonds to atoms or
groups located below the ring. As in the case of the 2-butene stereoisomers, disubstituted
cycloalkane stereoisomers may be designated by nomenclature prefixes such as cis and trans.
The stereoisomeric 1,2-dibromocyclopentanes shown to the right are an example.

In general, if any two sp3 carbons in a ring have two different substituent groups (not counting
other ring atoms) stereoisomerism is possible. This is similar to the substitution pattern that gives
rise to stereoisomers in alkenes; indeed, one might view a double bond as a two-membered ring.
Four other examples of this kind of stereoisomerism in cyclic compounds are shown below.
If more than two ring carbons have different substituents (not counting other ring atoms) the
stereochemical notation distinguishing the various isomers becomes more complex.

Examples of the IUPAC Rules in Practice

When one substituent and one hydrogen atom are attached at each of more than two positions of
a monocycle, the steric relations of the substituents may be expressed by first identifying a
reference substituent (labeled r) followed by a hyphen and the substituent locator number and
name. The relative configuration of other substituents are then reported as cis (c) or trans (t) to
the reference substituent.

When two different substituents are attached at the same position of a monocycle, then the
lowest-numbered substituent named as a suffix is selected as reference group. If none of the
substituents is named as a suffix, then that substituent of the pair of substituents having the
lowest number, and which is preferred by the sequence rule, is chosen as the reference group.
The relationship of the sequence-rule-preferred substituent at geminally substituted positions,
relative to the reference group, is cited as c- or t-, as appropriate.

An alternative system which specifies the absolute configuration of substituted carbon atoms
may also be used. This system, known as the Cahn-Ingold-Prelog rules, uses and elaborates the
priority rules developed earlier.

PROCHIRAL CARBONS

When a tetrahedral carbon can be converted to a chiral center by changing only one of the
attached groups, it is referred to as a ‘prochiral' carbon. The two hydrogens on the prochiral
carbon can be described as 'prochiral hydrogens'.
Note that if, in a 'thought experiment', we were to change either one of the prochiral hydrogens
on a prochiral carbon center to a deuterium (the 2H isotope of hydrogen), the carbon would now
have four different substituents and thus would be a chiral center.

Prochirality is an important concept in biological chemistry, because enzymes can distinguish

between the two ‘identical’ groups bound to a prochiral carbon center due to the fact that they
occupy different regions in three-dimensional space. Consider the isomerization reaction below,
which is part of the biosynthesis of isoprenoid compounds. We do not need to understand the
reaction itself (it will be covered in chapter 14); all we need to recognize at this point is that the
isomerase enzyme is able to distinguish between the prochiral 'red' and the 'blue' hydrogens on
the isopentenyl diphosphate (IPP) substrate. In the course of the left to right reaction, IPP
specifically loses the 'red' hydrogen and keeps the 'blue' one.

Prochiral hydrogens can be unambiguously designated using a variation on the R/S system for

labeling chiral centers. For the sake of clarity, we'll look at a very simple molecule, ethanol, to
explain this system. To name the 'red' and 'blue' prochiral hydrogens on ethanol, we need to
engage in a thought experiment. If we, in our imagination, were to arbitrarily change red H to a
deuterium, the molecule would now be chiral and the chiral carbon would have
the R configuration (D has a higher priority than H).
For this reason, we can refer to the red H as the pro-R hydrogen of ethanol, and label it HR.
Conversely, if we change the blue H to D and leave red H as a hydrogen, the configuration of the
molecule would be S, so we can refer to blue H as the pro-S hydrogen of ethanol, and label it HS.

Looking back at our isoprenoid biosynthesis example, we see that it is specifically the pro-
R hydrogen that the isopentenyl diphosphate substrate loses in the reaction.

Prochiral hydrogens can be designated either enantiotopic or diastereotopic. If either H R or HS on
ethanol were replaced by a deuterium, the two resulting isomers would be enantiomers (because
there are no other stereocenters anywhere on the molecule).
Thus, these two hydrogens are referred to as enantiotopic.

In (R)-glyceraldehyde-3-phosphate ((R)-GAP), however, we see something different:

R)-GAP already has one chiral center. If either of the prochiral hydrogens HR or HS is replaced
by a deuterium, a second chiral center is created, and the two resulting molecules will be
diastereomers (one is S,R, one is R,R). Thus, in this molecule, HR and HS are referred to
as diastereotopic hydrogens.

Finally, hydrogens that can be designated neither enantiotopic nor diastereotopic are
called homotopic. If a homotopic hydrogen is replaced by deuterium, a chiral center
is not created. The three hydrogen atoms on the methyl (CH3) group of ethanol (and
on any methyl group) are homotopic.

An enzyme cannot distinguish among homotopic hydrogens.