Lewis Dot structures

There are three rules for forming Lewis dot structures:

1) Count the total number of valence electrons (N) needed to account for the
atoms (based on the column of the atom in the periodic table) and charge (add
one electrons for each negative charge; subtract one electron for each
positive charge).
2) Draw the framework with single bonds. Some knowledge of the way the
atoms are connected may be required.
3) Using lone pairs, complete octets around the noncentral atoms.
4) Count the number of electrons depicted (two for each bond and two for each
lone pair). If this number is less than N, then add electrons to the central atom
until the total number of electrons depicted is N.
5) If the octet rule is not satisfied for the central atom and lone-pair electrons are
nearby, use those electrons to make double or triple bonds to the central atom.
6) Check each atom to see if it has a formal charge. (Singly bonded oxygen will
require a negative charge, for example.)

All atoms have to follow the octet rule or duet rule for hydrogen

Exceptions: Sometimes atoms break the octet rule. Molecules with such atoms include
molecules with an odd number of electrons, molecules with an atom having less than
an octet, and molecules with an atom having more than an octet!!

Compounds containing boron (B) and beryllium (BE) may contain less than an
octet!!

Exceptions

Molecules containing more than an octet must contain an atom from the third
period or greater in the periodic table because only these atoms have vacant D
orbitals available for hybridization!!!
The column # of the periodic table tells you the number of electrons in the outer ring of
the atoms in that column. Outer electrons are called "valence electrons".

(Halogens, other than fluorine, are capable of making more than one bond)

It is also useful to know the formal charge of an atom.

Formal Charge (for a single atom) is given by:

(valence electrons) - (# nonbonding e + .5 x # bonding electrons)

valence electrons for an isolated atom: 1 for H, 4 for C, 5 for N, 6 for O, 7 for F, etc. (this
is the number of electrons in the highest energy shell for the isolated atoms)

Total charge of molecule = sum of all formal charges

For instance, in the cyanide ion carbon has a pair of nonbonding electrons and one
electron from each bond in the triple bond for a total of five bond.

A neutral carbon atom has only four electrons, so the formal charge on the carbon in the
cyanide is minus one. It is important to know that, although the sum of the formal
charges for each atom in a molecule or ion represents the total charge on that molecule or
ion, the formal charge on a given atom doesn’t represent a real charge on that
atom!! The actual charge distribution requires consideration of electronegativity
differences among all the atoms in the molecule!!

Site: http://www.stolaf.edu/depts/chemistry/courses/toolkits/123/js/lewis/

(This site def helped me in understanding Lewis Dot structures)

Other Structures

Fischer projection

The wedge and dash representations of stereochemistry can often become cumbersome,
especially for large molecules which contain a number of stereocenters. The Fischer
Projection represents every stereocenter as a cross. The horizontal line represents
bonds extending out of the plane of the page, whereas the vertical line represents
bonds extending into the plane of the page!!
 

Figure 1.1: Drawing Fischer Projections

Manipulations of Fischer Projections

 
When working with Fischer Projections, keep in mind the following rules:

1) Because the "up" and "down" aspects of the bonds don't change, a
Fischer projection may be rotated by 180 degrees without changing its
meaning.

2) A Fischer projection may not be rotated by 90 degrees. Such a rotation

typically changes the configuration to the enantiomer.

3) To find the enantiomer of a molecule drawn as a Fischer projection,

simply exchange the right and left horizontal bonds.

4) To determine whether the molecule in Fischer projection is a meso compound,

draw a horizontal line through the center of the molecule and determine
whether the molecule is symmetric about that line.
 
 Figure 1: Operations on Fischer projections

For the fischer projections the vertical lines are assumed to be oriented into the page.
The horizontal lines are assumed to be oriented out of the page.

Note: For Fischer projections you can swap an 2 atoms 2 times and still have
the same compound

Newman projections

These projections are drawn by looking directly along a particular bond in the system
(here a C-C bond) and arranging the substituents symmetrically around the atoms at each
end of that bond. The protocol requires that the atoms within the central bond are defined
as shown below:
In order to draw a Newman projection from a wedge-dash diagram, it is useful to imagine
putting your "eye" in line with the central bond in order to look along it. Let's work
through an example, consider drawing a Newman projection by looking at the following
wedge-dash diagram from the left hand side.

1) First draw the dot and circle to represent the front and back C respectively
2) Since the front carbon atom has an H atom in the plane of the page pointing
up we can add that first
3) The back carbon atom has an H atom in the plane of the page pointing down
4) Now add the other bonds to each C so that it is symmetrical
5) The groups / bonds (blue) that were forward of the plane of the page in the
6) original wedge-dash diagram are now to our right
7) Those behind (green) the plane are now to our left

8) Try the same thing, but looking from the right to generate the other Newman
projection

Note: The sum of atomic radii is a reasonable approximation of bond length!

Index of Hydrogen Deficiency

The index of hydrogen deficiency indicates the number of pairs of hydrogens a
compound requires to become a saturated alkane.

Note: A saturated alkane contains 2n + 2 hydrogens (where n is the

number of carbons).

By calculating the index of hydrogen deficiency (IHD), we can tell from the molecular
formula whether and how many multiple bonds and rings are involved. This will help cut
down the possibilities one has to consider in trying to come up with all the isomers of a
given formula. Refer to your textbook for a more complete discussion of this. Here is a
summary of how the index of hydrogen deficiency (IHD) works.
 A double bond and ring each counts as one IHD.
A triple bond counts as two IHD.

Hydrocarbons (CxHy):

IHD = [(2x + 2) – y]/2

(where x and y stand for # of C and H respectively.)

Example 1: IHD for C2H4 is [(2(2) + 2) – 4]/2 = 1

This means it can have either one double bond or one ring. It cannot have a triple bond.
Since you cannot form a ring with only two C’s, it must have a double bond.

Example 2: IHD for C4H6 is [(2(4) + 2) – 6]/2= 2

This means it can have either one double bond and a ring, or two double bonds such as
CH2=CH−CH=CH2 or CH2=C=CH−CH3 or two rings, or one triple bond, such as
CH3C≡CCH3.

Compounds Containing Elements Other than C and H:

- O and S atoms do not affect the IHD.

- Halogens (F, Cl, Br, I) are treated like H atoms. (CH2Cl2 has the same
IHD as CH4.)

- For each N, add one to the number of C and one to the number H. (CH5N
is treated as C2H6. CH4N2O is treated as C3H6 by adding 2 to # of C and 2
to # of H.)

Note: Of course, the index of hydrogen deficiency for any saturated alkane
will be zero.

Site: http://student.ccbcmd.edu/~cyau1/200_02_IndexofHdeficiency2006.pdf

Functional groups

Alkane Alkene Alkyne

 Alcohol Ether Amine

Aldehyde Ketone Carboxylic acid

Ester Amide

Formation of hemiacetals

Formation of hemiketals
 or – AR
Aryl group (phenyl as a substituent) benzyl group

CH3SO2O-R

Tosyl (TS) group (good leaving group) Ms – Mesyl group

anhydride.

–OR – OH

Alkoxyl Hydroxyl

Vinyl group Allyl group

Hydrazine (reducing agent/ reactive base) Hydrazone

Nitrile Epoxide

Nitro Nitroso

Enamine tautomers imine

oxime
Nomenclature

Number of
IUPAC
carbons

meth 1

eth 2

prop 3

but 4

pent 5

hex 6

hept 7

oct 8

non 9

dec 10
 n-butyl
n-propyl

isobutyl

sec-butyl isopropyl

tert-butyl

The following are the IUPAC rules for nomenclature:

1) The longest carbon chain with the most substituents determines the base
name
2) The end carbon closest to a carbon with a substituent is always the first
carbon. In the case of a tie, look to the next substituent
3) Any substituent is given the same number as its carbon
4) If the same substituent is used more than once, use the prefixes di-, tri-,
tetra, and so on
5) Order the substituents alphabetically.

When deciding alphabetical priority, prefixes are ignored if they are

separated by a hyphen or if they refer to a number!!!

Ex. Sec-butyl or dimethyl

Bond Energy
Bond energy is a measure of bond strength in a chemical bond. The higher the bond
energy the less energy there is in the system.

The higher the bond energy the higher the strength of the bond, thus more energy
must be put in to break it!!!!
Bond energy is also a measure of bond length. The higher the bond energy, the
stronger the bond, thus the smaller the bond length will be!!!

Bonding

Electrons are negatively charged. They are attracted to positively charged nuclei.
It is the electrostatic force between the electrons and the nuclei that creates all
molecular bonds. Both nuclei tug on both electrons, and the result is a bond
between the two nuclei.

Electrons are transitory passengers on their respective nuclei. They are in constant
search of ways to unload some of their energy and will do so whenever possible.
They (electrons) are at their lowest energy state when they are nearest to a
positive charge and farthest from a negative charge!! Because negative charge
in proximity to electrons raises their energy level, electrons will share an orbital
with, at most, only one other electron. The only thing which prevents an
electron from releasing all its energy and crashing into the positively charged
nucleus is the quantization of energy. The electron must give up a minimum
quantum of energy. This minimum amount is greater than the amount that
would be released if the electron collided with the nucleus!!!

A bond is formed when a pair of electrons can lower their energy level by
positioning themselves between two nuclei in such a way as to take advantage
of the positive charge of both nuclei!!!

Two electrons are required to form a bond. Each of the bonded nuclei can donate
a single electron to the bond, or in a coordinate covalent bond, one nucleus can
donate both electrons.

A coordinate covalent bond (also known as dative covalent bond) is a special

type of covalent bond in which the shared electrons come from one of the atoms
only. Once the bond has been formed, its strength is no different than that of
a covalent bond.

Coordinate covalent bonds are formed when a Lewis base (an electron donor or
giver) donates a pair of electrons to a Lewis acid (an electron accepter).

Coordinate bonds can be found in many different substances, such as in simple

molecules like carbon monoxide (CO), which contains one coordinate bond and
two normal covalent bonds between the carbon atom and the oxygen atom, or the
ammonium ion (NH4+), where a coordinate bond is formed between a proton (a H+
ion) and the nitrogen atom.
Coordinate bonds are also formed in electron deficient compounds , such as in
solid beryllium chloride (BeCl2), in which every beryllium atom is bonded to
four chlorine atoms, two with normal covalent bonding, and the other two
with coordinate bonds, which will give it a stable octet of electrons!!!

Coordinate bonding can also be found in coordination complexes involving

metal ions, especially if they are transition metal ions!!! In such complexes,
substances in a solution act as Lewis bases and donate their free pairs of electrons
to the metal ion, which acts as a Lewis acid and accepts the electrons.

Coordinate bonds form and the resulting compound is called a coordination

complex, while the electron donors are called ligands.

Ligands composed of ions such as F– or small molecules such as H2O or CN–

possess more than one set of lone pair electrons, but only one of these pairs can
coordinate with a central ion. Such ligands are said to be monodentate (“one
tooth”.) Larger ligands may contain more than one atom capable of coordinating
with a single central ion, and are described as polydentate. Thus ethylenediamine
(shown below) is a bidentate ligand. Polydentate ligands whose geometery
enables them to occupy more than one coordinating position of a central ion act as
chelating agents and tend to form extremely stable complexes known as chelates.
Some of the more common ligands (chelating agents) are shown here:

There are many chemicals with atoms that have lone pairs of electrons, often
oxygen, sulfur, nitrogen and halogens or halide ions, which, in solution, can
donate their electron pairs to become ligands. A common ligand is water (H2O),
which will form coordination complexes with any hydrated metal ions, like Cu2+,
which will form [Cu(H2O)6]2+ in aqueous solution. Other common simple ligands
are ammonia (NH3), fluoride ions (F-), chloride ions (Cl-) and cyanide ions (CN-).

The coordination number is the number of donor atoms bonded to the central
metal atom/ion!!!

Sigma and Pi Bonds

A sigma bond forms when the bonding pair of electrons are localized directly
between the two bonding atoms. Since the electrons in a sigma bond are as close
as possible to the two sources of positive charge (the two nuclei), a sigma bond
has the lowest energy and is the most stable form of covalent bond. Thus
sigma bonds are strong. A sigma bond is always the first type of covalent bond to
be formed between any two atoms; a single bond must be a sigma bond.

If additional bonds form between two sigma atoms, the new bonds are called pi
bonds. Because the sigma bond leaves no room for other electron orbitals directly
between the atoms, the orbital of the first pi bond forms above and below the
sigma bonding electrons. A double bond now exists between the two atoms. If
still another pi bond, the new orbital is formed on either side of the sigma bond. A
triple bond now exists between the two atoms. Double and triple bonds are
always made of one sigma and one or two pi bonds.

Although a pi bond is weaker than a sigma bond (less energy is required to

break the bond), pi bonds are always added to an existing sigma bond, and
thus strengthen the overall bond between the atoms. Since bond strength is
inversely related to bond length, the additional pi bonds shorten the overall bond.
The bond energy of a double bond is greater than that of a single bond.

The electrons in a pi bond are further away from the nuclei than the electrons
of a sigma bond and therefore at a higher energy level, less stable, and form a
weaker bond. This is important because less stability means pi bonds are
more reactive!!

Note: Phosphorous forms pi bonds with oxygen in nucleotide phosphates

such as ATP

Third row elements form weaker pi bonds than second row elements.

Double and triple bonds are rare for all atoms except carbon, nitrogen,
oxygen, and sulfur.

- This is because of nonsignificant or absence of overlap of the p orbitals

Another important point about pi bonds is their effect on spatial arrangement. The
atoms bonded to a single sigma bond are free to rotate about the bonding axis but
a pi bond locks its atoms into one spatial orientation preventing rotation!!

Hybridization

If we examine the electrons of a long carbon atom in its ground state we would see
that its four valence electrons are in their expected atomic orbitals, two in the
orbital of the s subshell and two in orbitals of the p subshell. The p electrons are
at a higher energy state than the s electrons.

Valence orbitals

S, P, P, P  unhybridized
sp3, sp3, sp3, sp3  SP3
sp2, sp2, sp2, p  SP2
sp, sp, p, p  SP

However, if we examine a carbon with four sigma bonds, we find that the four
bonds are indistinguishable. Since the bonds are indistinguishable, the orbitals
which form them must be equivalent. In order to form four sigma bonds, the
electrons form four new orbitals. The new orbitals are hybrids of the old S and
P orbitals and are equivalent to each other in shape and energy.
When one of these hybrid orbitals overlaps an orbital of another atom, a sigma
bond is formed in the area where the orbitals coincide. Pi bonds are formed by
the overlap of pure P orbitals (so pi bonds have 100% P character)!!!

There are several types of hybrid orbitals:

1) sp
2) sp2
3) sp3
4) dsp3
5) d2sp3

In order to figure out the type of hybrid orbital formed by an atom on the
MCAT, simply count the number of sigma bonds and lone pairs of electrons
on the atom. Match this number to the sum of the superscripts in a hybrid name
(letters without superscripts are assumed to have the superscript ‘1’). Remember,
there is one orbital in the S subshell that must be formed first, three orbitals in the
P subshell that must be formed next, and five orbitals in the D subshell to be
formed only after the S and P orbitals are formed.

Note: If an atom has 1 or more lone pair of electrons and is attached to

an sp2 atom then that atom is also sp2!!!

For example, water makes two sigma bonds and has two lone pairs of electrons.
Thus the sum of the superscripts in the name of the hybrid must add up to four.
The oxygen in water must be sp3 hybridized.

A hybrid orbital resembles in shape and energy the S and P orbitals from which it
is formed to the same extent that S or P orbitals are used to form it. This extent is
referred to as character.

The superscript indicate the character as follows:

1) sp orbital is formed from one S and one P orbitals and thus 50.0% S
character and 50.0% P character

2) sp2 orbital is formed from one S and two P orbitals and thus 33.3% S
character and 66.7% P character

3) sp3 orbital is formed from one S and two P orbitals and thus 25.0% S
character and 75.00% P character
 Note: the more S character a bond has, the stronger, more stable,
shorter it is

The electrons in an orbital seek to minimize their energy by moving as far away
from other electron pairs as possible, thus lessening repulsive forces. This leads to
specific bond angles and molecular shapes for different numbers and combinations
of sigma and lone pair electrons

Hybridization Bond Angle Shape

Sp (strongest) 180 Linear
Sp2 120 Trigonal planar or
Bent
Sp3 (weakest) 109.5 Tetrahedral,
pyramidal or Bent
Dsp3 90, 120 Trigonal bypyramidal,
Seesaw, T-shaped,
Linear

Where more than one possible shape exists, the shape depends upon the number
and position of lone pairs. Lone pairs, pi electrons, and ring strain can distort the
predicted bond angles. Lone pairs and pi electrons (dbl bonds/sp2 atom with a
lone pair) require more room than bonding pairs, and thus decrease the bond
angles.

Electron Delocalization

Sometimes bonding electrons are spread out over three or more atoms. These
electrons are called delocalized electrons. For MCAT purposes delocalized
electrons result from pi bonds.

- To have delocalized electrons you must have more than one pi bond
in an alternating single-double bond carbon, this is called
conjugation!!!

Molecules containing delocalized electrons can be represented by a combination

of two or more Lewis structures called resonance structures. The weighted
average of these Lewis structures most accurately represents the molecule.

- This is why the bonds between carbons in benzene are shorter than
single bonds in a normal alkane but longer than double bonds in an
alkene
The real molecule must be at a lower energy than any single Lewis structure
representing it since otherwise it would simply retain that structure . This
difference between the energy of the real molecule and the energy of the most
stable Lewis structure is called resonance energy. Remember, the real molecule
does not resonate between these structures but is a stable weighted average of all
of the contributing structures.

Here are the rules for writing resonance structures:

1) all contributing structures must have the same number of valence

electrons (cant add/remove atoms)
2) All contributing structures must obey the rules of covalent bonding; no
contributing structure may have more than two electrons in the valance
shell of hydrogen or more than eight electrons in the valance shell of a
second period element. Third period elements, such as phosphorous and
sulfur, may have up to 12 electrons in their valence shells
3) Atoms must not be moved; Move electrons not atoms
4) Number of paired and unpaired electrons must remain the same!!

The contribution made to the actual molecule by any given structure is roughly
proportional to that structure’s stability; the most stable structures make the
greatest contribution and equivalent structures make equal contributions.

Here are rules for precedence of resonance structures:

1) Structures in which all atoms have filled valence shells.

2) More number of covalent bonds and minimizes formal charge!!!
3) Least separation of unlike charges!!!
4) Negative charge on a more electronegative atom

Two conditions must exist for resonance to occur:

1) a species must contain an atom either with a p orbital (sp2) or an

unshared pair of electrons
2) That atom must be single bonded to an atom that possesses a double or
triple bond.

The adjacent p orbital in a conjugated system may contain zero

(carbocation), one (a radical), or two electrons (as in another pi bond)
The p orbital allows the adjacent pi bond to extend and encompass more than two
nuclei.

The above two conditions are required but not always sufficient for resonance.
Ring structures must also satisfy Huckel’s rule, which states:

- Planar monocyclic rings with 4n+2 pi-electrons (where n is any integer,

including zero) should be aromatic (display resonance)

Note: Can’t have more than 1 lone pair of pi electrons on one atom

Ex. So if we have an sp2 atom with 1 lone pair of electrons that is

connected to a double bond those two lone electrons aren’t
pi electrons because the double bond pi electrons is using that
one p orbital.

Ex. If we have an sp2 atom with two lone pair electrons only one of
those lone pair electrons are considered pi electrons because
we have only one P orbital. The other lone pair is part of one of
the sp2 orbitals

Video: http://www.youtube.com/watch?v=UYCJFcKT6gw&feature=related

In order to be considered aromatic it must also be flat, cyclic and completely

conjugated ((sp2) p orbital at every position in the ring). Aromatic molecules
are very stable and anti-aromatic (non 4n+2 pi electrons) are unstable. If a
molecule isn’t flat, cyclic or completely conjugated its non-aromatic.

Note:
A + charge indicates a p orbital w/ no electrons.
A - charge indicates a p orbital w/ 2 electrons
 Note: An 8 membered ring with alternating single and double bonds
isn’t flat

Dipole Moment

A dipole moment occurs when the center of positive charge on a molecule or

bond doesn’t coincide with the center of negative charge. A dipole moment can
occur in a bond or molecule. All the positive charge in a molecule comes from the
protons of the nuclei. All the negative charge comes from the electrons. The
dipole moment is measured in the units of debeye, D, and given by the equation:

p = qd

The potential energy of a dipole is PE = qEcos(theta)

Where q is the magnitude of charge of either end of the dipole and d is the distance
between the centers of charge.

A molecule or bond which has a dipole moment is referred to as polar; a

molecule or bond without a dipole moment is referred to as nonpolar.

A polar bond results from the difference in electronegativity of its atoms.

Atoms with greater electronegativities attract the electrons in a bond more
strongly, pulling the center of negative charge toward themselves, and thus
creating a dipole moment.
A molecule with polar bonds may or may not have a dipole moment. Since a
dipole moment is a vector, it is possible for the sum of the dipole moments in a
polar molecule to equal zero, leaving the molecule without a dipole moment.
Therefore we can see that dipole moments depend on the electronegativity of
atoms as well as the geometry/orientation of the atoms.

Ex. CCl4 has polar bonds, but doesn’t have net dipole moment

A dipole moment can be momentarily induced in an otherwise nonpolar molecule

or bond by a polar molecule, ion, or electric field. The polar molecule or ion
creates an electric field, which pushes the electrons and nuclei in opposite
directions, separating the centers of positive and negative charge. Such dipole
moments are called induced dipoles.

- Induced dipoles are common in nature and are generally weaker

than permanent dipoles

An instantaneous dipole moment can exist in an otherwise nonpolar molecule.

Instantaneous dipoles arise because the electrons in a bond move about the orbital,
and at any given moment may not be distributed exactly between the two bonding
atoms even when the atoms are identical. Although instantaneous dipoles are
generally very short lived and weaker than induced dipoles, they can act to
induce a dipole in a neighboring atom.
Intermolecular attractions (attractions between separate molecules) occur
solely due to dipole moments. The partial negatively charged side of one
molecule is attracted to the partially positively charged side of another molecule.
Dipole forces are much weaker than covalent forces. The attraction between
two molecules is roughly proportional to their dipole moment.

There is a very simple rule for Hydrogen bonding:

- Molecule must have H bonded to any one of these atoms N, O and F

(FON). If this is missing, there is no self-hydrogen bonding. You
can apply it on any molecule and its always right.

- The more electronegative the atom bonded to the hydrogen is the

stronger the hydrogen bond that forms…..so F forms the strongest
hydrogen bond, then O, and then N

Ex. How many hydrogen bonds is H3BO3 capable of producing.

- the answer is 9 because every hydroxyl group can participate in 3

hydrogen bonds (2 on the oxygen and then 1 from the hydrogen)

Like ethers  R-O-R , here there is no H on O atom so no self H bonding

Tertiary amines (R)3N ,here again no H on N so no H bonding.

Ethers can act as hydrogen bond acceptors, but not as hydrogen bond donors. The
same is true of deprotonated tertiary amines, since they have a heteroatom
(nitrogen in this case) with a lone pair to be a hydrogen bond acceptor. They can't
act as hydrogen bond donors because they don't have a hydrogen directly attached
to an electronegative heteroatom.

The point of all of this is that, if a molecule can act as a hydrogen bond
acceptor but not a donor, it can participate in hydrogen bonding ONLY if
another molecule that can act as a donor is present.

On the other hand, if you look at a deprotonated primary amine (R-NH2). It has
one lone pair that can act as a hydrogen bond acceptor, and two N-H bonds to act
as hydrogen bond donors. So primary amines can hydrogen bond with one
another. So this is an example of self hydrogen bonding. Water is the classic
example of this

R-OH, RNH2, RCOOH they all will show H bonding because they have H bonded
to most electronegative atom N and O. This is also applicable on big molecules
like proteins, DNA, etc.
Hydrogen bonding is the strongest type of dipole-dipole interaction.

The weakest dipole-dipole force is between two instantaneous dipoles. These

dipole-dipole bonds are called London Dispersion Forces. Although London
Dispersion forces are very weak, they are responsible for the phase changes of
nonpolar molecules!!

Note: Larger the molecule the larger the London dispersion forces!!!

Note: The shapes of the molecules also matter. Long thin molecules
can develop bigger temporary dipoles due to electron movement
than short fat ones containing the same numbers of electrons!!!

Collectively these forces make up van der Waal’s forces:

 permanent dipole–permanent dipole forces
 permanent dipole–induced dipole forces
 instantaneous induced dipole-induced dipole (London dispersion forces).

These are relatively weak and if these are the predominant forces, then the
compound will have a low boiling point.

Isomers

Two molecules are isomers if they have the same molecular formula but are
different compounds.

Conformational Isomers

Conformational isomers are different in their spatial orientations of the same

molecule. At room temperature, atoms rotate about their sigma-bonds resulting in
a mix of conformers at any given moment.

- ** If there is a Pi-Bond there is no free rotation **

The Elipsed conformation always has more energy than the staggered
conformation, and the anti always has the least energy

There will always be 7 energy levels in a conformation-energy projection

The larger the atoms and the closer they are together the more energy that
conformation will have:

- if we have all the atoms of equivalent size ANTI to each other then we
are at the lowest possible energy conformation

- Full eclipsed as shown above is the conformation with the most energy

- It will always go from staggeredeclipsed, or eclipsedstaggered via a

60 degree rotation

** Staggered conformation can sometimes be isolated at low temperature **

Structural (constitutional) isomers have the same molecular formula but

different bond-bond connectivity (i.e. isobutene and n-butane)!!!

Chirality

Chiral molecules differ from their mirror images, therefore can’t be superimposed
 - All chiral molecules have a mirror image which is their enantiomer.
- Are never the same as their mirror image
- Rotate polarized light

Achiral – can be superimposed are the same as their mirror image. An easy way
to find if a molecule is achiral is to look for a plane of symmetry if there is one
then the molecule is achiral.

- Achiral compounds are optically inactive (cant rotate polarize light)

- Don’t have chiral centers

Chiral center - is any carbon w/ FOUR!! (4) DIFFERENT substituents

To detect chiral carbons:

- first detect which ones have 4 substituents on them
- if they have two of the same such as 2 H’s then its not
- if not then continue onto the others and follow their trail to see if
they match

Designating R & S (Absolute Conformation)

- # substituents by atomic weight

- higher weight = higher priority
- If 2 of the atoms are the same go look at their substituents
- Substituents on double or triple bonds are counted 2 or 3 times
respectively
- Rotate so lowest priority group faces away (if you cant then R becomes
S and S becomes R), if you cant rotate it away then R becomes S and S
becomes R.
- R = clockwise and S = counter-clockwise

- ** FOR FISCHER PROJECTIONS WE REVERSE S AND R **

The absolute configuration of a molecule DOESN’T give information about the

direction in which the compound rotates plane polarized light!!!

The mirror image of a chiral molecule always has the opposite absolute
configuration!!
Relative Configuration – two molecules have the same relative conformation
about a carbon if they differ by only one substituent and the other substituents are
oriented identically about the carbon. It is NOT related to absolute conformation.

Note: Relative configuration can remain the same but absolute

conformation can change

In a Sn2 reaction it is the relative configuration that is inverted.

Observed Rotation

The direction and the degree to which a compound rotates polarized light is given
by its observed rotation!!!

A single photon can be described by a changing electric field and its

corresponding magnetic field, both fields being perpendicular to each other and to
the direction of propagation.

A polarimeter screens out photons with all but one orientation of electric field.
The resulting light consists of photons with their electric fields oriented in the
same direction. This light is called plane-polarized light.

When a photon reflects off any molecule, the orientation of the electric field
produced by that photon is rotated. The mirror image of that molecule
(enantiomer) will rotate the electric field to the same degree but in the
opposite direction!!

Optically inactive compounds don’t rotate polarized light!!!

Compounds that are optically inactive:

1) no chiral centers (achiral)
2) meso compounds
3) racemic mixtures

A racemic mixture, or racemate, is one that has equal amounts of left- and right-
handed enantiomers of a chiral molecule.

In contrast to the two separate enantiomers, which generally have identical

physical properties, a racemate often has different properties from either of
the pure enantiomers. Different melting points and solubilities are very common,
but different boiling points are also possible.
When plane polarized light is projected through an optically active compound, the
orientation of its electric field is rotated.

- If the compound rotates the light clockwise it is designated with a ‘+’ or

‘d’ for dextrotorary
- If the compound rotates the light counterclockwise it is designated with
a ‘-’ or ‘l’ for levorotary

The direction and number of degrees that the electric field in plane-polarized light
rotates when it passes through a compound is called the compound’s observed
rotation. Specific rotation is simply a standardized form of observed rotation that
is arrived at through calculations using observed rotation and experimental
parameters such as:

- temperature
- length of the polarimeter
- type of wavelength used
- concentration of the solution

Spec. rotation [a] = observed rot. (degrees)/ (length (dm) x concentration

(g/ml))

Specific rotation is equal to observed rotation after these adjustments have been
made.

Stereoisomers

Stereoisomers are two molecules with the same molecular formula and the
same bond-bond connectivity but aren’t the same compound.

UNLESS THEY ARE GEOMETRIC ISOMERS, THE COMPOUND MUST

HAVE AT LEAST ONE (1) CHIRAL CARBON!!

There are two (2) types of stereoisomers:

1) Enantiomers
2) Diasteromers

A chemical reaction is steroselective when a certain stereoisomer or set of

stereoisomers predominate as products. A reaction is sterospecific if different
isomers lead to isomerically opposite products!!
ENAMTIOMERS
Enantiomers – have the same molecular formula, have the same bond-bond
connectivity, are mirror images of each other, but not the same molecule.

Enantiomers MUST have opposite absolute configuration (R&S) at EVERY

chiral carbon

- Enantiomers have the same physical and chemical properties except

for 2 cases:
1) reactions with other chiral compounds
2) reactions with polarized light

- So we can separate them via those ^^ methods

- Enantiomers rotate plane-polarized light in opposite directions but

with the same magnitude.
- Ex. R-2-butanol is -13.52 while S-2-butanol is +13.52

- When enantiomers are mixed together in equal concentration the

resulting mixture is a racemic mixture.
- Racemic mixtures don’t rotate plane polarized light b/c of
equal concentrations they will cancel each other out.

- The ratio of actual rotation (for a mixture with uneven concentrations of

enantiomers) to the rotation of pure sample is called optical purity.

- The ratio of pure enatiomer to racemic mixture is called enantiomeric

purity

Enantiomeric excess = %R-%S or vice versa

For example, if a mixture consists of 75% of the R enantiomer and 25% of the S
enantiomer, the enantiomeric excess is 50 % pure R, and the other 50% is (R/S).

e.e = % optical purity = ([a] sample / [a] pure enatiomer) x 100%

- Optical purity = Enantiomeric purity, ALL THE TIME

|observed specific rotation (assuming only enantiomers)| = e.e. x rotation of pure (+)-
enantiomer,
 - The separation of enantiomers is called Resolution!!!

DIASTEREOMERS
Diastereomers – have the same formula, bond – bond connectivity, but are NOT
mirror images of each other, and aren’t the same compound

Diastereomers formed by inverting some but not all stereocenters.

Diasteromers have different physical and chemical properties, which can be

separated due to their different physical (Ex. Crystallization, boiling points,
or melting points) and chemical properties

An example of diasteromers are cis and trans isomers, which are geometric
isomers.
 - Cis isomers have their substituents on the same side while trans are on
opposite sides. (remember to label the priority of the groups)

- Geometric isomers have different physical properties

- so they can be separated due to their different physical (Ex.
Crystallization, boiling points, or melting points)

- It is important to know that cis molecules have a dipole moment

while trans doesn’t!!!

- Due to their dipole moments, cis molecules have stronger

intermolecular forces leading to higher boiling points but b/c of their
lower symmetry they have lower melting points!!!

- Also steric hindrance is present in cis molecules which produce

higher energy levels resulting in higher heats of combustion!!!

a) (higher heat of combustion = less stable)

For tri and tetra substituated alkenes we use the terms E and Z instead of cis and
trans:
- To label it according to this label the highest priority substituents on
each carbon according to weight and if the higher priority substituent for
each carbon exists on both sides it is Z (cis) or if on opposite sides it is
E (trans)

Etrans
Zcis
 Max # of optically active stereoisomers = 2^n
n = # of chiral centers

A molecule with n chiral centers:

1. can have up to 2n - # meso structures = stereoisomers in its
family
2. if a compound is achiral it does not have an enantiomer
3. if a compound is chiral it has only one enantiomer
4. if a compound is chiral it can have up to 2n-2 diasteromers

Four possible stereoisomers of 2-bromo-3-chlorobutane and Two diasteromers

Meso compounds (are another type of stereoisomer) contains two or more

chiral centers but is optically inactive (can’t rotate polarized light).

They have a plane of symmetry, therefore they are achiral. If there are two
chiral centers, one is R and the other is S.

They can be superimposed when the mirror image is taken either by rotating 180
degrees or by taking the mirror image in a different way that you can just shift the
image over onto the other. THEY ARE THE SAME COMPOUND!
Diasteromers that differ at only one chiral carbon are called epimers

A more selective term, epimer, is used to designate diastereomers that differ in

configuration at only one chiral center.

- An anomer is a special type of epimer. It is a stereoisomer (diastereomer,

more exactly) of a saccharide (in the cyclic form) that differs only
in its configuration at the hemiacetal (or hemiketal) carbon, also called
the anomeric carbon.

The anomeric carbon can be identified as the only carbon which is attached to 2
oxygens because its alcohol group may point upwards or downwards on the ring
structure resulting in either the a(down) or B(up) anomer.

example: α- and  β-D-glucose