Chapter 1:

Organic chemistry deals with compounds made of carbon.

Analogs compounds of similar structure.
Electrostatic attraction the attraction between opposite charges, holds ions together
and is the same in all directions.
Bond order and bond length relationship is that bond length increases with increasing
period (right to bottom). Triple bonds are shorter than double bonds always.
Dihedral or torsional angle is the angle between two planes.
Resonance structures are like the average of two same molecules. Something that is in
between two similar structures. For example a nectarine is like a hybrid between a plum
and a peach.
Resonance is used because we are not sure where the electron density is at. It could be
on one side or the other of a compound; and the difference in electron densities of two
compounds is what causes reaction.
An orbital with principal quantum number n has n -1 nodes.
Principle quantum number (n) is the main energy level occupied by the electron, also
called the shell. Energy increases with increasing shell number. Subshells are
represented by L.
Angular momentum quantum number (l) describes the shape of the orbitals. Allowed
values go from 0 up to n-1.
Magnetic quantum number (ml) indicates the orientation of an orbital around the
nucleus. Its values go from -L to +L. For example, when L = 0, then mL is just 0, which
makes sense because S orbital (a sphere) can only be oriented in one way since its a
sphere.
Spin quantum number (mS) describes how the electron is spinning (spin up +1/2 or spin
down -1/2)
Molecular orbitals are orbitals of entire molecules unlike orbitals of single atom. They
are the region an electron is most likely to the found. MOs result from combination of
atomic orbitals. MOs are arranged in increasing energies. Electrons in bonding MOs
occupy space around the nuclei and between the nuclei (acting as cement or glue
holding the two nuclei together). Orbitals that are out-of-phase with one another are
antilbonding orbitals because they cancel out the wave. For example a top half cycle
of sign function cancels out with bottom half cycle. Bonding orbitals come together
constructively, whereas anti bonding come destructively. Phases are either (+) or (-) to
their wave up or wave down. A node occurs where the phase changes from (+) to (-)
direction. Electron finding chances are zero at nodes. An MO bond involving symmetry
w/r/to rotation around the bond axis is called sigma bond. If the orbital maintains its
original character even after rotation around the sigma bond, then the bond is defined
as garage, g; if character changes, then it it called underage, u. Orbital energy
increases with nodes; more nodes = more energy = less stable. Fewer nodes = less
energy = more stable. Higher bond order = more stable molecule. No bond order (i.e. is
0) = molecule does not exist. Sigma bond is more stable than pi bond. Molecules are
stable if anti bonding orbitals are empty. Sharing of electrons between nuclei does not,
in some cases, contribute to bonding (i.e. when they occupy the anti-bonding MOs).
The number of MOs of the molecules is equal to the overall number of AOs of all atoms.
Orbitals of atoms in MO are different than their regular AOs but they are still made from
the same AO orbitals by combining different AOs to make hybrid orbitals. Hybrid orbitals
are combination of different orbitals with characteristics thats in-between. For
example, 1 part s and 3 part p orbital is called sp3 orbital. Electron density is highly
directional in space in sp3 orbital.
In hybridization, a p-orbital from each atom is needed to form pi bond, leaving behind
two other p-orbitals for hybridization (sp2), if the molecule has triple bond then two p-
orbitals are needed, leaving behind one p-orbital for hybridization (sp). If all bonds are
single bonds, then no pi bond is present so all three p-orbitals can be used for
hybridization (sp3).
General notes on MO Diagrams:
-Y-axis represents total energy of the orbitals.
-Individual atomic orbitals (AO) are arranged on far left and right of the diagram.
-Overlapping AOs produce MOs located in the middle of the diagram. These MO
overlap with either sigma or pi bond in bonding, nonbonding, or anti bonding manner
w/r/to their phases.
-Electrons from AOs are assigned to MOs following all the rules (i.e. Pauli exclusion,
Hund, etc).
Cylindrical symmetry is when you have a bond and no matter how you turn the molecule
around the bond, its electron density look the same. Bonds with cylindrical symmetry is
called sigma bonds.
The formula for bond order = electrons in bonding MOs - electrons in anti-bonding MOs
* 1/2.

How to form MO Diagram:

1. Find VE configuration of each atom (these e- will be placed on AO of that atom.)
2. Decide if atoms are homo or heteronuclear. If molecules is symmetric (is
homonuclear), the AOs will be symmetric. If hetero, the more electronegative atom will
be placed lower on the diagram because lone pairs of electrons are more stable on the
electronegative atoms. More stable = less energy.

Chapter 2: Alkanes
Hydrocarbons only contain hydrogens and carbons.
Hydrocarbons are divided into two categories: aliphatic and aromatic.
Aliphatic hydrocarbons include alkanes, alkenes, and alkyls.
Alkanes are also called paraffins.
Aromatic hydrocarbons include benzene and its derivatives.
Unbranched alkanes are called normal alkanes or n-alkanes.
CH2 is called the methylene group.
The conformation of molecule is the spatial arrangement of all of its atoms when all the
dihedral angles are specified.
Two Newman conformation: staggered or eclipsed. In eclipsed conformation, the
smallest dihedral angle is 60. In eclipsed conformation, the smallest angle is zero.
Torsional strain is the repulsion between electrons of CH bonds in two carbons.
Internal rotation is the rotation of a carbon atom relative to another in staggered
conformation. It is like jump from one staggered conformation to another.
Gauche conformation have angles of -+60 (or 300). Anti conformation have dihedral
angles of 180. A conformation is more stable if there are less gauche interactions
among adjacent carbons.
Van der Waal repulsions exist when two atoms are close enough that they almost
overlap a bit.
Compounds that have the same molecular formula are called isomers.
Constitutional or structural isomers have different connectivity (or atoms
arrangement).
A carbon is said to be primary if it is only connected to one other carbon; secondary if it
is connected to two other carbons, tertiary if connected to three, and quaternary if
connected to four other carbons in a molecule. Same thing for the hydrogen, if a
hydrogen is on a primary carbon, it is called primary hydrogen.
Cycloalkanes are closed-loop carbon chains. Cycloalkanes have two less hydrogens
than open-ended alkanes, thus their formula is CnH2n.
Skeletal structures (squiggly lines) show only the carbon-carbon bonds.
A functional group is a characteristically bonded group of atoms with same reactivity
regardless of whichever compound it occurs in.

Chapter 3: Acids and Bases

Electron-deficient compounds have a tendency to undergo reactions that fulfill their
valence-shell octets.
A lewis acid is an electron-pair acceptor. A lewis base is electron-pair donor. When lewis
base and lewis acid combines, the reaction is called lewis acid-base association
reaction.
Curved arrow notation keeps track of electron movement. Two arrows are required if the
reaction is electron displacement reaction.
Nucleophile (nucleus loving) is a specie that donates an electron to form a new bond.
The atom in the nucleophile group that actually donates the electron is an nucleophilic
atom or nucleophilic center. An electrophile is a specie that accepts the electron and the
atom of the electrophile that takes the electron is the electrophilic atom or center. The
group that accepts electron from a bond is called the leaving group.
A specie that donates a proton (H+) is called a Bronsted acid. A specie that accepts a
proton is called a Bronsted base. In Bronsted acid-base reaction, the the electrophilic
center is a proton. When the electrophilic center is a proton, the electron donor is called
a Bronsted base, while a Bronsted base is the species that provide a proton to the base.
If the electrophilic center is something other than a proton (H+) then the donor of
electron is not Bronsted base but is just called nucleophile.
When a Bronsted acid loses a proton, it becomes a conjugate base, the receiving base
becomes a conjugate acid.
Compounds that can act as either acids or bases are called amphoteric compounds.
The strength of Bronsted acids can be assessed based on how well it transfers a proton
to a standard Bronsted base. The strength of a Bronsted acid is measured by the
magnitude of its acid dissociation constant. Stronger acids have large K_a constant (or
smaller pKa values).
A stronger Bronsted base is the one whos conjugate acid has the greatest pKa value.
The equilibrium in the reaction of an acid and base always favor the side with the
weaker acid and weaker base.
Dissociation state (whether an acid or base is present in conjugate-acid or conjugate
base form or as a mixture) depends on the pH of the solution.
Bronsted acidity increases as the atom to which the acidic hydrogen is attached has a
greater atomic number with in a column (Group) of the periodic table. Also, the acidity
increases as the atom to which the acidic hydrogen is attached is farther to the right in
the periodic table. So, going down, and to the right, the acidity increases.
The effect of changing the directly attached atom A on the acidity of HA is called the
element effect.
Acid dissociation involves breaking the bond to hydrogen, so smaller bond dissociation
energies promote increased acidity. Once the bond is broken, the second step is the
removal of electron from hydrogen atom. The energy required for this step is the
ionization potential of hydrogen (it is the same for all bronsted acids). The third step of
acid dislocation is the transfer of electron to A to form anion. The energy required for
this step is called electron affinity. Larger electron affinity corresponds to greater acidity.
Electron affinity is like electron attraction. The major factor governing acid strength is the
HA bond. Weaker bonds mean strong acid.So going down a group, acidity increases
because of weaker bonds. Going to the right of a period the acidity increases because
of greater electron affinity/attraction by the atom. The charge effect also affects acidity
as a positively charged atom has more attraction for electrons. Also, the closer an
electronegative atom is to the acidic hydrogen, the greater its effect on acidity. Factors
that affect acidity include CARIO: charge, atomic size, resonance, induction, and orbital
hybridization.
There is a direct proportional relationship between dG and pKa. Lowering the energy
(dG) increases acidity. If the net effect of a dipole is attractive, then it is stabilizing and
thus increasing acidity. An effect on chemical properties caused by the interactions
between charges, dipoles, or both is called a polar (or inductive) effect. Halogens have
acid-strengthening effect. Halogens and electronegative groups exert electron-
withdrawing polar effect raising acidity (lowering pKa). Non-electronegative groups exert
electron-donating polar effect (increasing the pKa) and lowering acidity. Stabilization of a
conjugate acid or base alters the energy dG and effects its pKa.

Chapter 4: Alkenes
Alkenes, also called olefins, are hydrocarbons with one or more carbon-carbon double
bonds.
Alkenes are unsaturated hydrocarbons because they have fewer C-H than alkanes,
which are called saturated hydrocarbons.
Sp3 orbitals are associated with tetrahedral geometry. Sp2 orbitals are associated with
trigonal planar geometry.
Sigma bond: The first bond made with any other atom (CC). Sigma bonds are made
from hybridized orbitals.
Pi bond: Any 2nd or 3rd bond made with any other atom (C=C). Pi bonds are made from
leftover p-orbitals. Side to side overlap of p-orbitals make up pi bond.
Compounds with identical atomic connectivities that differ in the spatial arrangement of
their atoms are called stereoisomers. The cis and trans notation describes how atoms
are arraignment across a double bond. Double bond stereoisomers are related by the
internal 180 rotation of the groups attached to the carbons on either side of the double
bond. The double bond carbons of double-bond stereoisomers are called
stereocenters.
Unsaturation number or degree of unsaturation indicates the number of rings or
double bonds in a molecule. Unsaturation number can be found by getting total number
of hydrogens hydrocarbon supposed to have minus the amount it actually has and
divided by two.
Heat of formation of a compound is the energy change that occurs when a compound
is formed from its elements in their natural state at STP.
A trans-alkene is more stable than a cis (think of repulsions in cis arrangement). Alkene
with more alkyl (or side groups R) around the double bond is more stable.
Bond strength increases with the fraction of s character in the component hybrid
orbitals. More s character means stronger bond. Also, more s character means more
electronegativity. Then, sp2sp3 CC bond is stronger than sp3sp3 CC bond.
This also means then that sp2sp3 is more polar than sp3sp3. Alkenes with four R
groups around the C=C bond is more stable than one with three groups which is table
than one with two R groups.
In addition reaction pi bond of carbon is broken and single bond of XY is broken,
new bonds are then formed CXCY.
Hydrogen halides HF, HCl, HBr, and HI undergo addition to C=C to give
products called alkyl halides, compounds in which a halogen is bound to a saturated
carbon atom. If many products are possible as a result of halogen addition, then the
main product is that isomer that is attached to the carbon with more alkyl substituents,
and the hydrogen goes to the carbon with fewer substituents. When one of the possible
isomers is formed in excess over the other, the reaction is called regeoselective
reaction. Hydrogen halide addition to alkenes is highly regioselective. If the number of
substituent around the C=C is equal, then no noticeable effect is observed on which
isomers is dominant. Only number of substituents around the C=C matters, size does
not matter.
A carbocation is a positively charged cation of carbon. Carbocations are examples of
reactive or unstable intermediates, that is they react so rapidly that they do not
accumulate too noticeably.
A complete description of a chemical reaction (pathway), including its reactive
intermediates, is called the mechanism. It completely describes how the reaction
happen. Hydrogen halide addition is a two step mechanism: a carbon of pi bond is
protonated, and a halide reacts with the resulting carbocation. The regioselectivity of
hydrogen halide addition is due to the formation of only one of the two possible
carbocations (the one that has faster reaction rate).
In rearrangement, a group from starting material moves to a different position.
Rearrangement is favored by the increased stability of the rearranged ion. A hydride
shift is the migration of a hydrogen with its two bonding electrons.
Two pathways for carbocation reactions: through reaction with a nucleophile and
through rearrangement towards more stable carbocations.
Chapter 5: Addition reaction of alkene
Addition reactions are characterized by two groups adding across a double bond.
Regioselectivity describes which side of the product gets the adding groups. Does X go
to the right of the molecule or the left and vice versa. Regiochemistry is only relevant
when the adding groups are different (i.e. H and Br); if the groups are the same (i.e. H
and H) or if the molecule is symmetrical, then regioselectivity is irrelevant.
Syn addition is when you add the adding groups on the same side of the plane. Anti
addition is when you add the adding groups across each other through a plane.
Enantiomers are non-superimposable mirror images of each other. A stereo center is a
point in molecule where the exchange of two groups will produce a stereoisomer.
Chiralcenter is atom with four DIFFERENT groups attached to it. A carbon is a stereo
center if it is sp3 hybridized and bonded to four different groups; or if in a ring, the two
half of the ring around it are different. Stereochemistry is irrelevant if less than two
stereo centers are created.
In hydrogenation reaction, Hs are added across double bonds in alkenes using a
metallic surface as a catalyst. Regiochemistry doesnt matter because adding same
groups (Hs). H2 first gets adsorbed (glues) to the metallic surface freeing each H for
grab. The alkene then grabs the Hs on the same side of the alkene. So therefore it is a
syn-addition.
In hydrogen halide addition, the regioselectivity will be determined by the preference for
the reaction to proceed via the more stable carbocation intermediate. Higher order
carbocation are more stable than lower order ones (i.e. tertiary carbocation is favorable
compared to secondary). A hydride shift can occur to produce a more stable
carbocation. Carbocation rearrangement can occur either via hydride shift or methyl
shift; a carbon will always rearrange an H before rearranging methyl.
Addition reaction of HBr in the presence of peroxide (ROOR) is anti-Markovnikov.
Hemolytic breaking of the bond means radicals are formed because the bond is split
in half where each group receives one electron. Higher order radicals are more stable
than lower order radicals. This is why HBr addition is anti-Markovnikov because Br*
attacking the less substituted carbocation results in a more branched (higher order)
radical.
So hydrogen halide addition follows Markovnikov rule, but in the presence of radicals
(ROOR) it then follows anti-Markovnikov.
The process of adding a water across an alkene is called hydration. The mechanism of
acid-catalyzed hydration is similar to the machinism of hydrogen halide addition without
radicals presence (ionic pathway).
Hydroboration-oxidation is anti-Markovnikov and syn. Addition of BH3 is
hydroboration.
Cycloaddition is a reaction that forms a ring, ozonolysis is an example of that.
Electrophlic addition is a reaction that begins with the donation of an electron pair
from a pi bond to an electrophilic atom.
A bromonium ion is a species that contains a bromine bonded to two carbon atoms; it
has an octet and a positive charge. Why doesnt Br2 addition proceeds the same was
HBr addition, meaning, why should a bromonium ion be formed instead of a carbocation
(just like a carbocation is formed when HBr is added)? It is because when bromonium
ion is formed, each atom in the molecule has an octet of electrons (8e-) as opposed to a
carbocation with only 6es.
A bromohydrin contains both an OH and a Br group. Bromohydrin is an example of
halohydrins, meaning, a product contain a halogen and OH group.
Oxymercuration follows Markovnikov while hydroboration is anti-Markovnikov. The
overall result of oxymercuration-reduction of an alkene is the addition of OH and H
across a double bond that follows Markovnikov's rule.
A reaction that occurs in a single step without intermediates, like hydroboration, is said
to have concerted mechanism because everything occurs simultaneously.
Ozonolysis is the splitting of the carbon to carbon double bond. Under oxidative
conditions (OH) is added, under reductive condition just H is added. The fist step of
ozonolysis is example of concerted mechanism where the pi bond of CC attacks
oxygen, at the same time, the other oxygen electrons attacks the other carbon, while the
pi bond between the two OO attacks the middle oxygen, resulting in a ring structure
that is unstable called the ozonide.
Addition of Hbr in presence of peroxide reverses regioselectivity from Markovnikovs to
anti-Markovnikov. Only addition of Hbr is affected by peroxide, not other chemicals such
as HI or HCl.
Any specie with at least one unpaired electron is called a free radical.
A free radical chain reaction involves free-radical intermediates and three core steps:
initiation steps, propagation steps, and termination steps.
In the initiation steps, the free radicals form from a free-radical initiator (this is the source
of the free-radicals).
In an atom-abstraction reaction, a free radical removes an atom from another molecule
and a new radical is formed. In the propagation steps radicals react with non-radical
starting materials to give other radicals. This step occurs repeatedly. In the termination
steps, free radicals combine to give nonradical products (forming a covalent bonding).
Radical recombination is the reverse of hemolysis.
Free radicals can be classified as primary, secondary, or tertiary. tertiary radicals >
secondary radicals > primary radicals (in terms of stability). The reason why Br atom
would bond with the less substituted carbon to give a tertiary radical is because Br is
large atom that experiences van der waals repulsion, so squeezing it in a congested
area increases the repulsion; whereas forming bond at less congested area is more
stable (steric effect).

Chapter 6: Stereochemistry
An object or molecule that is not superimposable on its mirror image is chiral, like our
hands (thumbs are at different locations on each hand). The higher the atomic number
of an atom directly attached to a chiral carbon, the higher the priority. Stereoisomers
are compounds with same atomic connectivity but a different spatial arrangement.
Molecules that are non-congruent (i.e. do not align) are called enantiomers.
Enantiomers are can be chiral, the property of handedness (like pair of hands that are
images but not congruent).
An asymmetric carbon is a carbon to which four different groups are attached. A
molecule that contains only one asymmetric carbon is chiral. Other terms for
asymmetric carbon are chiral center and stereo center.
Any molecule with a plane of symmetry is achiral.
Naming enantiomers using R & S priority rule: if the circle goes clockwise, then it is R
configuration; if the circle goes counterclockwise, then it is S configuration.
The melting points and boiling points of a pair of enantiomers are the same. A
substance that rotates the plane of polarization of light is said to be optically active.
Individual enantiomers of chiral substances are optically active. Note: learn optical
rotation calculation. Enantiomers rotate the plane of polarized light by equal amounts in
the opposite directions (i.e. if S-2-butanol rotates light +30C then R-2-butanol will rotate
it -30C). Positive rotation is dextrorotatory and negative rotation is levorotatory.
Enantiomerically pure substances have the same chirality. But usually mixtures of both
enantiomers occur. Enantiomeric excess, EE, is just the difference between % of the
major enantiomer % of the minor enantiomer. A mixture containing equal amounts of
either enantiomers is called a racemate or racemic mixture. Racemates have physical
properties different than pure enantiomers (due to having different crystals, which then
affect melting or boiling points).
Stereoisomers that are not mirror images are called diastereoisomers or
diastereomers. Diastereomers differ in all of their physical properties.
A meso compound is an achiral compound that has at least two stereo centers (they
are optically inactive).
The separation of two enantiomers is called enantiomeric resolution.
Amines are derivative of ammonia in which one or more of the hydrogens have been
replaced with organic groups.
Conformational isomers differ by rotation about single bonds (sigma). Conformational
isomers are non-superimposable mirror images, but they interconvert very rapidly with
their mirror images that they cannot be isolated as separate chiral conformation.

Chapter 7: Cyclic Compounds

Monocyclic compounds are compounds with only one ring. Cyclohexane have same
empirical formula, a formula that gives the smallest whole-number proportions of the
elements CH2. The relative stabilities of cycloalkanes can be compared by looking at
their heat of formations. Cyclohexane, which has the lowest (most negative) heat of
formation, is the most stable.
Torsional strain (or the eclipsing strain) results from eclipsed bonds. Torsional strain
is the increase in potential energy of a molecule due to repulsion between electrons in
bonds that do not share an atom. Steric strain results from atoms being too close
together. Angle strain results from distortion of bond angles from normal values.
High heat of combustion imply unstable molecules.
Alkane rings are not (always) planer but rather often plucked, which relieves angle
strain. A conformation of a cyclic organic molecule is a specified shape the ring could
assume.
Cycloalkanes can change conformation via internal rotation (but several carbons must
rotate at the same time because its a ring).
Look at a model of cyclohexane, the substituents (or hydrogens) that are perpendicular
(straight up or straight down) are called axial-substituents. The remaining substituents
are on the edges of the sphere so they are called equatorial substituents. Equatorial
substituents are more stable because they face away from each other as compared to
facing each other in axial setting. Axial conformation is less stable due to having 1,3-
diaxial interactions or dixaxial strain which are interactions between the axial methyl
substituent (carbon one) and the axial hydrogen or substituent on carbon three.
Another name for axial strain is gauche-butane interactions, because both
interactions look the same and cost the same amount of energy per one interaction
(about k.7 kJ per mol).
-The cis-trans relationship doesnt change if a molecule undergoes conformation
change. Keep this in mind when looking for diastereoisomers of a molecule (i.e. if a
molecule is cis then its distereomers must also be cis).
-To determine which chair conformation a molecule is more stable, look at the large
substituent, if it is in equatorial position then that is more stable.
-A compound can in principle be isolated in optically active state at room temperature if
the compound is achiral (i.e. its mirror image is non-superimposable).
The investigation of molecular conformations and their relative energies is called
conformational analysis.
When two adjacent substituents on a ring have the same relative orientation both up
or down the substitution pattern is called cis (cis is added in the name). When one
substituent is up and the other down, this is called trans.
Cyclopentane (which is less stable cyclohexane) exists in a puckered conformation
called the envelope conformation. Cyclopropane (3C) is planar so puckering cannot
provide relief.
If two rings share two or more atoms, the compound is called a bicyclic compound. If
only one single atom is shared between the two rings, the compound is called a
spirocyclic compound.
The atoms at which the two rings are joined are called bridgehead carbons. When the
two bridgehead carbons are adjacent like so: CC, then the compound is
classified as fused bicyclic compound. If the bridgehead carbons not adjacent (i.e.
have another atom in between) like so: CAtomC, the compound is called
bridged bicyclic compound. The bond connecting two bridgehead carbons in a fused-
ring system is considered to be a bridge with zero carbons (i.e. bicyclo[4.4.0]decane).
Compounds with more than two rings joined together are called polycyclic
compounds.
In small rings, only cis fusion is observed because trans fusion puts too much strain on
the ring (i.e. bicyclo[1.1.0]butane). In larger rings, both conformations are observed, but
trans-fused isomers are more prevalent because it reduced axial strain on the ring.
Bretts rule states that in a bicyclic compound, a bridgehead carbon of small rings
(seven or fewer carbons) cannot be part of a double bond.
A steroid is a compound with four fused rings (tetracyclic). Steroids have to methyl
groups called angular methyls because they are bonded to bridgehead carbons 10 and
13.
Enantiomers react at the same rates with an achiral reagent. Principle of enantiomeric
differentiation states that enantiomers react at different rates with a chiral reagent.
When chiral products are formed from achiral starting material, both enantiomers of a
pair are always formed at identical rates (product is a racemate).
Enantiomers are formed at different rates from achiral starting material in the presence
of a chiral catalyst.
Diastereomers have different reactivities (rates) with any reagent, whether chiral or not.
In substitution reaction, one group is replaced by another.
Retention of configuration is when a group Y replaces X but doesnt change spatial
orientation (i.e. if X as in the front, then why replaces it and stays in the front).
Inversion of configuration happens when Y replaces X by also changing position (i.e.
if X was in the front, then Y replaces X but moves to the back instead of staying at the
front).
A stereoselective reaction favors the production of a particular stereoisomer over the
others.
The electrophilic addition of Br2 to alkenes occur through a bromonium ion
intermediate. Br- attacks opposite to the CBr bond of the cyclic intermediate.
Bromination addition is anti addition (adds to opposite face).
Hydroboration-oxidation follows anti-Markovnikov and syn addition.
Catalytic hydrogenation (H2/Pd) follows syn addition (there is no markov rule since
both same things are added).
Oxymercuration follows Markovnikovs rule and is typically anti addition.
Chapter 8: Nonycovalent Intermolecular Interactiona
Alkyl substituent is an alkane missing one hydrogen. An alkyl halide is a compound in
which a halogen (F, Cl, Br, I) is bound to the carbon of an alkyl group. An
alcohol is a compound in which a hydroxy group(OH) is bound to an alkyl group.A
thiol is a compound in which a mercapto (or sulfhydryl) group (SH) is bound to the
carbon of an alkyl group. Thio generally means sulfur in place of oxygen. Thiol is an
alcohol is which a sulfur has been substituted for oxygen.
Aryl group is derived from an aromatic hydrocarbon by the removal of a hydrogen atom
(i.e. benzene ring). In alcohols, the OH group is bound to an sp3 carbon (i.e. the
carbon is not part of a double or triple bond). In aryl halides, the halogen is attached to
an sp2 carbon of a benzene ring.
Halides in which halogen is attached to an sp3 carbon that is next to a C=C double
bond is called allylic halides. The halides in which the halogen is attached to sp2
carbon that has a double bond with another carbon is called vinylic halides.
Ethers are compounds in which an oxygen is bound to two carbon, alkyl or aryl, groups
(ROR). Sulfides (thioethers) are compounds in which a sulfur is bound to two
carbon groups (RSR).
The carbon that is attached to a side group such as a halogen, an alcohol, or an ether,
is called the alpha-carbon (a). A primary halide or alcohol has one alkyl group
attached, a secondary halide or alcohol has two alkyl, a tertiary has three alkyl groups
attached to the alpha-carbon.
Naming of alkyl halides, alcohols, ethers, this, and sulfides can be done using
substitutive nomenclature, or common nomenclature. The common name of alkyl
halide is constructed from the name of the alkyl group followed by the name of the
halide as a separate word (i.e. ethyl chloride, butyl bromide, etc). These compounds
name and formulas should be learned: allyl chloride (three carbons with a double bond
C=CCCl), benzyl bromide (PhCH2Br), vinyl chloride (two carbons with a
double bond C=CCl), and carbon tetrachloride (CCl4). Benzyl group is a phenol
group with an additional methyl group.
The haloforms are methyl trihalides, meaning, a methyl group (CH) has three halides
(i.e. Br3 or Cl3) attached to it: chloroform (HCCl3), bromoform (HCBr3), or (HCI3).
The substitutive nomenclature of alkyl halide follows same rules as alkane and alkene
naming (i.e. 2-chloro-3-methylhexane).
Common nomenclature of alcohols and thiols is derived by specifying the methyl group
to which the OH is attached (i.e. H3COH is methyl alcohol, PhCH2OH is benzyl
alcohol, etc). Compounds with two or more OH groups on different carbons are called
glycols. When naming glycols (more than one OH), remember to add diol, triol, and
so on suffix without dropping the e of the alkane (i.e. propane-1,2-diol or 1,2-
propanediol). If both OH and SH are present in a compound, the compound is
alcohol where SH is just a substituent called marcapto (i.e. 7-mercapto-5-methyl-3-
hept-2-ol).
Thiols are named in the common system as mercaptans (i.e. CH3CH2SH is called
ethyl mercaptan).
Substitutive nomenclature of alcohols and thiols involves a concept called the principle
group, a group on which the name is based (i.e. OH or SH are principle groups).
The principle group is also the name changing group; order the carbons such that the
principle group is closest to and part of the main parent chain. Name the alkane (alkene)
and group the e at the end and then add ol to it in case of alcohols (i.e. CH3CH2OH
is ethane + ol = ethanol). Same rule for thiols (i.e. Ch3H2SH is ethane + thiol =
ethanethiol) but e is not dropped.If there is no principle group then the compound is
named using substituted hydrocarbon rules.
Common nomenclature of ether is constructed by writing as separate words the two
groups attached to ether oxygen in alphabetical order and then adding the word ether at
the end (i.e. ethyl methyl ether). Sulfides are named in similar fashion but adding
sulfide at the end (i.e. ethyl methyl sulfide).
In substitutive system, ethers and sulfides are treated as side groups (not principle
group); the yl is dropped from the side group and oxy is added to it (i.e. C2H5O
group is ethyl + oxy = ethoxy). Sulfides are named similarly but the yl is not dropped,
just thio is added to the substituent (i.e. methylthio).
Cyclic compounds with rings that contain at least one atom other than carbon are called
heterocyclic compounds. Some common heterocyclic compounds should be learned:
furan, tetrahydrofuran, 1,4-dioxane, oxirane.
Epoxides are a class of three-membered rings of heterocyclic ethers that contain an
oxygen.
Intermolecular repulsion (non-covalent interaction) raises the energy of the interacting
species (it is energetically unfavorable). Intermolecular attraction lowers the energy of
the interaction species (i.e. ionic bond).
Boiling point can be used as a crude measure of intermolecular attractive forces. The
stronger the forces, the higher the boiling point. The boiling point of compounds
generally increases about 20C per carbon atom (i.e. boiling point go up with increasing
size or mass).
Larger molecules have greater Van der Waals attractions because of greater surface
area of interacting electron clouds. It is the surface area, not the volume of the molecule
that controls the boiling point. BP tends to be lower for highly branches molecules as
less area is available for Van der Waals attraction.
The polarizability of a molecule is a direct measure of how easy it is energetically for
an external charge (dipole) to alter electron distribution or cloud in a molecule or atom; it
is a measure of squishiness of electron clouds. Polarization increases van der Waals
attraction, and thus, raises the boiling point.
Hydrogen bonding is an intermolecular attraction that results from the association of a
hydrogen on one atom with an unshared electron pair on another. Hydrogen bond
requires two partners: the hydrogen bond donor (the atom to which H is attached
permanently) and the hydrogen bond acceptor (the atom with pair of electrons to be
shared). Hydrogen bonding accounts for the unusual high BP of alcohols.
Melting point is the temperature above which a solid is spontaneously transformed into
a liquid. Symmetry affects MP; it increases the MP. Symmetry lowers enthalpy of a
crystal.
Solutions are mixtures of molecules. A solvent shell, or solvent cage forms when
solute molecules are surrounded by and in direct contact with solvent molecules.
Entropy is a measure of probability. If a system goes from less probable state to a more
probable state, then entropy has increased.
A protic solvent consists of molecules that can act as hydrogen-bond donors (i.e.
water, alcohols, carboxylic acids). Solvents that cannot act as hydrogen bond donor are
said to be aprotic solvents (i.e. ethers, dichloromethane, hexane).
Polar solvents have higher dipole moments, hence, higher dialectic constant (e => 15).
Apolar solvents have low dielectric constant.
Donor solvents consist of molecules containing oxygen and nitrogen that can donate
unshared electron pairs (molecules can act as Lewis bases). Non-donor solvents cannot
donate unshared pair of electrons.
Larger alcohols are almost insoluble in water (because they are more alkanes than
alcohols). Hydrocarbon groups reduce solubility while hydrogen bonding increases it.
Xenobiotic is any substance that is not a normal constituent of living organisms.
Hydrophobic bonding is the association of hydrocarbon groups in aqueous solution.
Ionic compounds can exist in a solution in two states: ion pair, each ion is closely
associated (hang out with) with a molecule of opposite charge; dissociated ions are
free of opposite charge and are surrounded by solvent molecules called solvation cage
or shell. Solvation refers to the favorable interaction of a dissolved molecule with
solvent. When solvent molecules interact favorably with an ion, they are said to solvate
the ion.
Attractions between ions are called electrostatic attractions. The interaction between
a solvent molecule that donates a pair of electron (acting as a Lewis base) to a cation is
called the donor interaction. The interaction between the dipole of a solvent molecule
and the charge of an ion is called charge-dipole interaction. If a solvent is protic and
an anion can accept hydrogen bonds, the solvent can solvate the negative ion by a
hydrogen-bonding interaction; which stabilizes the ion.
A lipid is a compound that shows significant solubility in apolar solvent. Phospholipids
are lipids that contain phosphate group. Phospholipids have a polar head group (made
of ethanol amine, choline, and esterified phosphate), and a non-polar tails (made up of
hydrocarbons). The polar head group is ionic so it is well solvated by water. Molecules
that have discrete hydrophilic and hydrophobic groups, like phospholipid) are called
amphiphatic.Lipid bilayer is an example of hydrophobic bonding.
Ionophores are molecules that form strong complexes with ions.
Crown ethers are heterocyclic ethers containing a number of regularly spaced oxygen
atoms; they are synthetic ionopores. Crypttands, are nitrogen-containing analogs of the
crown ethers.

Chapter 9: Alkyl Halides

In a nucleophilic substitution reaction, a nucleophile donates an electron pair to an
electrophile to displace a leaving group. Conjugate bases of alcohols are called
alkoxides. In elimination reaction, two or more substituents are removed from a
molecule. In an alkyl halide, the carbon bearing the halogen is referred to a-carbon
(alpha-carbon), and the adjacent carbons to it are called b-carbon (beta-carbon).
Then, an elimination from two adjacent carbons to form a double bond is called B-
elimination. Think of B-elimination as a reverse of an addition reaction of alkenes.
The reaction for primary alkyl halides is typically nucleophilic substitution in the
presence of a strong base; and B-elimination for tertiary alkyl halides. For secondary
alkyl halides the reaction is in competition (50-50); they occur at comparable rates. Just
like acid-base reactions favor the production of a weak base (or acid), the nucleophilic
substitution reaction equilibrium also favors weaker acid/base production as a final
product. The rate of two reactions are compared by comparing their rate constant k. If
standard free energy of activation (G) is large, the rate is slow (and K is small), if it is
small, the rate is fast (and K is large).
A mechanism in which electron-pair donation by a nucleophile to an electrophile (usually
carbon) that displaces a leaving group from the same atom in a concerted manner
(without formation of intermediates) is called the SN2 mechanism. SN2 stands for
substitution-nucleophilic-bimolecular. Bimolecular means that both the nucleophile and
the substrate are involved in the rate-determining step. Increased alkyl halide
substitution on B-carbon slow downs an SN2 reaction due to steric effect. There is
inverse relationship between basicity and nucleophilicity between atoms in the same
group. Atoms with strong hydrogen bonding (i.e. F compared to I) will have relatively
slower reactions due to the bonding strength (harder to break). SN2 reactions are much
faster in polar aprotic solvents compared to protic solvent.
Protic solvents have O-H or N-H bonds. Why is this important? Because protic solvents
can participate in hydrogen bonding, which is a powerful intermolecular force.
Additionally, these O-H or N-H bonds can serve as a source of protons (H+). Aprotic
solvents may have hydrogens on them somewhere, but they lack O-H or N-H bonds,
and therefore cannot hydrogen bond with themselves
Nucleophilicity involves bond formation to atoms other than hydrogen, whereas basicity
involves bonding to hydrogen atoms.
The best leaving group in SN2 reactions are the one that give the weakest bases as
products. Weak base is a poor nucleophile.
Factors that determine a good nucleophile: charge, electronegativity, solvent, and steric
hindrance. Nucleophilicity increases with increasing electron density on a atom. So a
conjugate base is always a stronger nucleophile. Nucleophilicity (NP) increases with
decreasing electronegativity (because it is easier to snatch the electrons). Remember
nucleophilicity is the donation of an electron pair. In polar protic solvents, NP
increases going down the periodic table because of less and less hydrogen bonding
shell around the molecule in question making it easier to snatch the electrons. In polar
protic solvents, NP increases going up the periodic table.
A good leaving group is a weaker conjugate base. In substation reactions, we
generally go from stronger base (nucleophile) to a weaker base (leaving group).
Nucleophilic SN2 substitution mechanism involves opposite-side substitution and
inversion of stereo configuration. Reactivity is reduced with increasing substituents (on
both A- and B-carbons). Alkyl halides with three B-branches are unreactive.
A mechanism involving removal of a proton (H) by a base and loss of a halide ion (i.e.
Br-, Cl-, etc) is called an E2 mechanism (B-Removal).
The transition state is the state corresponding to the highest energy along the reaction
timeline (energy diagram). It has more free energy in comparison to the substrate or
product; thus, it is the least stable state.
A reaction in which the B-hydrogen being transferred (during the rate-limiting step) is
replaced by deuterium isotope (heavy hydrogen) will have a slower reaction. This effect
(of slowing down the reaction) is called primary deuterium kinetic isotope effect, or
simply, kinetic isotope effect (KIE). Substitutions of non-B-hydrogens have little or no
effect on the reaction rate. KIE is just the ratio of the rates of the two reactions (i.e.
Kh/Kd). The reason why the reaction is slower for deuterium is due to the stranger bond
of CD as compared to CH.
Syn-elimination is when the groups leave from the same side. Anti-elimination is
when the groups leave from opposite sides. Most E2 reactions are stereoselective anti-
eliminations. Anti-elimination happens more because there is no eclipsed conformation
in the transition state (unlike sun-elimination), and the base and leaving groups are on
opposite sides so no steric interference unlike syn-addition.
If more than one B-hydrogen present, then more than one alkene products possible; the
most stable (alkenes with most number of substituents at their double bond) is formed in
larger number. The higher the number of B-substituents & a-substituents, the more
change of B-elimination to take place relative to substitution. Highly branched base
favors elimination relative to substitution. Alkyls with no B-hydrogens cannot undergo B-
elimination. E2 B-elimination is promoted by strong bases.
A reaction of an alkyl halide with a solvent that acts as nucleophile (and where no other
base or nucleophile has been added) is called a solvolysis (bond breaking by solvent).
Solvolysis cannot occur via E2 because no strong base is present.
A substitution mechanism that involves a carbocation intermediate is called an SN1
mechanism. A B-elimination mechanism that involves a carbocation intermediate is
called an E1 mechanism. The rate-limiting step for both SN1 and E1 of an alkyl is its
rate of ionizationthe rate at which it forms carbocations. The product-determining
steps determine the relative amounts of different products formed.
SN1-E1 reactions are fastest in polar, protic, donor solvents.
Tertiary and secondary alkyl halides undergo solvolysis reactions by the SN1 and E1
mechanisms; tertiary alkyl halides are much more reactive.
If an alkyl halide has B-hydrogens, then both E1 and SN1 will occur (both products will
form).
Compounds that contain carbon-metal bonds are called organometallic compounds.
A Grignard reagent is a compound of the form RMgX (where X could be I, Br, or
Cl).
Organolithium reagents are compounds of the form RLi.
A carbon atom with three bonds and an unshared pair of electrons, and a negative
charge is a carbon anion called carbanion.
Protonolysis is any reaction with the proton (H) of an acid that results in the breakage
of chemical bonds.
Carbene is neutral divalent carbon atom with two unshared electrons and two bonds R
CR; it is highly reactive and unstable. It is formed by alpha-elimination. a-
elimination involves elimination of two groups from the same carbon. A carbene acts as
both an electrophile and a nucleophile. The empty 2p orbital attracts Pi electrons of
alkenes, thus acting as electrophile; and the unshared pair of electron wants to be
donated, thus acting as a nucleophile.
Reaction of a haloform with base in presence of alkenes gives 1,1-dihalocyclopropane
generally. The reaction is concerted and sun-addition. Cyclopropane without halogen
atoms can be prepared by reacting alkenes with methylene iodide in the presence of zn-
cu couple (zinc-copper alloy); this reaction is called Simmons-Smiths reaction. A-halo
organometallic compounds are sometimes called carbenoids. A carbenoid is a reagent
that is not a free carbene but has carbenelike reactivity. Addition of carbenes or
carbenoids to alkenes forms new carbon-carbon bonds.
Free-radical substitution reaction occurs by a free-radical chain mechanism. A more
reactive species (i.e. chlorine) is less selective (regioselective), and less reactive
species (i.e. bromine) is more selective. This inverse relationship of reactivity and
selectivity is called reactivity-selectivity principle.

Summary:
SN2 substitution reactions occurs with the inversion at chiral centers (i.e. if R to S or S
to R). The reaction is dependent on concentration of both substrate and nucleophile.
The reaction proceed via backside attack (180 from CHalide bond). This explains
inversion of configuration and also why alkyls with more substituents proceed slower
(i.e. due to steric hindrance).
SN1 substitution occurs with racemization of products, meaning a mixture of retention
and inversion at a stereo center. The reaction rate only depends on concentration of
substrate. Its a stepwise mechanism. After carbocation forming, the nucleophile can
attack from front or back resulting in mixture of retention. Faster for 3>2>>1 because
tertiary carbocation are more stable. Whatever factor stabilizes the carbocation,
increases the rate at which leaving group leaves, and thus, the reaction rate.
One key factor determining that a nucleophilic reaction will occur or not is the identity
of the leaving group.
SN2 tends to proceed with strong nucleophiles (i.e. negatively charged) such as
CN(-), HO(-), etc. SN1 occurs with weak nucleophiles (i.e. neutrally charged) such as
CH3OH, H2O, etc.
For elimination reactions, more substituted alkene is the most stable. The major
product of an elimination reaction is the more substituted alkene (Zaitesev rule). E1 is
stepwise while E2 is concerted. The hydrogen removed in E2 must be anti to the leaving
group (i.e. 180). If you have strong base, E2 most likely to occur.

Chapter 10: Alcohols and Thiols

Summary from Youtube videos:
The conjugate bases of alcohols are generally called alkoxides.
Tertiary alkoxides are more basic in solution than primary alkoxides. Primary alcohols
are more acidic in solution than tertiary alcohols. Alcohols are ROH, enters are R
OR, and thiols are RSR.
To convert OH into a good leaving group, use strong acid. Mechanism: first step, acid
protonates the alcohol. Second step, water leaves leaving carbocation behind. Third
step, proton (H) from adjacent carbon is lost to a water molecule or other base, and the
two carbons then form pi bond. Reaction proceeds via E1 for 3 and 2 (3 is the
fastest); 1 proceeds via E2. Carbocation rearrangements may occur. Removing water
via acid (sulfuric acid) or distillation shifts equilibrium towards right (products).
Alcohol dehydration will give alkene which is most stable (i.e. where the double bond
has most R groups coming off of it).
Mesylotes and tosylates are excellent leaving groups. Alcohols react with tosyl chloride
(TsCl) and pyridine to form tosylate (with retaining of stereochemistry).
Alcohols can be turned into sulfonate ester in the presence of sulfunylchloride (i.e. TsCl)
and pyridine (pyridine deprotonates things). Reason for doing this is so we can follow it
up with SN1 or SN1 reaction. Mechanism is as follow: alcohol attacks sulfur (which as
partial pos+ charge), which causes chloride to be kicked off. We are left with protonated
ester product as a result. To rid off the proton, pyridine in the solution will come and grab
the proton (giving the e- pair to oxygen) giving us final product, the sulfonate ester (also
called ROTs; R = side group, O=oxygen, Ts=tosylate). This is then followed by SN2 or
E2 reaction.
Most oxidation reactions we encounter are essentially glorified E2 reactions where the
leaving group is on oxygen. The oxidants used (PCC, H2CrO4, etc) are just different
ways of replacing OH bond with OLG (good leaving group).
Oxidation of primary alcohol with HOCl: OH attacks H from the acid and gets
activated. Next, SN2 occurs when OCl- attacks carbon while water leaves. Next, some
base will attack a-hydrogen; the donated e- pair will form double with oxygen, and the
oxygen will kick off the leaving group. The result is an aldehyde, a protonated base, and
an anion.

Notes from book:

Reaction which results in water lost is dehydration.
Dehydration of alcohols is a three step mechanism. First step is protonation of alcohol
group by catalyzing acid. Second step is water molecule departing resulting in
carbocation. Third step is B-hydrogen removal conjugate base of the catalyzing acid or
water resulting in alkene.
Loss of proton from carbocation is the rate-liming step in alcohol dehydration. OH in
alcohols must be converted to a good leaving group (H2O) first. One method is to use
acids. Another method is to use convert alcohols into sulfonate easters, which are
derivative of sulfonic acids (RSO3H). A sulfonate ester is a compound in which the
acidic hydrogen is replaced by an alkyl or aryl group. Sulfonate anions are weak bases
and good leaving group. A more reactive sulfonate ester than tosylate and mesylate is
triflate group (trifluoromethanesulfonate), OTf.
Thionyl chloride (SOCl2) can be used to convert primary alcohols to alkyl chloride. SN2
conditions can be achieved by reacting halide ion with a sulfonate ester in polar aprotic
solvent. Converting alcohols to alkyl bromide, triphenylphosphine dibromide (Ph3PBr2)
can be used.
Summary: Alcohols can be converted to alkyl halides using three methods discussed:
reaction with hydrogen halides, formation of sulfonate esters followed by SN2 with
halide ions, or reaction with thionyl chloride or triphenylphosphine dibromide. These
methods are used when non-rearrangement products are desired.
Carbonyl compounds are compounds containing group R,RC=O.

2 alcohols are oxidized to ketones in the presence of Na2Cr2O7 & H2SO4 (which
reacts to form chromic acid which is then used to oxidize the OH). Another reaction:
alcohol with K2Cr2O7 in presence of H2SO4 and then reacted with water gives
carboxylic acid.
1 OH can be converted to carboxylic acid by reacting with KMnO4 in basic (-OH)
solution.

1 can be oxidized to give aldehyde or they can be further oxidized to give carboxylic
acid. Using chromic acid will move reaction all the way to carboxylic acid. To stop
reaction at aldehyde formation only, milder reagent must be used. For example, PCC
(pygidinium chlorochromate) can be used to oxidize primary alcohol to aldehyde.

Groups that are chemically equivalent behaves the same way towards some chemical
reagent. If groups are chemically nonequivalent, then they have different behavior
towards some reagent. Groups in a molecule are chemically equivalent if they have the
same constitutional connectivity (p.489). So if two groups are constitutionally
different, then their chemical reactivity will also be different. But what if the two groups
are constitutionality equivalent? To see if they are also chemically equivalent, their
stereochemical relationship needs to analyzed. This can be done via substitution test.
This is done by rotating groups (120) via some specified axis and see if the original
molecule is obtained. If identical molecule is obtained, the constitutionally equivalent
groups are said to be homotopic. Homotopic groups are chemically equivalent and
undistinguishable under all circumstances (meaning they all react in same manner
towards some reagent). When substitution test gives enantiomers, the constitutionally
equivalent groups are said to be enantiotopic. Enantiotopici groups are chemically
nonequivalent towards chiral reagents but chemically equivalent towards achiral groups.
If substitution test gives diastereomers, then the constitutionally equivalent groups are
said to be diastereotopic. Diastereotopic groups are chemically nonequivalent under all
conditions.

Chapter 12: Spectroscopy

Spectroscopy is the study of interaction of matter and light. Absorption spectroscopy can
be used for structure determination. Matter absorbs energy form electromagnetic
radiation, which is a function of wavelength.
IR spectroscopy provides info about what functional groups are present in a molecule.
Nuclear magnetic resonance (NMR) provides info on the number, connectivity, and
functional-group environment of carbons and hydrogens.
UV spectroscopy provides info about the types of pi-electron systems that are present.
These techniques differ only in the frequency of radiation used.
Wave number ~v (nu) is the inverse of wavelength (lambda) so nu = 1 / lambda. Wave
number is just the number of wavelengths contained in a meter.
v = c / lambda = c(~v). Also, Energy = E = hv (h = plancks constant).
Percent transmittance (T) tells you how much light is absorbed. It is the ratio of the
intensity of the light emerging the sample (I) to the intensity I_o of the light entering the
sample. T = I / I_o. Where I is light transmitted back, and I_o initial intensity of light from
some source.

A higher force constant k means a stiffer "spring" (i.e. stronger bond). Therefore, a
stronger bond has a higher IR frequency.
Each peak in the IR spectrum corresponds to the absorption of light by a bond (which
makes the bond to vibrate). Understanding IR spectrum: some absorptions are
diagnostic, that is they indicate with reasonable certainty that certain functional groups
are present. Other peaks/absorptions are confirmatory; that is similar peaks can be
found in other types molecules. In other words, it gives a list of molecules that could be
present. To right of diagnostic absorption is the fingerprint region; its like the fingerprint
or identifier of a molecule.

The vibration frequency for a bond between two atoms of different masses depend more
on the mass of the lighter atom. The absorption frequency is also affected by the types
of vibration. Two types of vibration are stretching vibration and bending vibration.
Bending vibrations occur at lower frequencies (higher wavelengths) than stretching
vibrations of the same groups. Types of stretching vibrations: symmetrical, where both
atoms are stretching in and out of the central atom at the same time, antisymmetrical,
where one atom is going away from the central atom and the other one is going towards
the central atom. Types of bending vibrations: scissoring, where both atoms are coming
together and then away from each other in the plane of paper; rocking, in-plane vibration
where both atoms are rocking bath and forth like a pendulum; wagging, when both
atoms are coming out and into of the page at the same time; twisting, when one atom is
coming out of page while the other is going into the page. The bond length does not
change in bending vibration.

Molecular absorptions that occur but do not give rise to IR absorptions are said to be
infrared-inactive. Molecular vibrations giving rise to IR absorptions are said to be IR
active. A molecule is IR active if a change in dipole occurs. Symmetrical stretch has no
dipole change so it is IR inactive. Asymmetrical stretch and bending does result in
dipole change so it is IR active. Absorption peak does not happen if there is no change
in dipole moment.

A broad signal is indicative of polar objects (OH, NH, H-bonding) or C=O, so these
bonds tend to broad. Non polars (i.e. C=C or C to C triple bond) have sharp signal. As
mass increases wave number decreases. As bond energy increase wave number also
increase. As conjugation increase wave number decrease.

Internal alkenes have double bond in the middle (i.e. CC=CC) whereas terminal
alkenes have double bond at the end (i.e. CC=C).
Some useful absorptions frequencies:
Polar bonds (OH or NH) is between 4000-3000 cm-1.
OH band is about 3500-3300 cm-1.
C=O bond is between 1870-1700 cm-1.
CO bond is 1100 cm-1.
C=C bond is between 1670-1600 cm-1.
NH (1 amine) is 3500-3300 cm-1.
sp2 CH bond is 3000-3030 cm-1.
CH stretching ~2800-3000 cm-1.
Carbonyl stretch ~1735 cm-1.

Characteristic peaks of alkene stretching C=C occurs ~1650cm-1.

Double peaks at 910-990 cm-1 is indicative of CH=CH2 presence.
CH bending is ~800 cm-1 (presence of methyl).

Mass spectroscopy is used to determine the mass of a compound.

Original molecule denoted by M. Reaction of mass spectroscopy is follow: M + 1e >
M.(+) + 2e.
m/z is ratio of mass to charge but for all practical purposes, m/z is just going to be the
mass of the cation (not radical) since all particles will have charge of 1; so m/1 is just m.
Base peak is the highest peak vertically on the mass spectrum (it is 100%). If M is some
compound, then M+1 refers to isotope of M on a mass spectrum. Given % (or
abundance) of M and M+1, finding the ratio of (M+1)/M will you the number of carbon
present. Indicative of bromine presence is two peaks equal heights two units over.
Indicative of chlorine presence is two peaks two units over with one peak only 1/3 as tall
as the other.

Ionization and fragmentation in M.S.

Relative stability of the resulting radical and cation dictate the likelihood of each bond
breaking.
In a fragmentation reaction, a radical cation literally comes apart (dissociates). The
ionic part of the fragmentation is called a fragment ion. In spectrometer, ions are
separated based on mass to charge ratio (m/z). Only ions are detected by mass
spectrometer. The ion derived from the electron ejection before any fragmentation
occurs is called the molecular ion, M. Ms mass is equal to m/z. The base peak is the
ion of greatest relative abundance (and is assigned a relative abundance of 100%).
Chapter 13: NMR spectroscopy