CHM1321

http://www.saplinglearning.ca/ibiscms/course/view.php?id=5823
 Atomic structure
nucleus: p+ and ºn
atomic number: # of p+, identity of the atom
neutral ē = p+
 The electronic structure of an atom determines its chemical reactivity
 Orbitals (spdf)  each one of them can contain a max of 2ē
 An atomic orbital is a mathematical equation that describes the energy of an
electron
 **the square of the equation for the atomic orbital defines the probability of
finding an ē within a given region of space
 quantum numbers
 all s orbitals are spherically symmetrical
 the 2s orbital is larger than the 1s orbital
 the 2s orbital is farther from the nucleus and it has a higher energy than a 1s
orbital

 the three p orbitals in a shell are not spherically symmetrical

 ē density in each p orbital is concentrated in two regions or lobes: one on each
side of the nucleus
 the 2 lobes together are the orbital
 the p orbitals are often designated as px, py and pz.
 They are mutually perpendicular to one another and they are aligned along the x,
y and z axes
 Although the orientations of the px, py and pz orbitals differ, the ē in each p
orbital have equal energies

 The + and – signs on the orbitals refer to the phase of the orbital, not to the
charge of the orbital

Chapter 1. Carbon and its compounds

1.2. Organic Molecules from the inside out I: the modelling of atoms
 S orbitals:
*the probability of finding an ē is highest near the nucleus
*the probability of finding and ē decreases as the distance from the nucleus
increases
 P orbitals:
*equal probability of finding ē in either lobe of a p orbital
*the probability of finding an ē in the nodal plane of a p orbital is 0
 Ground state electronic configuration of atomic carbon:
*The carbon atom in the ground state has 6 ē occupying s-orbitals and p-orbitals
* shells further from the nucleus contain an increasing number of orbitals and
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 have a greater capacity for ē
*the first shell consists of a 1s-orbital containing 2 ē
*the 2nd shell is made up of one 2s-orbital and three 2p-orbitals which have a
combined capacity for 8 ē
 The ground state electronic configuration of an atom describes the arrangement
of ē in the lowest-energy state and is assigned by following 3 simple rules:
I. the lowest-energy orbital is filled first (Aufbau principle)
II. Each orbital can accommodate 2 spin-paired electros  (Pauli exclusion
principle)
III. Orbitals of equal energy successively accept a single ē until all are half full
(Hund’s rule)
 Applying these rules to carbon, the two lowest-energy ē are placed in a 1s-
orbital, the next two ē are placed in a 2s-orbital and the final 2 ē are placed with
parallel spins  in two of the 3 available 2p-orbitals (2px^1, 2py^1)
 The ground state electronic configuration of a carbon atom is 1s2, 2s2, 2p2

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 electrons 2 6 10 14
0 1 2 3
s p d f

E  
---- ---- ----
2px 2py 2pz


---- 2s


---- 1s

 (^^carbon) The three 2p orbitals are degenerate and have identical energies
 the 2nd most stable atomic orbital has this energy (2nd row from top to bottom)

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 ^^ 4 valence orbitals and 4 valence ē
 the most stable orbital is the one of lowest energy  two spin-paired ē in the 1s
atomic orbital
 valence orbitals: occupied orbitals of highest energy and any accompanying
empty orbitals of similar energy
 valence electrons: electrons found in valence orbitals

1.3 Organic molecules from the inside out II: bonding

 Ionic bonds: *occur when ē transferred from one atom to another
*electrostatic attraction between opposite charges
i.e.: NH4+Cl- CH3CO2- Na+ {salts}
 Covalent bonds: *arise due to sharing of ē between atoms
*each bonding atom usually contributes one ē to a bond (opposite spin)
i.e.: HH {high probability of finding ē between the 2 nuclei, since they are
equally attracted to both}

1.4 Organic molecules represented as Lewis Structures

textbook used (picked by myself not by my prof): get ready for organic chemistry
(2nd edition) Joel Karty
Lewis structures:
 Bonds are shown as lines between the elemental symbols of the atoms
 Reminder: valence electrons are the electrons that are ultimately involved in
bonding and chemical reactivity
 Lewis structures are only concerned with valence electrons
 The group number of the group in which an atom is found is the same as the
number of valence electrons it has
 Lewis structures show covalent bonding
 Atoms are especially stable when they have completely filled valence shells
 Non-bonded electrons are shown as dots arranged in pair around the atom they
are associated with

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 Systematic procedure for constructing Lewis structures of molecules
1. Count the total number of valence electrons
a. The number of valence electrons contributed by each neutral atom is the
same as its group number
b. If the total charge is -1, -2 or -3, ADD 1, 2, or 3 valence electrons,
respectively
c. If the total charge is +1, +2 or +3, SUBTRACT 1, 2 or 3 valence electrons,
respectively
2. Write the skeleton of the molecule, showing only the atoms and a single
covalent bond connecting each pair of atoms that you know must be bonded
together
3. Subtract 2 electrons for each single covalent drawn in step 2
4. Distribute the remaining electrons as lone pairs around the atoms
a. Start from the outside atoms and work inward
b. Attempt to achieve a complete valence shell for each atom
5. If an atom is lacking an octet, convert lone pairs from neighboring atoms into
bonding pairs of electrons, thereby creating double and/or triple bonds
 For convenience, lone pairs of electrons are often not shown explicitly. Unless
you are provided enough information to suggest otherwise, you can assume that
all atoms will have their octets

Formal charge:
 A deficit or excess of electrons
 Some atoms carry formal charges
 The formal charge is calculated by subtracting he number of bonds and non-
bonded electrons from the group number of the atom
oxygen is in group 6
it is surrounded by 3 bonds and 2 non-bonded electrons
FC= (group #) – (# of bonds) – (# of non-bonded electrons)
FC= 6- 3- 2 = +1

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Method of drawing Lewis structures (follow previous steps from 1 to 5 + the
steps below)

*A lone pair of ē on an atom is assigned to that atom

*For each bonding pair of electrons between atoms, one electron is assigned to one
atom and the other ē is assigned to the other atom
*After doing this, we just have to compare the number of valence electrons
assigned to an atom to the number of valence electrons the atom would have as an
isolated neutral atom (same as group number)
Then:
*An atom in a molecule has a formal charge of 0 if the number of valence electrons
it is assigned is the same as its group number
*Each extra electron contributes an additional -1 formal charge to the atom
*Each missing electron contributes an additional +1 formal charge to the atom

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 The sum of the formal charges on all the atoms in a species must equal the total
charge of the species
 Exceptions to the octet rule:
*incomplete octets: common for 1st row elements (C, B)
*expanded octets: common for elements in 2nd row and beyond (S, P)

1.5 Covalent bonds: overlap of valence atomic orbitals

 Covalent bonds are the result of overlap of atomic orbitals
 Direct (head-on) overlap results in a sigma bond

 Indirect (side by side) overlap results in a π bond

because a π bond involves indirect orbital overlap, it is weaker than a sigma

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 bond

 Unequal sharing of electrons: electron-rich and electron-deficient atoms:

Electronegativity:
 The ability of an atom to pull electrons toward itself from the surrounding atoms
to which it is bonded

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1.6 The shapes of atoms in organic molecules
 Tetrahedral (CH4), angle = 109º
 Trigonal planar (CH2O), angle =120º
 Linear (C2H2), angle= 180º

Predicting shape using VSEPR theory

 Valence, shell, electron, repulsion
 Most stable structure for a molecule is the one in which valence electron pairs
are as far apart as possible
 Minimizes electron-electron repulsion
 Repulsions dictate geometry
 AXmEn (A: central atom, X: bonded atom, E is a nonbonding valence electron
group, m and n are integers)
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1.7 the valence bond approach to electron sharing
 Linear geometries require sp orbitals

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 1.8 Resonance forms: molecules represented by more than one Lewis structure

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 a tool to describe electron delocalization in a molecule

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 1.9 Molecular orbital approach to electron sharing

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 This molecular orbital model can be used to explain why He2 molecules don't
exist. Combining a pair of helium atoms with 1s2 electron configurations would
produce a molecule with a pair of electrons in both the bonding and the *
antibonding molecular orbitals.

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 The total energy of an He2 molecule would be essentially the same as the
energy of a pair of isolated helium atoms, and there would be nothing to hold
the helium atoms together to form a molecule.
 The fact that an He2 molecule is neither more nor less stable than a pair of
isolated helium atoms illustrates an important principle: The core orbitals on an
atom make no contribution to the stability of the molecules that contain this
atom.
 The only orbitals that are important in our discussion of molecular orbitals are
those formed when valence-shell orbitals are combined. The molecular orbital
diagram for an O2 molecule would therefore ignore the 1s electrons on both
oxygen atoms and concentrate on the interactions between the 2s and
2p valence orbitals.

1.10 Other representations of organic molecules

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see pdf Get ready for Orgo Joel Karty Ch2

CH2. Anatomy of an Organic Molecule

2.2 Structural features of molecules
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Structure boiling point, color, chemical reactivity, mass, solubility, interactions
with light, mass
Functional group an atom or group of atoms that, because of its structure,
exhibits its own distinct patter of chemical reactivity

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2.3 Functional groups and intermolecular forces

 intermolecular forces: weak forces that exert on each other when they are in
close proximity
 types:
1- electrostatics
2- dipole-dipole interactions
3- hydrogen bonding
4- London forces
 they result from charge interactions
 electrostatic potential map: a plot of forces on a point charge measured at a fixed
distance from a molecule (figure: blue means electron deficient, red is electron
rich and green to yellow colors are in the middle)

1. electrostatic interactions: result from the presence of formal charges

2. dipole-dipole: attractive force between the negative end of a permanent dipole
in a molecule and the positive end of a permanent dipole in a neighboring
molecule or vice versa
a polar molecule has a net overall dipole

3. hydrogen bonding: attractive force between a lone pair of N or O atom in a

group and a H atom that is covalently bonded to a N or O atom in a

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 neighboring group

 Polar protic solvents act as hydrogen bond donors (Ex: H2O)

4. London forces aka dispersion forces: attractive interactions that exist between
all molecules in close proximity to each other. Result from small temporary
dipoles induced in each molecule by the other. Particularly important for non-
polar molecules (no net dipole)
The larger the difference in electronegativity, the larger the dipole moment. The distance between the
charge separation is also a deciding factor into the size of the dipole moment. The dipole moment is a
measure of the polarity of the molecule.

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 Formation of temporary dipoles:

2.4 Relation between intermolecular forces, molecular structure, and

physical properties
 Boiling point and melting point

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  Relative strength of intermolecular forces

 Solubility: like dissolves like

classes of organic solvents:

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2.5 Naming organic compounds

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IUPAC

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CH3
Molecules in Motion: conformations by rotations

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3.3 Steric strain

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3.4 Strains in cyclic molecules

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3.5 Conformations of six-membered rings

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3.6 Six-membered rings flip their chairs

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3.7 Six-membered rings with substituents

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Ch4
Stereochemistry: three-dimensional structure in molecules
4.2 Constitutional Isomers and Stereoisomers

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4.3 Chirality centers

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4.4 Cahn-Ingold-Prelog nomenclature

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4.5 Drawing enantiomers

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4.6 Diastereomers

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4.7 Meso Compounds

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4.8 Double-bond stereoisomers

substituents will stay on the same ( ) or opposite side (trans) of the double
bond  ≠  ….. trans -1,3-dimethylcyclohexame (example)

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4.9 Physical properties of enantiomers and diastereomers

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4.10 Optical rotation

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4.11 Optical purity
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4.12 Fischer Projections

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CH5
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Organic Reaction Mechanism (using curved arrows to analyze reaction
mechanisms

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5.3 Curved arrows and formal charges

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5.4 Intramolecular reactions

5.5 The stabilizing effect of delocalization

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5.6 Constructing resonance forms

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5.7 Evaluating Resonance form contributions

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5.8 Resonance and Orbital structure
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5.9 Patterns in mechanism

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5.10 Patterns in resonance

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------------------------------------------2nd midterm-------------------------------------
CH6
Electron movements in Brønsted Acid-Base reactions

o Acid is a proton donor

o Base is the acceptor
o A Lewis base donates an ē pair to a proton
o In all reactions, electrons move from a region of high electron density
(electron source), such as a lone pair or bonding pair of electrons, to a region
of lower electron density (electron sink), such as an empty orbital.
o When a Brønsted acid loses a proton, its conjugate base is formed; when a
Brønsted base gains a proton, its conjugate acid is formed. In any Brønsted
acid–base reaction there are two conjugate acid–base pairs. The conjugate
acid–base relationship is always across the reaction arrow. This is an acid-
base reaction between the two functional groups located on the ends of a
bigger structure. Recall that curved arrows indicate the flow or \"movement\"
of electron pairs. A curved arrow is always drawn with its tail at the source of
electrons (a bond or unshared pair) and its head at the destination.
o Electron-withdrawing substituents increase the acidity of carboxylic acids
due to the inductive effect. The more electronegative an atom is, the more
electron-withdrawing the substituent. Since fluorine is the most
electronegative, the fluorine-substituted carboxylic acid is the most acidic,

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 followed by the chlorine-substituted carboxylic acid, and the bromine-
substituted carboxylic acid.
o Consider the influence of carbon hybridization on the pKa of each
hydrocarbon class; sp carbon atoms are more electronegative, and thereby
more acidic, than sp3 carbon atoms. Likewise, sp2 carbon atoms have an
electronegativity and acidity between that of sp and sp3 carbon atoms.
The acidity of an alkyne (pKa ≈ 25) is greater than that of amines (pKa ≈
35–40), so HC≡CH > H3CNH2. Although HF isn't considered a strong acid, it
is relatively the strongest acid of the given choices. Thus, the final ranking
is HF > HC≡CH > H3CNH2 > H2C=CHCH3 > CH4
o  sp>sp2>sp3 acidity for hydrocarbon groups
o alkyne > alkene > alkane  HC≡CH > H2C=CHCH3 > CH4.
o Carboxyl group: carbon atom double bonded to an oxygen atom and single
bonded to a hydroxyl group (OH) (another way to view it is a carbonyl group
(C=O) that has a hydroxyl group (O-H) attached to the carbon atom.
Commonly written as: -C(=O)OH or –COOH

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 o Carboxylic acids (pka ~ 4) > acidic than alcohols (pka ~15) due to the
resonance stabilization of the conjugate base’s negative charge on the
carboxylate oxygen. The easier a proton is to remove, the more acidic the
compound, and the lower the pka
o Electron-withdrawing substituents will also increase acidity of both
carboxylic acids and alcohols, due to the inductive effect.
o The carbonyl group will help stabilize the negative charged formed after
proton loss
o The stronger the acid, the weaker will be its conjugate base
o The larger the pka of the conjugate acid, the stronger the base
o Electronegativity increases, acidity increases
o CNOF
P S Cl
Br
I increasing electro(-)
o DON’T FORGET: the lower the pka the higher the acidity
o Be careful not to confuse relative strength with classification. The conjugate
of a weak acid is not a strong base, it is simply a stronger weak base than
the conjugate of a stronger acid. The conjugate of a strong acid is so weak
that it is neutral, and arguably not a base at all.
o The Equilibrium arrow: This shows a reaction that is reversible, usually in
the context where the reversibility is being highlighted (such as in a reaction
mechanism). To further highlight the position of an equilibrium, you may also
occasionally see one of the arrows being longer than the other, showing that
the equilibrium favors the starting materials or products
o If
 the
 arrow
pointing
 towards
 the
 reactants
 is
 longer
 than
 the
 arrow

pointing
 to
 the
 products,
 it

reflects
 that
 the
 reaction
 will
 reach


equilibrium
 when
 there
 are
 more
 reactants
 than
 products
 presen

t
 in


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 the
reaction.
 If
 the
 arrow
 pointing
 to
 the
 products
 is
 longer,
 it
 sho
ws
the reaction reaches equilibrium
when
 there
 are
 more
 products
 present.


o Prediction of equilibria: pka values can be used to predict whether an acid-

base equilibrium will favor the reactants or the products:
1- the acid has the highest pka and is the weakest acid equilibrium favors
towards it
o when making qualitative predictions, compare the stabilities of the charged
species
ACID–BASE PROPERTIES OF CARBOXYLIC ACIDS
o acidity of carboxylic acids is one of their most important chemical properties.
This acidity is due to ionization of the O—H group
o http://www.saplinglearning.com/media/loudon/loudon5ech20sec04.pdf
o http://www.saplinglearning.com/media/loudon/loudon5ech03sec04.pdf
o http://www.chemistry-drills.com/functional-groups.php?q=simple
o the conjugate bases of carboxylic acids are called generally carboxylate ions.
o Carboxylate salts are named by replacing the ic in the name of the acid with
the suffix ate
o E.g.: sodium acetate (acetic – ic + ate = acetate)
o Carboxylic acids are among the most acidic organic compounds.
o Carboxylic acids are more acidic than alcohols or phenols, other compounds
with O—H bonds
o So basically when going from acid to base (carboxyl group), the conjugate
base is composed of an cation (+) and an anion (-)  negative charge on the
single bonded oxygen
R-C=O
O(-) Na+
o don’t forget that curved arrows indicate movement of electrons (loss)
o the closer the electro(-) atom is to the carboxylic acid, the more acidic the
compound is due to the inductive effect
o http://www.saplinglearning.com/media/loudon/loudon5ech14sec07.pdf

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 o the stronger the acid, the lower the pka
o across a row in periodic table, acidity increases with the increase in
electronegativity
o as we go down a group, acidity increases with the decrease of
electronegativity
o The ionization process depends upon the breaking of the bond to hydrogen, so
the weaker the H–X bond, the stronger the acid. Bond energies usually
decrease down a group, because the distance between nuclei increases. In
other words, a greater charge separation between H and the atom it is directly
bonded to causes that H to be more acidic. A more electronegative atom
attracts electrons more than a less electronegative atom. Recall that
electronegativity increases as you move up and to the right in the periodic
table. A positively charged atom attracts electrons much more than a
neutral atom of the same element.
o Element effect: identity of the atom to which the acidic hydrogen is attached.
Brønsted acidity increases as the atom to which the acidic hydrogen is
attached has a greater atomic number within a column (group) of the periodic
table.
o How halogen substituent affect acidity? Electronegative substituent groups
such as halogens increase the acidities of carboxylic acids by stabilizing their
conjugate-base carboxylate ions
o They have an acid-strengthening polar effect on the acidity of carboxylic acids
o Polar effect = inductive effect =
o The increase in acidity that results from increasing the positive charge on the
atom bonded to the acidic hydrogen = charge effect
Protonation
o Acids  protonated form when ph < pka
o Deprotonated from when ph is > pka
o If ph ~pka, a mixture of protonated and deprotonated state is observed
o Acidity  acetic acid > acetamide > acetone
CH7

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 o ELECTROPHILE: a group or atom that accepts electrons, carbon atom
of carbonyl group is electrophilic (the one affected by the most
electronegative or movement/resonance of pi bonds)
o NUCLEOPHILE: a group or atom that donates or shares electrons (most
electronegative, also, pi bonds have high density)

o An electrophilic site is electron deficient. When a carbon is bonded to an

electronegative heteroatom, the bond is polarized, and a partial positive charge
on the carbon makes it electrophilic. A nucleophilic site is an electron-rich
atom that can share its electrons with an electron-deficient atom (an
electrophile). Heteroatoms with a lone pair of electrons are nucleophilic. Both
reactant molecules have an electronegative heteroatom with lone pairs of
electrons: oxygen in ethanol and bromine in ethyl bromide. You need to
determine which one acts as a nucleophile in this reaction. Look at the organic
product molecule, diethyl ether. What new bond was formed in the reaction?
What atoms formed this new bond? What atom acted as a nucleophile? What
electrophilic atom did it attack? Select only one atom for the electrophilic site
and one for the nucleophilic site.
o If a site is more stable  the site is more basic

o Nucleophilic reaction involving a prochiral ketone carbon atom reacts with a

nucleophilic hydride ion source (K- or LiAlH4) and subsequently a proton
source H2O or H+
o The first reaction presented is a hydrogenation, where two hydrogens are
added to each alkyne carbon. The reaction is a reduction, since there is an
increase in the number of C–H bonds in the product. Recall that oxidation
number is the charge an atom would have if bonding electrons were arbitrarily
assigned to the more electronegative atom. The oxidation number of each
alkyne carbon also decreases from 0 to –2, confirming the reaction is a
reduction. The second reaction presented is a bromination, where two
bromines are added to each alkyne carbon. The reaction is an oxidation.
Like oxygen, bromine is more electronegative than carbon and an
increase in the number of oxygens (or electronegative atoms) on a carbon
is an oxidation. Thus, the oxidation number of each alkyne increases from 0
to 2, confirming the reaction is an oxidation. The last reaction presented is a
hydration where one oxygen is added to one alkyne carbon and two
hydrogens are added to the other alkyne carbon. The overall reaction is
neither an oxidation nor a reduction. One carbon increases the oxidation
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 number from 0 to 2, while the other decreases the oxidation number from 0 to
-2. Thus, the overall oxidation state remains the same.

o The Grignard reagent is an anionic source of carbon that acts as a

nucleophile. This nucleophile will attack the electrophilic aldehyde at the
carbonyl carbon breaking the carbon-oxygen pi bond and giving the
electrons to the oxygen in the first step. The resulting alkoxide forms an ion
pair with the magnesium bromide. The addition of acid in the second step
provides the oxygen anion with a hydrogen from the hydronium ion. In this
step, non-bonding electrons from the alkoxide oxygen attack a hydrogen on
the hydronium to form an alcohol and a water molecule. The final organic
product is a secondary alcohol.
o Grignard reagents are very strong bases and good nucleophiles. If a
functional group is acidic or reactive to nucleophiles and it resides on the
Grignard bearing compound, then there will be a self-reaction usually in the
form of a cyclization (when a electrophile is present) or destruction of the
Grignard reagent (when an acidic proton is present)
o Feasible vs unfeasible reagents: ***not all functional groups are compatible
with Grignard reagents:
o Alkyl, alkenyl, and aryl functional groups are compatible with Grignard
reagents.
o Grignard reagents will deprotonate carboxylic acids and alcohols in an acid–
base reaction. unfeasible
o Grignard reagents can act as nucleophiles and react with carbonyls.
o

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