Molecular modeling kid for organic chemistry

Review Chapter 1 and also do the assigned problems for the class
Chapter 1
-Organic chemistry is the study of the covalent compounds of carbon and the transformations that
they undergo
*Reactions occur as a result of the motion of electrons
-Distinction between organic and non-organic compounds
-Difficult to isolate and purify (organic)
-Upon heating, they decomposed more readily than inorganic compounds
-Vitalism (nonorgo can't turn into orgo. comp without outside force)
-Dealt blow with Wohler and his conversion of ammonium cyanate to urea
-Led to new definition of organic and nonorganic matter based on carbon atom presence
-The Structural Theory of Matter
-August Kekule, Archibbald Couper, Alexander Butlerov
-Defined that substances are defined by a specific arrangement of atoms, their constitution
-Same molecular formula with different constitution - constitutional isomers
-Also, Theory stated each element will generally form predictable number of bonds
-Carbon, four bonds, tetravalent
-Nitrogen, three bonds, trivalent
-Oxygen, two bonds, divalent
-Hydrogen, one bond, monovalent
-Carbon is unique
-2*10^7 compounds of carbon
-10^5 compounds of all other elements
-Why carbon forms so many compounds?
*Carbon forms strong covalent bonds to both electropositive and electronegative
elements
*Carbon has a valence of 4
*Carbon atoms bond strongly to each other making long chains and ring structures possible
-Average bond dissociation energy
~Close to 83, C-C, pretty high
-Usually bonding to themselves disfavors high BDEs
Electrons, Bonds, Lewis structure
-Existence of electrons proposed in 1874 by George Stoney
-J.J Thompson provided evidence of Stoney, known for discovering the electron
-Gilbert Lewis defined covalent bond
-Result of two atoms sharing a pair of electrons
-Energy diagram for two hydrogen atoms trying to bond
-As each atoms approaches either

1897

-Force of repulsion arising between negatively charged electrons

-Force of repulsion by positvely charged nuclei arising
-Force of attraction between positive and negatively charged electrons
arising
-Under these circumstances, electrons move to minimize repulsive forces,
maximize attraction forces
-Leading to net force of attraction, lowering energy of system, lost as heat
-Nuclei get close until nuclei achieve separation of 0.74 angstroms, causing
energy to increase, explains energy diagram (pg 5)
-Lowest point of diagram most stable due to lowest energy, determines bond
length and bond strength
-Lewis used idea of bonds to create lewis structures
-Octet rule- atoms have tendency to achieve electron configuration of noble
eight valence electrons
-Lone pair- nonbonding pair
-Formal charge- Appropriate number of valence electrons are not present on
-For formal charge, bond will count only as 1 electron
-Oxygen for ex. if it has seven V. elec. it has a negative formal charge

gas,

atom

-Bonds in three categories

-Covalent
-Polar Covalent
-Ionic
-Based on electronegativity of atoms or the ability to attract electrons
-If difference in electronegativity is less that 0.5, consider covalent
-Between 0.5 and 1.7, consider polar covalent
-Leading to induction or withdraw of electrons toward atom, leading to
partial positives and partial negatives
-Greater than 1.7, electrons are not shared at all, ionic bond result of
attraction between two oppositely charged ions
-Some bonds are not so clear cut in what type they are
-Atomic Orbitals
-Louis de Broglie suggested that electrons exhibit wavelike properties
-Schrodinger, Heisenberg, and Dirac proposed mathematical description of the wavelike
properties of electrons
-Called quantum mechanics
-Wave equation used to describe total energy of hydrogen atom, wavelike
properties of electrons
-Wave equation solved to provide solutions called wavefunctions (psi)
-Used to describe energy of electron is quantized, discrete energy levels
-Wavefunction is function of spatial location, allows assignment of numerical value for each
location in 3D space relative to nucleus

-Square of number is probability of finding electron in that location

-All combined to produce atomic orbital
-Wavefunction is dependent on location
-Like wavefunctions, orbits can also have negative, positive, and zero
values/nodes to indicate phases
-No electron density at node
-Electronic structure of atoms
-Orbitals are regions in space around the nucleus of an atom where an electron is
be found, occupied by electron density
-Orbital vs. Cloud analogy
-Clouds come in various sizes, electron clouds only come with limited
shaped spaces and sizes
-Clouds have lots of rain molecules, electron cloud more like one entity
-Clouds with defined edges, electron clouds have no defined edges,
electron density
-Examples of atomic orbitals are s, p, d, f orbitals
-Atomic orbitals cont.
-Energy of electron depends on type of orbital that it occupies
-Electrons lowest in energy when occuping a 1s orbital, closest to nucleus and it
nodes is reason why
-2s orbital has one node and is farther away from the nucleus so more energy
-Degenerate orbitals- like three 2p orbitals, same energy level

likely to

has

no

-Aufbau principle- filling lowest energy orbitals first

-Hund's rule- With degenerate orbitals, one electron is placed in each orbital first
before
electrons are paired up
-Pauli exclusion principle- Each electron has unique set of quantum numbers, each orbital
can have at max two electrons w/ opposite spins
-For each period, n increases by 1
-Valence bond model and molecular orbital model
-Covalent bonds are formed by overlap of atomic orbitals, these two models are
describe nature of overlap

used to

Valence bond Theory

-Wave properties of electrons are reflected by how orbitals interact
-Interference occurs between either valence shell orbitals or atomic orbitals
-Can be constructive to produce larger amplitude or destructive to make a node
-VBT- bond is sharing of electron density between two atoms from constructive
interference of atomic orbitals (Linus Pauling), also known as localized electron
pairing

-The smaller the particle, the bigger the wave

-Area of space where you can find the electron of a nucleus- wave^2
-Sigma bond- circular cross section with respect to bond axis, distinguished by cylindrical
symmetry along nuclear axis (free rotation along bond axis 360),
strongest
Molecular Orbital Theory
-Overlap of atomic orbitals described constructively and Deconstructively
*VBM does not have molecular orbital
-Math method- LCAO, used to combine and produce new orbitals called MOs
-Forms two MOs (bonding and anti bonding)
*Bonding- most of electron density are between two nuclei (zero nodes), lower
energy, constructive
*Anti bonding- barely any electron density between two nuclei (one node),
higher energy, destructive
-Both electrons occupy MO to be in lower energy state = essence of bond
*In MO model, the atomic orbitals are replaced by molecular orbitals that cover
entire molecule, to summarize atomic orbitals are assoc. with individual atoms, while
MO are assoc. with entire molecules
-HOMO- Highest Occupied, -LUMO- Lowest Unoccupied
Hybridized Atomic Orbitals
-A valid model of bonding must rationalize molecular shape, bond angles, bond lengths, and bond
dissociation energies
-Methane- colorless gas, smelly
-Shape- tetrahedral
-Bond angles of 109.5
-four equivalent bonds length 109pm (closer together due to hydrogen being smaller)
-C-H bond dissocation energy of 439 kJ/mol
-Electron configuration cannot satisfactorily describe bonding structure
-Look at energy diagram for electronic configuration of carbon
-Only two unpaired electrons, meaning that carbon can only form two bonds
-This is false, so imagine one electron was moved from 2s to 2p orbital, so it
would be in its excited state
-Now, four unpaired atomic orbitals exist, capable of up to four bonds
-However, methane had tetrahedral geometry of 109.5 on all bond angles
-Could not be explained with one 2s and three 2p orbitals. cannot make 109.5
bond angles because P orbitals are separated by only 90 degrees
-Linus Pauling found a solution, suggesting that by averaging or hybridizing
the
2s orbital and three 2p orbitals, they would be degenerate or even
hybridized
atomic orbitals, allowing for 109.5 bond angles
-Doesn't actually happen in real life, math procedure to explain concepts
-the *sp^3 atomic hybridized orbitals are not symmetrical, larger front lobe
allowing for more efficiency in forming bonds compared to p orbitals, will only

form single bonds, so if you see carbon with single bonds, assume hyridized
orbitals and it will be tetrahedral
-VBT: Four sigma bonds between overlap of sp^3 hybridized orbitals and 1s
orbital from hydrogen on methane
-Methane: assume a plane on carbon and two hydrogens, you will notice that
one hydrogen is pointed towards you, and one is pointing behind
MO cont.
-Combining of of sp^3 atomic orbital and 1s atomic orbital produce bonding
antibonding MO
-Notice that on the bonding MO, electrical density is focused on center
-By providing heat, you can excite one of the electrons from the bonding MO
the antibonding MO
-Hybridized = lower energy

and

to

C2H6 Ethane
-Sp^3- any carbon with single bonds is sp^3 remember!
-Carbon is tetravalent = forms four bonds = always
-1.54 Angs. or 154 pm
-Single bonds are longer than double bonds
Double bond and sp^2 hybrid.
Ethylene (ethene)
-Geometry: Planar
-Bond angles : close to 120
-Bond distances C--H = 110 PM and C=C = 134 PM
-Bond dissociation energy : 174 kcal/mol
-Gas, most produced organic compound in the world, much to plastic
-Naturally produced, used to ripen tomatoes, produced by plants in order to
and turn yellow/brown, winter is coming!!!!!!! CORN
Bonding of Ethylene
-Instead of using three 2p and one 2s, used two 2p and one 2s to make three
degenerate sp^2 orbitals with one atomic p orbital
-*Trigonal planar shape with sp2 bond angles of 120 always!
-sp^2 33.3% s orbital + 66.7% p orbital
Valence bonding
-Pi bond edge on overlap of two atomic p orbitals, no free rotation, but
interaction on both ends of the p orbitals
-Sigma bond end on overlap of two sp^2 hybrid carbon orbitals, free
rotation, with rest of sp^2 orbitals forming sigma bond with H atoms
Molecular bonding

die

-Pi bonding in molecular orbital model - Two atomic 2p orbitals form a

bonding and antibonding orbital
-Pi bonds are seen on p orbitals, edge on overlaps
Triple bonds and sp hybridization
Acetylene (ethyne)
-Geometry: linear
-Bond angles: 180
-Bond distances: C--H = 106 PM and C---C (triple) = 120 PM
-Bond dissociation energy = 230 kcal/mol
-Oxygen reacts with Acetylene to make a very hot flame
-Used alot in the polymer industry, colorless odorless gas
Bonding in Acetylene
-Linear Shape
-Sp bond angles of 180
-One s orbital hybrid. with one p orbital for sp hybrid.
-2 atomic p-orbitals left untouched
-2 hybrid sp orbitals and 2 atomic p-orbitals are results
-Sp = 50% s and 50% p
-Summary: formation of two degenerate sp orbitals
Valence bond model
-Triple bond of one sigma bond and two pi bonds which are only edge on
-For triple bond, overlap end on of two sp orbitals, two pi bonds from
overlap edge on of two pi orbitals
Molecular bond model
-Three orbitals of two p orbitals and 1 sp hybridized orbital found on both
sides of the model, leading to product of six MOs for bonding and
antibonding
-*You will end up with one MO for every AO
*Practice finding hybridization of carbons
Bond strength and bond length
-Single bonds
-Only one interaction
-Longest bond
-Also weakest
-Double bonds
-Only two interactions
-Stronger than single, weaker than triple
-Shorter than single

-Triple bonds
-Only three interactions
-Strongest between the two
-Shortest in length
-Steric number and VSEPR Theory
-Steric number- total number of sigma bonds and lone pairs, indicates number
electron pairs repelling each other
-Causing electron pairs to rearrange themselves to farthest distance
-Steric- 4- SP3, Steric- 3- SP2, Steric- 2- SP

of

-Dipole moments and molecular polarity

-Induction- presence of a electronegative atom
-Dipole moment- center of neg. charge and center of positive charge are
separated from one another by certain distance
-Dipole moments are used to indicate polarity, define as amount of partial
charge times the distance of separation
-Units of Debye (D) can be used
-When more than one polar bond is observed, necessary to take vector sum of
individual dipole moments, called molecular dipole moments
-Takes into account magnitude and direction of each individual dipole
moment
-Presence of lone pair has effect, dipole moment w/ every lone pair, does
not affect direction of MDM
-Intermolecular forces and Physical properties
-Physical properties ae determined by intermolecular forces
-All IF are electrostatic, forces occur as result of attraction between opp. charges
-Three types
-Dipole dipole
-Net attraction between molecules results in higher melting point and
boiling point
-Solid phase- align to attract each other
-Liquid phase- Dont really attract or repel, just tumble in space
-Hydrogen bonding
-Attractive dipole dipole interaction can occur with any protic compound.
This means any compound that has a proton connected to an
electronegative atom
-Strong because hydrogen is small, partial charges can get close to each
other
-Fleeting Dipole Dipole interactions
-Have no permanent dipole moments but strong intermolecular forces
-Hydrocarbons- BP increases with molecular weight, due to london
dispersion forces as electrons/center of partial negative charge moves
and does

not coincide with partial positve center at times

-Large hydrocarbons have more surface area, attractive forces faced w/
larger extent with more interactions
-Branching causes decrease in boiling point
-Isomers
-Compounds with the same molecular formula, but different bonding
arrangement in 3D space
-Constitutional/structural isomers are compounds with the same molecular
formula but possess different atom connectivity
-Formula: C2H6O
-Dimethyl Ether (BP of -23 C)
-Ethanol (BP of 78.4 C)
-1-butanol works as a great solvent and a fuel (extra)
-1. Number the carbons
-2. Identify the atoms with lone pairs
-3. Write down your lone pairs
-Kekule Structure vs. Lewis Structure: Kekule doesn't have lone pairs
-Condensed structure: bonds and lone pairs aren't visible, just writing it down
-Line structure and stick structure on top side, carbon and hydrogens are invisible
-Don't mix the types of structures or you'll get them wrong
Chapter 2
-Different types of structures
-Lewis structures: atoms and bonds drawn
-Partially condensed structures: C-H bonds aren't drawn
-Condensed structures: Single bonds are not drawn
-Too complicated for larger structures
-Bond-line structure used to simplify larger structures
-Lines are drawn between atoms to show covalent bonds
-Zigzag format with each corner or endpoint representing a carbon atom
-Double bonds are shown with two lines, triple lines are shown with three
-Bond line structures must represent bond angles
-For ex. Triple lines are not in zigzag format because it is sp hybridization or
degrees
-Hydrogen atoms bonded to carbon are also not shown
-How to Draw the Bond-line structures
-Carbons atoms in straight chain are in zigzag format
-Drawing double bonds, have angles as far apart as possible
-Direction of bonds for single bonds are irrelevant
-All heteroatoms or atoms other than oxygen and hydrogen must be drawn

180

-Label hydrogens on them as well

-Never draw carbons with more than four bonds
-Get more practie with skillbuilders
-Easier to find functional groups
-Characteristic group of atoms/bonds that possss a predictable chemical
behavior
-Classification of organic compounds is based on functional groups
-Memorize the functional groups given in the chart
-***A carbon atom will generally have four bonds only when it does not have a
charge
-Whether positive or negative, carbon will have three bonds rather than four
-When positive, carbon atom is missing an electron, only forming three
-When negative, one lone pair will be formed, allowing for three bonds
-Only difference is fourth orbital: to hold a lone pair or be empty

formal

-Identifying lone pairs

-Need to know number of lone pairs to know formal charge, vise versa
-Bond line structures are only complete when it contains all lone pairs or all
formal charges
-Three dimensional bond line structures
-Wedges and dashes to indicate dimensionality, W towards you, D behind
molecule
-Fischer projections for acyclic compounds while Haworth projections for cylic
-Defect of bond line structures
-Implies bonding electrons are confined to region of space in between two
atoms
-Not necessarily true, electron density could be spread out over the
entire/large region of the molecule
-Molecular orbitals fit the idea of thinking of the molecule as a whole
-Associated with two ends of the system rather than one
-How do we draw a positive charge that is spread out over two locations? How
we draw two Pi electons that are associated with three carbon atoms
-To deal with this, resonance is used
-Use theoretical concepts to draw more than one bond-line structure and
meld them together
-Separate the resonance structures with straight, two headed arrow and
brackets
-Used to indicate that drawings are of one entity, need both drawings
to show and explain the characteristics of the structure
-Show that the charge which is in this case positive is spread out over two

do

locations on allyl cation

-Spreading of charge is called delocalization, spreading of negative or positive
charge stabilizes a molecule called resonance stabilization
-Each curved arrow has a head and tail
-Just to represent the idea if the electrons moved to another location
-Not actually representing the actual motion of electrons
-Two rules that must be followed
-Avoid breaking any single bonds
-Never exceed an octet for second rule elements
-Not considered a violation if underviolating octet for 2nd row elements
-Delocalization of electrons (lecture)
-Electrons exist in orbitals that span a greater distance giving the electrons
freedom minimizing repulsions

more

-Formal charges in resonance structures

-Based on formation and use of lone pairs and bonds
-Formal charge affects stability and reactivity of molecules, must be able to
identify formal charges (lecture)
-Answers: 0, -1, 0, +1 (carbocation), -1
-If youre given the formal charge, can you find number of electrons
-#e = atom valence - # bonds - FC
-0, 1, 2, 2 talking about the electrons not paired, makes sense
-Five patterns of resonance structures
-Allylic lone pair
-In a carbon carbon double bond, the carbons connected via double bond
are in vinylic positions, while the atoms connected to the carbons are in
allylic
positions
-Identify lone pairs in allylic positions
-Draw one curved arrow going from lon pair to form pi bond
-Draw another arrow going from pi bond to form lone pair
-Allylic positive charge
-Identify positive charges in allylic positions
-Draw curved arrow from pi bond to form new pi bond, moving formal
charge to the opposite end of the system
-Two pi bonds separate from each other by one sigma bond - conjugated
-Never place the tail of a curved arrow on positive charge
-Lone pair adjacent to positive charge
-Draw curved arrow from lone pair to form a pi bond between lone pair
and positive charge

-Conservation of charges!
-Exception with nito group: must be drawn with charge
-Pi bond between two atoms of different electronegativity
-For example, C=O bonds
-Move pi bond up to electronegative oxygen as lone pair
-Creating charges on the way
-Conjugated pi bonds in a ring
-Pi bonds sparated from each other by sigma bond
-When conj. pi bonds are enclosed in a ring of alternating pi and sigma
bonds, push all pi bonds by one position
-Resonance structures and major contributors
-1. Minimize charges
-2. Electronegative atoms
-As long as atoms have octets, it is okay for N, O, Cl to have + charge
-3. Avoid drawing resonance structure in which two carbon atoms bear
opposite charges
-Remember, sp3 will not have any resonance structures since there are no
empty p orbitals
-2.11 The resonance hybrid will most resemble the more stable contributor
-Delocalized and localized lone pairs
-Whenever a lone pair is delocalized, it will occupy a p orbital rather than a
hybrid orbital in order to interact with pi orbitals in pi bond, must be taken
into account when thinking about geometry
-localized lone pair- does not participate in resonance due to reasons for
example like nitrogen where one pair is already being usd to overlap with
other p
orbitals
-Memorize the functional group and the name of the functional group of 2.3 on ppt.
and also memorize priority order, if carbon is bonded to three other things that are part of
functional group, meaning higher priority, one group with carbon
group
is
lower
priority, important in nomenclature
-Resonance structures (lecture additional)
-Can only move pi electrons to adjacent atomic p orbitals
-Never move electrons in hybrid orbitals
-Never move atoms
-Never move or break sigma bonds
-Resonance structures cannot have more than 8 electrons on an atom
-Resonance structures can have fewer than 8 electrons on an atom

-There must be conservation of overall charge on molecular resonance

structures
-Conservation of charges
-Negative charged carbon is usually sp3 hybridized
-Chapter 3
-Bronsted- Lowry acids and bases
-Transfer of H+ or proton
-Acid is proton donor, and base is proton acceptor
-Conjugate base and acids are products of reaction
-All actions completed with flow of electrons
-Using curved arrows to show flow of electron density or motion of electrons
-Arrows represent actual physical process by showing reaction mechanism
-Base functions to abstract proton from acid
-Two ways to predict whether proton transfer would occur:
1. a quantitative approach w/ pKa values
2. a qualitative approach w/ structure analysis of acids
-Review
-Equilibrium- rate of foward reaction is same as rate of reverse reaction
-Value of Ka used to measure acid strength
-Higher the Ka value, the stronger the acid
-pKa = -log Ka, so lower the pKa value the stronger the acid
-Also can use values to compare base strength
-The stronger the acid, the weaker the conjugate base
-Direction of equilibrium position
-Will point towards formation of weaker acid (higher pKa value)
-Compare acids without pKa values
-Look at conjugate base
-If conjugate base is very stable, meaning that it is very weak, then the acid
must be a strong acid and vise versa
-Chlorine is a electronegative atom, so it can stabilize a negative charge
-Chloride is very stable because it is electronegative so therefore the acid
would be a strong acid
-The acid can act as a proton donor because the conjugate base left behind is
stabilized
-Unlike atoms like chloride, a negative charge generated on a carbon atom
would show that it is unstable since carbon is not very electronegative and is
generally not capable of stabilizing a negative charge so weaker acid
Factors affecting stability of negative charge
-1. Charge

-Remember acidity increases with more positive charge on atom

-2. Atom
-Look at atom bearing negative charge and determine whether more
stable
-If in same row, determine by electronegativity. A more electonegative
atom is more likely to be stable with a negative charge since it is willling to
accept a new electron
-If in same column, determine by atomic radius. Easier to remove electron
if atomic radius is large, meaning electrons are farther apart from the
nucleus
-More stable meaning stronger acid
-3. Resonance
-First depronate and determine conjugate bases
-Concept of it is basically the conjugate base with more resonance
structures will be more stable since the negative charge is delocalized over
more than one atom, making a stronger acid
-Acidity is relative
-4. Dipole dipole (electron density) and Induction
-Can be used instead of pKa value comparison
-Draw conjugate bases and compare them
-Watch for highly electronegative atoms like chlorine that withdraw
electron density through induction
-Withdraw electron density away from negatively charged region of
molecule structure like negative oxygen for ex.
-Stabilizing the charge
-Allowing the molecule to be more acidic and more stable
-5. Orbitals
-As always draw conjugate bases first
-Hybridization states are key in discussing step
-Of the orbitals that accommodate the charges
-Basically because the sp-hybridized orbitals have electrons closer to
the nucleus than a pair electrons in a sp2 or sp3 orbital, the
electrons for the sp orbital are stabilized because they are closer to the nucleus.
So again, sp would be most stable and sp3 would be least stable
-A proton on a triple bond will be more acidic than a proton on a double
bond which is more acidic than a single bond
-Priority taken by given order: CARDIO
-There are exceptions to the rule ARIO
-Position of equilibrium and choice of reagents
-General rule: the equilibrium will always favor the more stabilized atom
-In the example regarding comparison between bases, the more stabilized
negatively charged base will be favored
-Leveling effect
-If a base stronger than HO- is dissolve in water, the base reacts with water to

produce

hydroxide
-In order to work with bases stronger than hydroxide, a solvent other than water
must be
used, like liquid ammonia or NH3
-Basically the leveling effect prevents bases stronger than the amide ion or H2Nfrom
dissolving in liquid ammonia and will instead destroy the base and convert it to H2N-For acids, the main difference between two different acids is the concentration of H3O+
-Solvating effects
-Sometimes interactions between conjugate bases and surrounding solvent molecules can be
used to determine the difference in stability of two molecules
-This method is weaker than ARIO
-Counterions
-Generally do not play a role in reactions
-Generally not even mentioned in reactions, but if they are, they are usually

spectator ions

-Lewis definition of acids and bases

-Lewis acids are electron pair acceptors
-Lewis bases are electron pair donators
-Much broader in definition
Chapter 4 Conformational analysis
-Alkanes and cycloalkanes- compounds that lack a functional group
-Introduction to alkanes
-Hydrocarbons that lack pi bonds are called saturated hydrocarbons or alkanes
-Usually end with -ane
-System of naming compounds called nomenclature
-System to name compounds called Geneva rules: IUPAC
Steps to identify an alkane:
-1. Identify the longest chain
-If there is competition in chains of equal length, go with the chain that has the most
substituents
-Substituents are groups connected to the main parent chain
-1.5 Cyclo- is used to indicate the presence of a ring in the structure of the alkane
-2. List all the substituents
-To name substituents, all we do is add he letters -yl as in methyl
-These groups are generically called alkyl groups
-When an alkyl group is connected to a ring, the ring is usually treated as the
parent only when there are more carbon atoms in the ring than there is in the
alkyl group
-When there are less carbons on the ring, the ring is called a substituent in
the form -cyclo----yl

-3. Naming complex substituents

-Naming branched alkyl substituents is difficult
-Begin by placing numbers on the substituent, going away from the parent
chain
-"1" would start on the carbon not on the parent chain but on the first carbon of the
substituent
-When naming a complex substituent, place parentheses around the name
-Ex. (2-methylbutyl)
-An alkyl group bearing three carbon atoms is called an isopropyl group when
branched
-Alkyl group bearing four carbon atoms can be branched into three different
ways
-Sec-butyl 1-methylpropyl)
-Isobutyl (2-methylpropyl)
-Tert-butyl (1,1- dimethylethyl)
-Alkyl group bearing five carbon atoms can be branched in two common ways +
more
-Isopentyl or isoamyl (3-methylbutyl)
-Neopentyl (2,2-dimethylpropyl)
-4. More rules for assembly
-We need numbers on the carbon atoms of the parent chain in order to
assemble the name of the alkane
-Locant- location of substituent identified with number
-Rules
-If one substituent is present, it should be assigned to lowest possible
number possible
-When multiple substituents are present, assign numbers so that first
substituent receives lower number, first locant to be low as possible
-If there is a tie, the second locant should be low as possible
-If both rules are not enough, go alphabetically (in a chain with
-chloro and -bromo, start counting from carbon next to -bromo)
-When a substituent appears more than once in a compound, use a prefix (di, tri, tetra,
penta, hexa)
-A hyphen is used to separate numbers from letters, and commas are used to
separate two numbers from each other
-When placing substituents in alphabetical order after having numbered and
identified each of them, prefixes like di and tri are ignored (so in dimethyl, you
look at the m and not the d), sec and tert are also ignored, however iso is not
ignored!!!
-Exception: When having complex substituents, the di, try, and other prefixes do
count in terms of order

-Naming bicyclic compounds

-Compounds containing two fused rings are called bicyclic compounds

-Similar process as naming alkanes but different rules are also observed
-For bicyclic systems, the term "bicyclo" is introduced in name of parent
-However this in itself is not specific enough
-In observing the structure, we need to identify the bridgeheads where the
rings are fused together on with two carbon atoms
-Begin by counting the number of carbon atoms for each path connecting to
the
bridgeheads but excluding the carbon atoms of the bridgeheads
-Order from largest to smallest like [2,2,1]
-Place in middle of parent like Bicyclo [2,2,1] heptane
-To number the parent, start at one of the bridgeheads in order to assign the
correct locant to the substituent
-Begin numbering at longest path, then to second longest path up to the
shortest
-Number in a way that would give substituents the lowest number
-Constitutional isomers of alkanes
-Number of possible constitutional isomers increase with increasing molecular size
-When drawing constitutional isomers of an alkane, be sure to avoid drawing same isomer
twice
-If they have the same name, they are the same compound
-Relative stability of Isomeric alkanes
-Stability of constitutional isomers can be observed from heat liberated when each undergo
combustion
- -DeltaH refers to heat of combustion
-Leads to conclusion that branched alkanes are lower in energy than straight chain alkanes,
meaning that they are more stable (branched alkanes)
-Sources and use of Alkanes
-Main source of alkanes is petroleum
-By distillation and differing boiling points, components can be separated
-Cracking and reforming techniques are used to increase yield of gasoline
Drawing Newman projections
-Rotation about C-C single bonds allow for compounds to adopt a variety of possible threedimensional shapes
-To show this, new kind of drawing called Newman projections are used
-Newman projections are basically 90 degree rotations of the wedge and dash structure
-Point at center represents first carbon
-Circle at back represents second carbon
-The sawhorse on the other hand represents a 45 degree rotation
-In the Newman projection of ethane, two hydrogen atoms appear to be separated by angle of 60
degrees, this angle is called the dihedral angle or torsional angle
-Lowest energy conformation - staggered conformation
-Highest energy conformation - eclipsed conformation
-All staggered conformations are degenerate, same amount of energy

-Dihedral angles are very small in comparison when potential energy is highest
-Torsional strain- difference in energy between staggered and eclipsed conformations
-Cause unknown, possible as staggered conformation has favorable
interaction between occupied bonding MO and unoccupied antibonding MO
-Interaction lowers energy of staggered conformation
-When C-C bond is rotated, the overlap is disrupted
-At room temperature, ethane gas will have 99% of its molecules as staggered
conformations
-In the Newman projection of butane, the three eclipsed conformations are not degenerate unlike
the eclipsed conformations of ethane, same with staggered conformation
-Looking the three staggered conformations, conformation with dihedral angle of 180 degrees
is called the anti-conformation, represents lower energy conformation of butane since methyl
groups achieve maximum separation
-The other two are higher in energy, gauche interactions are present. They are a type of
unfavorable steric interaction different from torsional strain
-Referred to as gauche conformations and are degenerate
-With eclipsed conformations, the higher conformation has methyl groups that are eclipsing
each other
-Using these rules, energy costs can be established
-Cycloalkanes
-Angle strain- the increase in energy associated with a bond angle that has deviated from preferred
angle of 109.5 degrees
-Compounds with smaller rings than five-membered rings prohibitive due to angle strain is what
Baeyer has concluded
-Evidence refuting Baeyer's conclusion came from dividing heat of combustion by number of CH2
groups
-Relative energy level does not increase with increasing ring size, opposing Baeyer's theory
-Baeyer's theory was incorrect because they were based on the incorrect assumption that
cycloalkanes were planar, in reality, the bonds of larger cycloalkanes can position themselves three
dimensionally to minimize total energy of compound
-Angle strain is not the only factor that contributes to the energy of a cycloalkane
-Ex. Cyclopropane
-Exhibits a lot of angle strain due to small bond angles, can be relieved a little bit by bending
orbitals that make up the bond outward
-Not as efficient due to overlap of orbitals
-Cyclopropane also exhibits a lot of torsional strain from eclipsing Hs
-Making cyclopropane very reactive in nature and susceptible to ring-opening reactions

-Ex. Cyclobutane
-Exhibits less angle strain but more torsional strain due to four sets of eclipsing Hs
-Best way to relieve strain is to adopt a slightly puckered conformation without gaining too much
angle strain
-Observed in image below
-Ex. Cyclopentane
-Had much less angle strain compared to cyclopropane and cyclobutane
-Can also reduce the torsional strain by adopting the following conformation

(lecture) Chapter 4 (look at 146, memorize the branches)

-Isopropyl occurs more in nature, very common
-Name: (

-COMPLETE Octets are most stable- More priority even if oxygen becomes positive
YOU Prefer the negative charge to be on an oxygen or nitrogen, positive charge on
carbon (lecture)

-Proteins are made with amide bonds (lecture)

-You would expect a little negative charge on oxygen and positive charge on
nitrogen
-Leads to tertiary structure of proteins
-Electrons must be in the p orbital not hybridized orbital, always be perpendicular to
the p system
-Chapter 3
-Conjugate acids and bases
-Be able to recognize the acids and bases based off structure
-Strong acid and weak acid chart memorize
-Especially acetic acid
-The equilibrium will always be in the direction of the weaker acid (higher
pka), 10^6 is usually the borderline for not being in equilibrium
-More effectively a conjugate base can stabilize its negative charge, the
stronger the acid
-Cardio!!!!!!
-Types of atom that carries the charge
-More electronegative atoms are better at stabilizing negative chage within a
period,
within a row***
-Compare the acidity of the two
-Practice with skillbuilder 3.5
-Bond length and bond strength also affect acidity
-The bigger the atom, the more acidic in a group
-Smaller the atom, the shorter the bond,
-Stronger the bond, lower acidity (high pka)
-Down a group, bond strength decreases and bond bond length and acidity increase
-Resonance
-Can function to greatly stabilize a formal negative charge by spreading it into
partial charges
-Formal charges must be observed
-The more stable the conjugate base, the stronger the acid
-Always through pi bonds
-Inductive effect
-Anything more electronegative than carbon will be electronegative atom
-Youre putting an electronegative atom close to carboxyl functional group
-Closer, bigger effect (pKa affected)
-Always through sigma bonds
-Orbital
-affect stability of formal negative charge
-negative charge on sp orbital is more acidic than negative charge on sp3
orbital
-Sp3 is furthest away from nucleus

-Should know acetylene has pka of 25, ethylene of 44 and ethane of 50

-Side with higher pka is where equilibrium moves toward to
-N-H bonds are usually more acidic than C-h bonds of course
-Hd > Hc > Hb > Ha
-Ha > Hb > Hc For resonance imagine ionization of hydrogen
-Solvents
-water 16 pka but alcohol just a little higher
-THF is best answer
-Solvation effects, bulky group hard to solvate, hard to predict
-Cesium effect
-Counterions of cesium have dramatic effect in reactions
-More soluble,
-But in general counterions have barely any effect
-When writing, do it in alphabetical order

Make sure to draw lone pairs for lewis structures but bondline structures are okay