Organic Chem 1 - Ch. 1-5

Isotopes

• atoms with the same number of protons but different number of neutrons

• atoms of the same element but with different atomic masses

Orbitals

• an allowed energy state for an electron bound to a nucleus

• the probability function that defines the distribution of electron density in space

  • up to two electrons can occupy each orbital if their spins are paired

Electron density

the relative probability of finding an electron in a certain region of space

Mass number

the sum of the protons and neutrons in an atom

Atomic number

the number of protons in an atom

Valence electrons

electrons on the outermost shell of the atom

Aufbau principle

states we must fill the lowest-energy orbitals first until we have the proper number of electrons

Hund’s Rule

states that when there are two or more orbitals of the same energy (degenerate), electrons will go into different orbitals rather than pairing up in the same orbital

Octet rule

• atoms generally form bonding arrangements that give them filled shells of electrons (noble-gas configurations)

• for the second-row elements, this configuration has eight valence electrons

  • elements in the third and higher rows can have an “expanded octet” of more than eight electrons

Ionic bond

• bonding that occurs by the attraction of oppositely charged ions

• usually results in the formation of a large, three-dimensional crystal lattice rather than individual molecules

• common in inorganic compounds but relatively uncommon in organic compounds

Covalent bond

• occurs by the sharing of electrons in the region between two nuclei

  • an unequally shared pair of bonding electrons is called a polar covalent bond

  • an equally shared pair of bonding electrons is called a nonpolar covalent bond

Lewis structure

• a structural formula that shows all valence electrons, with the bonds symbolized by dashes or by pairs of dots, and nonbonding electrons symbolized by dots

• allows you to see where all the electrons are and to determine if each atom obeys the octet rule

• a correct/true Lewis structure should show any lone pairs

Nonbonding electrons

• also called lone pairs

• valence-shell electrons that are not shared between two atoms

• lone pairs are nucleophiles — they participate in a host of chemical reactions

Valence

the number of bonds an atom usually forms

Dipole moment

a measure of the polarity of a bond/molecule, proportional to the product of the charge separation times the bond length

The electrons that contribute to an atom’s charge are…

1. all its unshared (nonbonding) electrons; plus

2. half the (bonding) electrons it shares with other atoms, or one electron of each bonding pair

Formal charge formula

formal charge (FC) = [group number] - [nonbonding electrons] - ½ [shared electrons]

Resonance hybrid

a molecule or ion for which two or more valid Lewis structures can be drawn, differing ONLY in the placement of the valence electrons

Resonance structures: general rules

1. All the resonance forms must be valid Lewis structures for the compound. Second-row elements (B, C, N, O, F) can never have more than eight electrons in their valence shells.

2. Only the placement of the electrons many be shifted from one structure to another. Electrons in double bonds and nonbonding electrons (lone pairs) are most commonly shifted.

3. Nuclei cannot be moved, and all bond angles must remain the same.

4. Sigma bonds are very stable, and they are rarely involved in resonance.

5. The major resonance contributor is the one with the lowest energy. The best contributors generally have the most octets satisfied, as many bonds as possible, and as little charge separation as possible.

6. Electronegative atoms such as N, O, and halogens often help to delocalize positive charges, but they can bear a positive charge only if they have octets.

7. Resonance stabilization is most important when it serves to delocalize a charge or a radical over two or more atoms.

Condensed structural formula

written without showing all of the individual bonds— each central atom is shown together with the atoms that are bonded to it; if there are two or more identical groups, parentheses and a subscript may be used to represent all the identical groups

Line-angle formula

a shorthand structural formula with bonds represented by lines— carbon atoms are implied wherever two lines meet or a line begins or bends; hydrogen atoms are not shown unless they are on a drawn atom

Molecular formula

the number of atoms of each element in one molecule of a compound

Empirical formula

the ratio of atoms in a compound

Molecular orbital

an orbital formed by the overlap of atomic orbitals on different atoms

Hybrid atomic orbital

a directional orbital formed from a combination of s and p orbitals on the same atom

Valence-shell electron-pair repulsion (VSEPR) theory

bonds and lone pairs around a central atom tend to be separated by the largest possible angles: about 180 degrees for two, 120 degrees for three, and 109.5 degrees for four

sp hybrid orbitals

• two orbitals (s and p) combine to form two sp orbitals

• linear electron pair geometry

• 180-degree bond angle

sp2 hybrid orbitals

• three orbitals (one s and two p) combine to form three sp2 orbitals

• trigonal planar geometry

• 120-degree bond angle

sp3 hybrid orbitals

• four orbitals (one s and three p) combine to form four sp3 orbitals

• the atom has tetrahedral electron-pair geometry

• 109.5-degree bond angle

Constitutional (structural) isomers

isomers that differ in the order in which their atoms are bonded together

Stereoisomers (configurational isomers)

isomers whose atoms are bonded together in the same order but differ in how atoms are oriented in space — example: cis- vs. trans-

Cis-trans (geometric) isomers

stereoisomers that differ in their cis-trans arrangement on a double bond or on a ring; must have two different groups on each end of the double bond

• the cis isomer has similar groups on the same side

• the trans isomer has similar groups on opposite sides

Functional group

• the reactive, non-alkane part of an organic molecule

• a specific combination of atoms that has a unique set of chemical properties

Dipole-dipole forces

attractive intermolecular forces resulting from the attraction of the positive and negative ends of the permanent dipole moments of polar molecules

van der Waals forces

the attractive forces between neutral molecules, including dipole-dipole forces and London dispersion forces

London dispersion forces

intermolecular forces resulting from the attraction of correlated temporary dipole moments induced in adjacent molecules

Hydrogen bond

a particularly strong attraction between a nonbonding pair of electrons and an electrophilic O—H or N—H hydrogen

Three main factors to consider when predicting relative boiling points:

1. hydrogen bonding

2. molecular weight and surface area

3. dipole moments

Hydrophobic

means “water-hating” — nonpolar substances or groups that do not readily dissolve in water (water-repellant)

Hydrophilic

means “water-loving” — polar substances or groups that readily dissolve in water (water-attractive)

Arrhenius acids/bases

• acid: substance that dissociates in water to give hydronium ions

• base: substance that dissociates in water to give hydroxide ions

Bronsted-Lowry acids/bases

• acid: any species that can donate a proton

• base: any species that can accept a proton

Lewis acids/bases

• bases: species with available electrons that can be donated to form new bonds — also called nucleophiles

• acids: species that can accept these electron pairs to form new bonds — also called electrophiles

Curved-arrow formalism

a method of drawing curved arrows to keep track of electron movement from nucleophile to electrophile (or within a molecule) during the course of a reaction

Hydrocarbons

Compounds composed exclusively of carbon and hydrogen.

• major classes: alkanes, alkenes, alkynes, aromatic hydrocarbons

• nearly all are nonpolar or only slightly polar

• tend to be hydrophobic

Alkanes

Hydrocarbons containing only single bonds.

• generally have the -ane suffix, and the first part of the name indicates the number of carbon atoms in the chain

Cycloalkanes

a special class of alkanes in the form of a ring

Alkyl group

an alkane portion of a molecule, with one hydrogen atom removed to allow bonding to the rest of the molecule; can be represented with the symbol R

Alkenes

Hydrocarbons that contain carbon-carbon double bonds.

• the double bond is the most reactive part, so it is considered the functional group

• end in the -ene suffix

• these bonds cannot rotate — show geometric (cis-trans) isomerism

Alkynes

Hydrocarbons with carbon-carbon triple bonds as their functional group.

• generally have the -yne suffix

• triple bond is linear, so there is no cis-trans isomerism

• to accommodate a triple bond, four atoms must be in a straight line —> cycloalkynes are rare and must contain at least eight carbon atoms

Aromatic hydrocarbons (arenes)

Hydrocarbons containing a benzene ring— a six-membered ring with three double bonds.

• look like cycloalkenes, but have different properties

• have a very stable bonding arrangement

• when it serves as a substituent, it is called a phenol group

Alcohols

Organic compounds that contain the hydroxy group (—OH) as their functional group.

• the general formula is R—OH

• classified as primary, secondary, or tertiary depending on whether the hydroxy group is bonded to a primary, secondary, or tertiary carbon atom

• among the most polar organic compounds —> hydrophilic

• end in the -ol suffix

Ethers

Compounds with two alkyl groups bonded to an oxygen atom.

• the general formula is R—O—R’ (the R’ means another alkyl group, which may or may not be the same as the first R)

• much more polar than hydrocarbons

• since they have no O—H hydrogens, they cannot hydrogen bond with themselves

• names are often formed from the names of the alkyl groups + the word “ether”

Carbonyl group

The C=O functional group.

• contains both aldehydes and ketones

• strongly polar—> hydrophilic

• can form hydrogen bonds with hydrogen-bond doners such as water, alcohols, and amines

Ketone

A compound containing a carbonyl group bonded to two alkyl groups.

• names generally have the -one suffix

• contains a carbonyl functional group (C=O)

Aldehyde

A compound containing a carbonyl group bonded to an alkyl group and a hydrogen atom.

• names generally use the -al suffix or -aldehyde suffix

• contains a carbonyl functional group (C=O)

Carboxylic acids

Any compounds containing the carboxyl group, —COOH as their functional group.

• general formula is R—COOH

• owe their acidity (pKa is about 5) to the resonance-stabilized carboxylate anions formed by deprotonation

• often uses historical names; systemic names would use -oic acid suffix

• strongly polar —> hydrophilic

Acid chloride

an acid derivative with a chlorine atom in place of the hydroxyl group

Ester

• an acid derivative in which the hydroxy group of the acid is replaced by an alkoxy group

• it is a composite of a carboxylic acid + an alcohol

Amide

• an acid derivative in which the hydroxy group of the acid is replaced by a nitrogen atom and its attached hydrogens or alkyl groups

• it is a composite of a carboxylic acid + an amine or ammonia

• among some of the most stable acid derivatives; form very weak bases

• form particularly strong hydrogen bonds —> strongly polarized

Amine

A derivative of ammonia with one or more alkyl groups bonded to the nitrogen atom.

• because of their basicity, naturally-occurring amines are often called alkaloids

• simple amines are named by naming the alkyl groups bonded to nitrogen and adding the word “amine”

• nitrogen atom is hydrophilic

Nitrile

A compound containing the cyano group.

• cyano group = a functional group that includes a carbon-nitrogen triple bond

• strongly polar; most small nitriles are soluble in water

• sp-hybridized bonding group

Common names

the names that have developed historically, generally with a specific name for each compound; also called trivial names

IUPAC (systematic) names

the systematic names that follow the rules adopted by the International Union of Pure and Applied Chemistry

“iso” grouping

branched alkyl group that has the formula (CH3)2CH

Degree of alkyl substitution

The number of alkyl groups bonded to a carbon atom in a compound or in an alkyl group.

• n- means primary (bonded to one other carbon atom)

• sec- means secondary (bonded to two other carbon atoms)

• tert- means tertiary (bonded to three other carbon atoms)

Combustion reaction

a rapid oxidation at high temperatures in the presence of air or oxygen

Catalytic cracking

heating large alkanes to cleave them into smaller molecules

Methane; CH4

• simplest alkane

• perfectly tetrahedral

• 109.5 degree bond angles predicted for an sp3 hybridized carbon

• four hydrogen atoms are covalently bonded to the central carbon atom

Ethane

• two-carbon alkane

• composed of two methyl groups with overlapping sp3 hybrid orbitals forming a sigma bond between them

• methyl groups are not fixed in a single position, and are able to rotate about the sigma bond that connects the two

• infinite number of conformations possible

Conformations

different arrangements of atoms caused by rotation about a single bond

Newman projections

A way of drawing the conformations of a molecule by looking straight down the bond connecting two carbon atoms

• front carbon atom is represented by three lines (bonds) coming together in a Y shape

• the back carbon is represented by a circle with three bonds pointing out from it

torsional strain

the strain associated with eclipsing of bonds in the ring

torsional energy

the energy required to twist a bond into a specific conformation

guache conformation

a conformation with a 60-degree dihedral angle between the largest groups

anti conformation

a conformation with a 180-degree dihedral angle between the largest groups; usually the lowest-energy conformation

steric strain

the interference between two bulky groups that are so close together that their electron clouds experience a repulsion

angle strain

sometimes called Baeyer strain; the strain associated with distorting bond angles to smaller (or larger) angles

ring strain (in cyclic compounds)

• the extra strain associated with the cyclic structure of a compound, as compared with a similar acyclic compound

• composed of angle strain and torsional strain

chair conformation

the most stable conformation of cyclohexane, with one part puckered upward and one part puckered downward

boat conformation

• the less stable puckered conformation of cyclohexane, with both parts puckered upward

• the most stable boat is actually the twist boat conformation; twisting minimizes torsional and steric strain

fused rings

rings that share a common carbon-carbon bond and its two carbon atoms

bridgehead carbons

• the carbon atoms shared by two or more rings in a bridged bicyclic compound

• three chains of carbon atoms (bridges) connect the bridgeheads

spirocyclic compounds

bicyclic compounds in which the two rings share only one carbon atom

mechanism

the complete, step-by-step description of exactly which bonds break and which bonds form, and in what order to give the observed products

Thermodynamics

• the study of the energy changes that accompany chemical and physical transformations

• allows us to compare the stability of reactants and products and predict which compounds are favored by the equilibrium

Kinetics

• the study of reaction rates, determining which products are formed fastest

• also helps to predict how the rate will change if the reaction conditions are altered

chain-reaction mechanism

a multistep reaction where a reactive intermediate formed in one step brings about a second step that generates the intermediate needed for the following step

initiation step

the preliminary step in a chain reaction, where the reactive intermediate is first formed

propagation steps

• the steps in a chain reaction that are repeated over and over to form the product

• the sum of the propagation steps should give the net reaction

termination steps

any steps where a reactive intermediate is consumed without another one being generated

substitution (displacement) reaction

a reaction in which an attacking species (nucleophile, electrophile, or free radical) replaces another group

reactive intermediate

a short-lived species that is never present in high concentration because it reacts as quickly as it is formed

free radical

• a highly reactive species in which one of the atoms has an odd number of electrons

• most commonly, a radical contains a carbon atom with three bonds and an “odd” (unpaired) electron

Four main ways that electrons move in polar reactions:

1. Nucleophilic attack on electrophile

2. Loss of a Leaving Group — heterolytic bond cleavage, an atom or group takes the electron pair

3. Proton Transfers (Acid/Base)

4. Rearrangements — carbocations can be stabilized by neighboring groups through slight orbital overlapping called hyperconjugation

Equilibrium

• a state of a system such that no more net charge is taking place

• the rate of the forward reaction equals the rate of the reverse reaction

Equilibrium constant

a quantity calculated from the relative amounts of the products and reactants present at equilibrium

homolytic (radical) cleavage

the breaking of a bond in such a way that each atom retains one of the bond’s two electrons —> produces two free radicals

heterolytic (ionic) cleavage

the breaking of a bond in such a way that one of the atoms retains both of the bond’s electrons —> forms two ions

transition state (activated complex)

• the state of highest energy between reactants and products

• a relative maximum (high point) on the reaction-energy diagram

• unlike the reactants or products, it is unstable and cannot be isolated