Organic Chemistry Intro Flashcards
Lewis Structure Rules
- Find total number of valence e-s for all atoms in molecule
- Use one pair of electrons to form a single bond between each pair of atoms
- Arrange remaining e-s in lone pairs and double or triple bonds to satisfy the duet rule for H and the octet rule for other atoms so total e-s matches total in #1
Exceptions: some atoms break the octet rule (Boron and Beryllium)
Valence of an atom
Number of bonds it usually forms Can be helpful when making Lewis dot structures C: tetravalent N: trivalent O: divalent H and halogens: monovalent S: 1-6 bonds, P: 1-5
Formal Charge
Number of valence electrons of an atom, minus number of bonds it is a part of, minus number of nonbonding electrons it has
Cyanide ion: CN^- has formal charge of -1
Dash formula
Bonds between each atom of a molecule
Does not usually display lone pairs
Does not show three dimensional structure of molecule
Condensed Formula
Shows neither bonds nor three-dimensional structure
Central atoms are usually followed by atoms that bond to them even when this is not the bonding order
CH3NH2, three H’s following C do not bond to N
Bond-line Formula
Line intersections, corners, and endings represent Carbon atom unless a different atom is drawn in
Hydrogen atoms that are attached to Carbons not usually drawn
Easy way of representing large molecules
Fisher Projection
Vertical lines are assumed to be oriented into the page
Horizontal lines are assumed to be oriented out of the page
Used to represent carbohydrates and are easy way to give information about 3D shape of molecule
Newman projection
View straight down axis of one of the sigma-bonds of a molecule
Both intersecting lines and large circle represent Carbon atoms
Give information about steric hindrance wrt particular sigma bond
Dash-line-wedge formula
Solid black wedges represent bonds coming out of page
Dashed wedges represent bonds going into page, and lines represent bonds in plane of page
Space-filling model
3D representation of a molecule, with spheres of various colors representing different elements wrt relative sizes
Ball and stick models
Atomic radii are drawn to scale, but bond lengths are twice their length for visibility
Give information about relative size of atoms and bond orientations
Sigma Bond
Bonding pair of electrons are localized to space directly between two bonding atoms
Electrons in sigma bond are as close as possible to two sources of positive charge (two nuclei)
Lowest energy, strongest, and most stable type of covalent bond
Always the first type of covalent bond to be formed between two atoms (single bonds)
Pi bond
Created by overlapping p orbitals
Double and triple bonds are made by adding pi bonds to sigma bonds
Sigma bond leaves no room for other electron orbitals directly between atoms, so first pi bond forms above and below sigma bonding e-‘s, forming double bond
Second pi bond forms on either side of sigma bond, forming triple bond
Double: one pi, one sigma
Triple: one sigma, two pi
Pi bond itself is weaker than sigma bond, but added to sigma they strengthen overall bond between atoms
Adding pi bonds shortens bond length and does not allow free rotation around bond
Hybrid Orbitals
To form four equal sigma bonds on Carbon, electrons occupy four orbitals that are hybrids of old s and p orbitals
Hybrid orbitals are equivalent to each other in shape and energy, averaging characteristics of s and p orbitals
Sigma bond formed in area where two hybrid orbitals overlap
Pi bond only with two pure p orbitals
Naming of hybrid orbitals
Named according to type and number of orbitals that overlap to create hybrid orbital: sp, sp^2, sp^3, dsp^3, d^2sp^3, etc.
Count number of sigma bonds and lone pairs of electrons on atom
match number to sum of superscripts in a hybrid name
Character of hybrid orbital: sp has 50/50% s and p character
Sp^3 has 25/75% s and p character
The more s character, the stronger, shorter, and more stable it is
Valence Shell Electron Pair Repulsion (VSEPR) Theory
Electrons in an orbital seek to minimize energy by moving as far away from other electron pairs as possible, minimizing repulsive forces between them
Sp: 180 deg, linear shape
Sp^2: 120 deg, trigonal planar
Sp^3: 109.5 deg, tetrahedral, trigonal pyramidal, or bent
Sp^3 d: 90 deg, 120 deg: trigonal-bipyramidal, see-saw, t-shaped, or linear
Sp^3 d^2: 90 deg, 90 deg: octahedral, square pyramidal, square planar
Lone pairs and pi electrons require more room, causing distortion
Bond Energy
Most stable bond has highest bond energy
Total energy required to break compound into constituent atoms divided by number of bonds in that compound
Delocalized Electrons
Bonding electrons spread out over three or more atoms
Can result from pi bonds and lone pairs
Molecules containing delocalized electrons can be represented by a combination of two or more alternative Lewis structures (resonance structures)
Weighted average of Lewis structure most accurately represents actual molecule
Real molecule exists at lower energy than any single Lewis structure that contributes to it
Resonance Energy
Difference between real molecule and energy of most stable Lewis structure in a molecule that exhibits resonance structures
Weighted average of Lewis structures most accurately represents actual molecule and exists at lower energy than energy of any of the structures
Rules for drawing resonance structures
- Atoms must not be moved: move electrons, not atoms
- Number of unpaired electrons must remain the same
- Resonance atoms must lie in the same plane
Most stable structure make greatest contribution to actual molecule’s structure
The lower the formal charges, the more stable
Separation of charges decreases stability
Destabilizing influences in a molecule
Charge separation
Bond angle strain
Steric hindrance
Stability and reactivity are opposites
What are the two conditions required for resonance to occur?
- Species must contain an atom with either a p orbital or an unshared pair of electrons
- Atom must be single bonded to an atom that possesses a double or triple bond (called a conjugated unsaturated system)
Adjacent p-orbital in conjugated system may contain 0, 1, or 2 e-
P-orbital allows adjacent pi bond from double or triple bond to extend and encompass more than two nuclei
Aromaticity
Increased stability of cyclic molecule due to e- delocalization (resonance)
Requires resonance requirements and Huckel’s rule
Huckel’s rule
Planar monocyclic rings whose number of pi-e- can be described with equation 4n + 2 (where n is integer, including 0) will be aromatic
Lone pairs count as pi electrons
What does electronegativity tell us about charge distribution in a molecule?
The more electronegative an atom is, the more time electrons will spend near that atom
Differences in electronegativity create dipole moments (partial ionic character, positive and negative)
Different functional groups have different electronegativities
Functional groups: groups of atoms on molecule that are involved in reactions and behave in predictable ways
Reactive, non-alkane portions of molecules
What are the two main types of functional groups?
- Nucleophilic functional groups
2. Electrophilic functional groups
Nucleophilic Functional Groups
Have partial negative charge and seek positively charged nuclei
Donate electrons and usually ‘attack’ functional groups w/ partial positive charges
E.g. amines, attack with lone pair of e- on N and donate electrons (also Lewis base)
Electrophilic functional groups
Have partial positive charge and seek electrons
Provide a center of positive charge and usually get ‘attacked’ by e- from other functional groups
E.g. Carbonyl carbons, reactivity increases as partial positive charge on carbon increases
Electron acceptors, so Lewis acids
Alkane
Carbon-carbon single bond (methane)
-C-C-
Alkene
Carbon-Carbon double bond
C=C
Alkyne
Carbon-Carbon triple bond
C-=C
Alcohol
Hydroxyl group attached to carbon
R-OH
Ether
Oxygen attached to two Carbons
R-O-R’
Amine
R-N-H
H
R-N-R’
H
R-N-R’
R”
Nitrogen attached to one or more carbons (has lone pair)Aldehyde
Carbon double bonded to Oxygen and attached to one carbon and one H
H
O=C
R
Oxygen has lone pairsKetone
Carbon double bonded to Oxygen and single bonded to two other Carbons
R’
O=C
R
Two lone pairs on OxygenCarboxylic Acid
C double bonded to Oxygen, single bond to Carbon on one side and single bond to hydroxyl on the other side
R
O=C
OH
Lone pairs on both oxygensEster
Carbon double bonded to Oxygen, with single bond to carbon on one side, and single bond to oxygen on other side
The additional oxygen is bonded to carbon on other side
R
O=C
O
R’
Amide
Carbon double bonded to Oxygen and single bonded to Nitrogen, other side of carbon is single bonded to Carbon
R
O=C
NH2
Stereochemistry
Three-dimensional structure of a molecule
Involves consideration of what can and cannot move in molecules in a rxn
- Single bonds free to rotate, double bonds locked
Isomers
Unique molecules that share the same molecular formula
“Iso” - “the same” or “equal” in Greek
Two molecules are isomers if they have the same molecular formula, but are different compounds
Three types on MCAT: structural (constitutional), conformational, and stereoisomers
Structural Isomers
Molecules with same molecular formula, but different bond-to-bond connectivity
E.g. isobutane and n-butane both have C4H10 as molecular formula
Conformational Isomers
Aka conformers
Not true isomers, because different spatial orientations of the same molecule
At room temperature, atoms rotate rapidly about their sigma bonds, resulting in a mix of conformational isomers at any given moment
Antistaggered, eclipsed, gauche, fully eclipsed, gauche, eclipsed, and antistaggered
High and low energy formations due to steric strain
Visualized with Newman projections
What are the high energy conformations of conformational isomers?
Eclipsed and fully eclipsed
Both have the groups overlapping each other
Eclipsed has lower steric hindrance groups overlapping each other
Fully eclipsed has highest sterically hindered groups overlapping, highest energy
What are the low energy conformations of conformational isomers?
Antistaggered and gauche
Both of these have staggered groups, where if a bound has three groups off of it, then each of the three bonds on the top bond are offset from each of the bottom bond’s three groups by 60 degrees
Gauche configurations still have the most sterically hindered groups close to each other, while antistaggered have the most sterically hindered groups opposite each other
Stereoisomers
Two unique molecules with the same molecular formula and the same bond-to-bond connectivity
Two major types of stereoisomers are enantiomers and diastereomers
Enantiomers
Non-superimposable mirror images of one another
Have the same molecular formula and connectivity, but are not the same molecule because they differ in their configuration
Must have opposite absolute configurations in each and every chiral carbon
Have same physical and chemical properties except fo rxns with other chiral compounds
Chirality
“Handedness”
Configurations of bonds in which the same bonds with all of the same groups are present, but two configurations are slightly different due to order of connections of the bonds
Molecules that have ‘handedness’ are called chiral molecules in chemistry
Chemical reactions sometimes can proceed only with one enantiomer and not the other
What is the requirement of a Carbon to have a chiral bond?
Must be bonded to four different substituents
Absolute Configuration
Describes the physical orientation of atoms about a chiral center in terms of R (right, rectus) and S (left, sinister)
Atoms attached to the chiral center are numbered from highest to lowest priority
Highest priority: atom with largest atomic weight
If two atoms are same element, substituents are sequentially compared in order of decreasing priority
Double and triple bonds have substituents marked 2 and 3 times
Draw a circle on the page from 1 to 2 to 3
Counterclockwise means S, Clockwise means R
Mirror image always has opposite absolute config
What is the process to determine the stereochemistry of a carbohydrate in a Fischer projection?
- Number bonds in order of substituent priority
- Ignore the lowest priority bond, bond 4 and draw an arrow in direction of highest priority to lowest priority
- Based on the direction of your arrow, determine whether the molecule is R or S
If lowest priority substituent is coming out of page on a horizontal bond, configuration must be reversed
Relative configuration
Two molecules have the same relative configuration about a chiral carbon if they differ by only one substituent and the other substituents are oriented identically about the carbon
Not related to absolute configuration
Does knowing the absolute configuration of a molecule tell you something about the rotation of plane polarized light?
No, this must be determined by experimental measurement for each enantiomer
Light
Made up of electromagnetic waves of perpendicular orientation
Changing electric and magnetic field that are oriented perpendicular to one another and to direction of propagation
Polarimeter
Screens out photons with all but one orientation of electric field
Resulting light consists of photons with their electric fields oriented in same direction and is called plane-polarized light
How do enantiomer’s rotate plane-polarized light with respect to each other?
Enantiomer of a molecule rotates the electric field of incident light to the same degree but opposite direction as the original molecule (optically active)
For compounds without enantiomers or in a mixture, there are so many millions of molecules colliding with photons that on average the photons leave the molecule with same incident electric field orientation (optically inactive)
- Optically inactive molecules can be compounds without chiral centers or molecules with internal mirror planes
How can you separate enantiomers?
Can separate by chemical (or in rare cases, physical) means
Results in pure ‘right-handed’ or ‘left-handed’ sample
What are designations for the direction of rotation of plane-polarized light?
If compound rotates plane-polarized light clockwise, designated as ‘+’ or ‘d’ or dextrorotary
If it rotates plane-polarized light counterclockwise, designated as ‘-‘, or ‘l’ or levorotary
Direction and number of degrees of rotation is called the compound’s observed rotation
Specific rotation
Standardized form of observed rotation that is calculated from observed rotation and experimental parameters
Dependent on length of polarimeter, concentration of solution, temperature, and wavelength of light
Racemic Mixture
Mixture of enantiomers in equal concentrations
Does not rotate plane-polarized light, rotations cancel each other out
When enantiomers mixed in unequal concentrations, light is rotated in same direction as it would be in a pure sample of enantiomer in excess, but only to a fraction of degree
ratio of actual rotation to rotation of pure sample is optical purity
Diastereomers
Type of stereoisomer
Molecules that have the same formula, and same bond-to-bond connectivity, but are NOT mirror images of each other and are NOT the same compound
Diastereomers with multiple chiral center shave same absolute config in one or more chiral center
Differ in physical properties (rotation of plane-polarized light, mp, bp, solubility) and chemical properties
What is the equation for the maximum number of optically active stereoisomers that a single compound can have?
(Diastereomers + enantiomers)
Max # optically active isomers = 2^n
Where n is the number of chiral centers
Meso Compound
Compound with multiple chiral centers, but is optically inactive
have a plane of symmetry through their center, which divides the molecule into two halves that are mirror images of each other
Symmetry means the plane-polarized rotation is exactly opposed by opposite side of molecule
Considered to be achiral
Epimers
Diastereomers that differ in configuration at only one chiral carbon
Anomers
Cyclic diastereomers that are formed when a ring closure occurs at an epimeric carbon
Chiral carbon of an anomer is called anomeric carbon
Carbohydrates are classified according to their configuration at the anomeric carbon
Cis/trans isomers
AKA geometric isomers
Special type of diastereomer that exist due to hindered rotation created by multiple bonds or a ring structure
Disubstituted, meaning each of two carbons has one non-hydrogen substituent
Cis-isomers are molecules with substituents on the same side
Trans-isomers are molecules with substituents on opposite sides
Have different physical properties (cis have dipole moment and therefore stronger intermolecular forces and higher bps, trans form crystals more readily and have higher mps)
Steric hindrance
Substituent groups on a molecule may crowd together, raising energy levels
E.g. cis isomers may have this issue
How do we refer to the isomers in alkenes or ring structures with 3 or 4 substituents?
Two substituents on each carbon are prioritized using atomic weight, similar to system used for absolute configuration
If higher priority substituents are on opposite sides of ‘locked’ bond, molecule is labeled E for entgegen, and if on the same side then Z for zusammen (zame zide!)
Substitution reactions
Reaction in which one group leaves and is replaced with another
Nucleophilic substitution: leaving group replaced by an incoming nucleophile
Two types: SN1 (unimolecular), SN2 (bimolecular)
Negative regions with high electron density attack positive regions with low electron density
SN1
Nucleophilic substitution that has two steps, but has a rate law that is dependent on only one of the reactants
First step: formation of the carbocation (slow, and rate-determining step)
- Rate is independent of conc of nucleophile, directly proportional to conc of substrate
- Leaving group breaks away on its own to leave carbocation behind
Second step: nucleophile attacks carbocation
Both enantiomers can be formed if substrate carbocation began as chiral center (planar intermediate)
What types of substrates are more likely to undergo SN1 reactions?
Carbocation must be formed spontaneously
A tertiary substrate is more likely to undergo SN1 than a primary or secondary
SN2
Nucleophilic substitution reaction that occurs in a single step
Rate is dependent on concentration of nucleophile and substrate
Nucleophile attacks the intact substrate from behind the leaving group and knocks the leaving group free while bonding to the substrate
Inversion of configuration: config is inverted, so relative config is changed, but absolute may or may not be changed
Steric hindrance important
What types of substrates are more likely to undergo SN2 reactions?
Rate of SN2 reactions decreases from primary to secondary, and do not typically occur with tertiary substrates
If nucleophile is a strong base and substrate is too hindered, an elimination (E2) reaction may occur instead (nucleophile picks up proton, leaving group leaves, and double carbon-carbon bond forms instead)
Bulky nucleophiles can also hinder an SN2 reaction
Nucleophilicity
Strength of nucleophile is not important for SN1 rxns, but important for SN2
Base is always stronger nucleophile than a conjugate acid, but basicity is not nucleophilicity (bases lead to elimination)
Characteristics associated with nucleophilicity: Less bulky, negative charge, polarizability
Characteristics opposite to nucleophilicity: electronegativity, going up to the right on periodic table (bad for nucleophilicity)
Leaving Groups
Best leaving groups are stable when they leave, always more stable than nucleophile
Weaker the base, the better the leaving group
Electron withdrawing effects and polarizability are also good
Solvents
Polar protic solvents (hydrogen bonding) stabilize nucleophile and carbocations, therefore slowing rate of SN2 and increasing rate of SN1 rxns
Polar aprotic solvents (no H bonds) increase rate of SN2 rxns and decrease rate of SN1 rxns
In SN1 rxns, solvent heated to reflux (boiled) to provide energy for formation of carbocation
Solvolysis: solvent acts as nucleophile
SN1 vs. SN2 reactions (nucleophile and five Ss)
SN2 requires strong nucleophile, while nucleophilic strength doesn’t affect SN1
1. Steric hindrance inhibits SN2 rxns (needs methyl, primary, or secondary substrate) and steric hindrance may stabilize carbocation, encouraging SN1 (requires secondary or tertiary substrate)
2. Highly polar solvent increases rxn rate of SN1 by stabilizing carbocation, slows SN2 by stabilizing nucleophile
3. Speed of SN2 depends on conc of substrate + nucleophile, speed of SN1 depends only on substrate
4. SN2 inverts stereochemistry, SN1 creates both enantiomers
5. Skeleton arrangements occur in SN1, but SN2 never rearranges carbon skeleton
Substitutions can run in revers and eliminations can accompany both kinds
