Organic Chemistry

What direction is the (R) form? What direction is the (S) form?

(R) = rectus (right) (S) = sinister (left)

hydroxyl group

(hydroxy-) A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.

geminal diols

-diols with hydroxyl groups on the same carbon (Geminal diols are like Gemini twins meaning that the hydroxyl groups are on the same carbon)

What are the rules for numbering a carbon chain?

1) Carbon numbered 1 will be the one closest to the highest-priority functional group 2) If functional groups have the same priority, numbering the chain should make the numbers of the substituted carbons as low as possible

What are the general steps for naming a compound?

1) Find the longest chain in the compound with the highest-order functional group 2) Number the chain 3) Name the substituents 4) Assign a number to each substituents 5) Complete the name

What are the rules for alphabetizing the substituents after priority has been assigned?

1) Name begins with the substituents and their names in alphabetical order with each substituent preceded by its number 2) Prefixes are normally ignored and alphabetizing depends on the name of the substituent 3) Exception: nonhyphenated roots are ignored in the following rule and are taken into account with alphabetization (Neo, iso, cyclo) 4) Numbers are separated by commas and from other words using hyphens 5) Finally, finish the name with the longest carbon chain and the highest order functional group as a suffix

How do you assign numbering priority to carbon rings?

1) Number begins with the highest substituted carbons like in carbon chains, giving lower numbers to the highest ordered carbons 2) However, when deciding between a double and triple bond for numbering, highest priority is assigned to a double bond

What are the four questions you should ask when determining the type of isomer?

1) Same connectivity? NO: structural (constitutional) YES: stereoisomers 2) Stereoisomer: requires bond breaking to interconvert? NO: Conformational YES: Configurational 3) Configurational: non-superimposable mirror images? NO: Diastereomers YES: Enantiomers 4) Diastereomers: differ in arrangement around an immovable bond? YES: cis-trans

How do you name multiple bonds found within the parent chain?

1) The double or triple bond is named like a substituent and is indicated by the lower-numbered carbon involved in the bond 2) The number may precede the molecule name (2-butene) 3) The number may be placed near the suffix (but-2-ene) 4) If there are multiple bonds, the numbering is generally separated from the suffix (1,3-butadiene) NOTE: if there are multiple bonds, this is indicated in the suffix as well like substituents

(R) and (S) Forms

1) Used the Cahn-Ingold Prelog priority rules to assign priority to the four substituents on the chiral center -only look at the atoms that are directly attached to the carbon -higher atomic number gets priority *if tie is there look at the combination of the atoms attached to the atom attached to the chiral center* -double bond, bonded to it twice 2) Draw a circle connecting 1 to 2 to 3 clockwise --> R - RIGHT counterclockwise --> S - LEFT (place the lowest priority in the back of the molecule) 3) If H is not going into the page (dashed lines or up/down) then opposite configuration

isopropyl alcohol

2-propanol

Chiral Center

A carbon with four different substituents and lack a plane of symmetry (often used to test knowledge on chirality)

Physical properties

A characteristic of a pure substance that can be observed without changing it into another substance Melting Point Boiling Point Solubility Odor Color Density

Meso compound

A compound with chirality centers and an internal plane of symmetry causing it to be an achiral molecule (these are the molecular equivalent of a racemic mixture)

Fischer Projection

A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes)

Newman projection

A method of visualizing a compound in which the line of sight is down a carbon-carbon bond axis (commonly visualized using a butane straight-chain

Racemic Mixture

A mixture that contains equal amounts of the (+) and (-) enantiomers. Racemic mixtures are not optically active.

Antibonding Orbital

A molecular orbital If the signs of the wave function are different, a higher energy (less stable) bonding orbital is produced

Bonding Orbital

A molecular orbital If the signs of the wave functions are the same, lower energy (more-stable) bonding orbital is produced

Chirality (what is chiral and achiral?)

A property of a compound to exist in both left and right forms; occurs whenever a compound contains an asymmetric carbon Chiral: mirror image cannot be superimposed on the original object; this implies that the molecule lacks an internal plane of symmetry Achiral: mirror images that can be superimposed

Chemical Properties

A property of matter that describes a substance's ability to participate in chemical reactions. Often determined by the functional groups present in the molecule

Absolute configuration Relative configuration

Absolute configuration: describes the exact spatial arrangement of groups of atoms independent of other molecules Relative configuration: the spatial arrangement of groups in a chiral molecule compared to another chiral molecule.

diols or glycols How do you name diols or glycols?

Alcohols with two hydroxyl groups Indicated with the suffix -diol The name of the hydrocarbon is preserved and -diol is added as a suffix (ex: ethane-1,2-diol)

What is an alpha carbon? What is a beta carbon? What is a gamma carbon? What is a delta carbon?

Alpha carbon = adjacent carbon to functional group Beta carbon = second carbon attached to functional group Gamma carbon = third carbon attached to functional group Delta carbon = fourth carbon attached to functional group

What is angle strain? What is torsional strain? What is non-bonded strain? (Van Der Waals repulsion)

Angle strain: results when bond angles deviate from their ideal values by being stretched or compressed Torsional strain: results when cyclic molecules must assume conformations that have eclipsed or gauche interactions Non-bonded strain: dominant source of steric strain in the flagpole interactions of the cyclohexane boat conformation

In the chair conformation, the hydrogen atoms that are perpendicular to the plane of the ring (sticking straight up or down) are called ______, and those parallel (sticking out) are called __________ These orientations alternate around the ring. Describe this

Axial, equatorial The wedge of C1 is axial, the dash on C2 will be axial, the wedge of C3 will be axial...

Interconversion of the chair conformation of a cyclohexane can be slowed by what? For these type of groups, what is the most favorable position to reduce non bonded strain?

Bulky groups (like tert-butyl) In rings with more than one substitute, the preferred chain form is determined by the larger group, which will prefer the equatorial position. These rings also have associated nomenclature

What are the suffixes for the following functional groups? Carboxylic acid Anhydride Ester Amide Aldehyde Ketone Alcohol Alkene Alkyne Alkane

Carboxylic acid = -oic acid Anhydride = anhydride Ester = -oate Amide = -amide Aldehyde = -al Ketone = -one Alcohol = -ol Alkene = -ene Alkyne = -yne Alkane = -ane

What are the prefixes for the following functional groups? Carboxylic acid Anhydride Ester Amide Aldehyde Ketone Alcohol Alkene Alkyne Alkane

Carboxylic acid = carboxy- Anhydride = alkanoxyloxycarbonyl- Ester = alkoxycarbonyl- Amide = carbamoyl- or amido- Aldehyde = oxo- Ketone = oxo= or keto- Alcohol = hydroxy- Alkene = alkenyl- Alkyne = alkynyl- Alkane = alkyl-

If both bulky groups on a cyclohexane are on the same side = ________ If both bulky groups on a cyclohexane are on different sides = ________

Cis Trans

Hydrocarbons

Compounds composed of only carbon and hydrogen

Diastereomers

Configurational isomers that are not mirror images of each other. These occurs when a molecule has two or more stereogenic centers and differs at some but not all of these center. These molecules will have different chemical properties. However, they may behave similarly in particular reactions because they have the same functional groups For any molecule with n chiral centers, there are 2^n possible stereoisomer

Ring Strain

Energy created in a cyclic molecule by angle strain, torsional strain, and nonbonded strain; determines whether a ring is stable enough to stay intact

What are the three carboxylic acid derivatives?

Esters Amides Anhydrides

flagpole interactions

For cyclohexane, the steric interactions that occur between the flagpole hydrogen atoms in a boat conformation

Anhydrides

Formed from two carboxylic acid molecules by dehydration (removal of one water molecule). Many anhydrides are cyclic (intramolecular dehydration) Named using the suffix anhydride in place of acid in the name of the corresponding carboxylic acid if the anhydride is formed using only one type of carboxylic acid (pthalic anhydride, succinic anhydride) If the anhydride is not symmetrical, both carboxylic acids are named without the suffix acid (ethanoic propanoic acid)

Molecular Orbitals

Formed when two atomic orbitals combine. They are mathematically obtained by adding or subtracting the wave functions of the atomic orbitals

Stereoisomers

Have the same chemical formula (like structural isomers) but also share the same atomic connectivity. They have the same structural backbone. They differ in how these atoms are arranged in space (their wedge and dash pattern), and all isomer that are not structural isomers fall under this category

Alkenes

Hydrocarbons with one or more carbon-carbon double bonds

Esters

Hydroxyl group of the carboxylic acid is replaced with an alkoxy group (-OR, where R is a hydrocarbon chain) Naming: The second term is the name of the parent acid, with -oate replacing -oic acid suffix from carboxylic acids Based on the naming conventions for carboxylic acids. The first term is the alkyl name of the esterifying group. Think of the first term as an adjective describing the ester, based on the identity of the alkyl (R) group. Ex: ethyl propanoate, propyl methanoate, methyl butanoate, propyl ethanoate

What is the anti conformation?

In a staggered conformation, this is when the two largest groups are antiperiplanar (in the same plane, but on opposite sides) to each other. This is the most energetically favorable type of staggered conformation

What does the n- prefix indicate?

Indicates that the substitute is "normal" and a straight-chain alkane

Configurational isomers What are the two types?

Isomer molecules that can only be interchanged by breaking and reforming covalent bonds Diastereomers Enantiomers

What does it mean if a compound is optically active?

It has the ability to rotate plane polarized light. Ordinary light is unpolarized, which means that is consists of waves vibrating in all possible planes perpendicular to its direction of propagation

Aldehydes and ketones do not have ________ _______ because they are only connected to the alkyl chains or in the case of aldehyde to hydrogen atoms Carboxylic acids and their derivatives do have _______ _______ connected to the carbonyl group

Leaving groups

Achiral

Mirror images that can be superimposed A carbon atom with only three different substituents have a plane of symmetry and would therefore be considered achiral (using a simple 180˚ rotation about the vertical axis)

What is eclipsed conformation?

Molecules pass through this conformation when they are being converted from anti to gauche conformation. It occurs when the two methyl groups are 120˚ apart and overlap with the hydrogen atoms on the adjacent carbon

Steric repulsion

Molecules take up space. Strong repulsion occurs when two molecules overlap due to Pauli electron repulsion. For example, when two He atoms come too close together, two of the electrons will need to move up to the antibonding orbital, leading to higher potential energy.

Enantiomer

Molecules that are non superimposable mirror images of one another and have the same connectivity, but opposite configurations at EVERY chiral center in the molecule. These have identical physical and chemical properties with two notable exceptions: optical activity and reactions in chiral environments

Structural Isomers (what is another name?)

Molecules that share their molecular formula, meaning that their molecular weights must be the same. Aside form this similarity, structural isomers are widely varied, with different chemical and physical properties

Aldehyde

Named by replacing the -e in the alkane with -al (typically does not receive a number because it is at the terminal end and normally takes higher priority) An organic molecule with a carbonyl group located at the end of the carbon skeleton

Ketone

Named by replacing the -e in the name of the parent alkane with the suffix -one. We will always assign a number to the carbonyl carbon when naming ketones (ensure to give the carbonyl the lowest possible number if it is the highest-priority group) An organic compound with a C=O carbonyl group within a carbon chain

_________ ________ decreased with more bonds to heteroatoms? What are heteroatoms?

Oxidation state (important for determining the highest priority carbon). Oxidation state decreases when bound to heteroatoms or with more bonds to hydrogen Heteroatoms occur whenever there is a carbon bound to anything besides a carbon or hydrogen (such as oxygen, nitrogen, phosphorus, or halogens)

In a more complex molecule with a highest-priority group that takes precedence over the carbonyl, we name aldehyde and ketones as substituents, using what prefix?

Oxo-

Cahn-Ingold-Prelog Priority rules

Priority is given by looking at the atoms connected to the chiral carbon or double-bonded carbons Whichever has the highest atomic number gets higher priority If there is a tie, one moves outward from the chiral carbon or double bond until the tie is broken

To alleviate steric strain, cycloalkanes attempt to adopt various nonplanar conformations _________ cyclobutane _________ cyclopentane _________ cyclohexane _________ cyclohexane _________ cyclohexane Which is the most stable conformation of the cyclohexane

Puckered cyclobutane Envelope cyclopentane Chair cyclohexane (most stable) Boat cyclohexane Twist-boat cyclohexane

Carboxylic Acids

Replace the -e in the name of the parent alkane with the suffix -oic acid Contain both a carbonyl group (C=O) and a hydroxyl group (-OH). They are terminal functional groups so their associated number is normally 1 in regard to naming This is the most oxidized functional group that appear on the MCAT, with three bonds to oxygen; only carbon dioxide, with four bonds to oxygen, contains a more oxidized carbon (highest priority group)

How are alcohols named?

Replacing the -e in the name of the corresponding alkane with -ol 1) Chain is numbered so that the carbon attached to the alcohol gets the lowest possible number 2) The hydroxyl group gets higher priority in naming than the multiple bonds if present (the alcohol gets a higher oxidation state than the multiple bonds) 3) If the alcohol is not the highest priority, it is a hydroxyl substitute

Potential energy vs. Degree of Rotation

Shows relative minima and relative maxima of potential energy of the molecule throughout its various conformations. Every molecule wants to be in the lowest energy state possible, so the higher the energy, the less time the molecule will spend in that conformation

Optical Isomers

Stereoisomers that are non-superimposable mirror images of each other. The different spatial arrangements of the groups in these molecules affects the rotation of plane-polarized light

cis-trans isomers (geometric isomers)

Stereoisomers that differ only with respect to their cis or trans arrangement on a ring or double bond (immovable bond)

What is the highest ordered functional group?

The functional group with the most oxidized carbon. This carbon and functional group will determine the suffix of the name

Amide

The hydroxyl group of a carboxylic acid is replaced by an amino group (nitrogen-containing group) More complex: the amino nitrogen can be bonded to zero, one or two alkyl groups. Similar to esters, except that the suffix becomes -amide Substituents attached to the nitrogen atom are labeled with a capital N-, indicating that this group is bonded to the parent molecule via a nitrogen (NOTE: substituents are included as prefixes in the compound name and are not numbered) Ex: N-ethyl-N-methylbutanamide, N,N-dimethylethanamide, propanamide

If there are two contiguous carbon chains with the same length of carbons, which one helps determine the name and suffix?

The most substituted chain with the highest order functional group

Conformational isomers

The same molecules, only at different points in their natural rotation around a single sigma bond. While double bonds hold their position, single bonds are free to rotate around the sigma bond They arise from the fact that the free rotation of atoms around the sigma bond can create varying levels of rotation and different levels of strain between the existing atoms

half-chair conformation

The unstable conformation halfway between the chair conformation and the boat conformation. Part of the ring is flat in the half-chair conformation

What is the more general name for aldehydes and ketones? What is the difference between the two?

They are both carbonyls Aldehydes are chain terminating meaning that they appear at the end of the parent chain Ketones have a carbonyl group in the middle of the chain

Why are geminal diols not commonly seen?

They are hydrates and spontaneously dehydrate (lose a water molecule) to produce carbonyl compounds with the C=O

What is gauche conformation?

This is a type of staggered conformation where the methyl groups are 60˚ apart.

Isomers

Two different molecules that have the same chemical formula. Isomerism describes a relationship; two molecules can be isomers to each other but no molecule can be an isomer of itself

(E) and (Z) nomenclature

Used for compounds with polysubstituted double bonds Start by identifying the highest priority substituent attached to each double-bonded carbon (Z) : two highest-priority substituents are on the same side of the double bond (E) : two highest-priority substituents are on the different sides of the double bond

What is a totally eclipsed conformation?

When the two methyl groups directly overlap each other with 0˚ separation, the molecule is said to be totally eclipsed and is in the highest-energy state. This conformation is the least energetically favorable because the two largest groups are synperiplanar (in the same plane on the same side)

What is the staggered conformation?

When there is no overlap of atoms along the line of sight in butane. This is the most stable conformation with two methyl groups oriented 180˚ away from each other In this position, there is minimal steric repulsion between the atom's electrons clouds because they are as far apart as possible and in their lowest energy state

Alkynes

a carbon compound with a carbon-carbon triple bond.

Carbonyl group

a chemical group consisting of a carbon atom linked by a double bond to an oxygen atom

Alkanes

a hydrocarbon containing only single covalent bonds

Optical activity

chiral molecules are optically active d = (+) = dextrorotatory = clockwise l = (-) = levorotatory = counterclockwise this cannot be predicted by structure, must be measured by polarimeter (determined experimentally) Not related to the absolute configuration of the molecule. For a molecule to have optical activity, it must not only have a chiral center within it, but must also lack a plane of symmetry

What are the two types of stereoisomers?

conformational and configurational

vicinal diols

diols with hydroxyl groups on adjacent carbons (Vicinal diols are in the vicinity of each other, meaning that they are on nearby or adjacent carbons)

acetylaldehyde

ethanal

ethylene glycol

ethane-1,2-diol

Acetic acid

ethanoic acid

What is ethyl alcohol?

ethanol

Molecules need a substantial amount of _______ in order to achieve energetically unfavorable conformations

heat (not room temperature normally)

Formaldehyde

methanal

Formic acid

methanoic acid

Chair flip

one chair conformation is converted to the other briefly passes through the half chain conformation all axial groups become equatorial all equatorial groups become axial dashed lines remain dashed wedges remain wedges conversion is slowed if there is bulky groups attached bulkiest group will favor the equatorial position

Alcohols

organic compounds containing hydroxyl groups

Alkyl halides

organic compounds in which one or more halogen atoms- fluorine, chlorine, bromine, or iodine- are substituted for one or more hydrogen atoms in a hydrocarbon fluoro-, chloro-, bromo-, iodo-

propionaldehyde

propanal

proprionic acid

propanoic acid

Specific Rotation

standardized form of observed rotation that is calculated from the observed rotation and experimental parameters

Parent Chain

the longest continuous chain of carbon atoms in a branched-chain alkane, alkene, or alkyne

Reacting two enantiomers with a single enantiomer of another compound will lead to _______. How does this allow researchers to separate two different enantiomers?

two diastereomers Because these two different products differ at some (but not all) chiral centers, they are necessarily diastereomers. They have different physical properties, allowing them to be separated by common laboratory techniques such as crystallization, filtration, and distillation. Once separated, these diastereomers can be reacted to regenerate the original enantiomers