U world organic chemistry

Fischer esterification and carboxylic acid nomenclature

* acid-catalyzed and they are when a carboxylic acid and an alcohol combine

Esters

Carboxylic acid derivative formed by fischer esterification * named first by stating the prefix that corresponds to the alcohol alkyl chain, followed by the name of the carboxylic acid. * suffix goes from '-ic acid' to just "-ate" as in ethyl hexanoic acid to ethyl hexanoate

Gas Liquid Chromatography

Highest Molecular Weight Eludes Last separates based on boiling point. Highest boiling point eludes last.

Mass Spectrometry (MS)

separates ions according to their mass-to-charge ratiom/z.

High performance liquid chromatography (HPLC)

Optimal for small sample sizes - solvent (mobile phase) is under pressure - separates compounds based on polarity

Rovibrational Spectroscopy

Remember from Quantum Chemistry Lab

substitution reactions

SN1 and SN2

R/S stereochemical Configuration

To Determine: The priority of substituents attached to the chiral carbon is assigned, with higher priority given to atoms with greater atomic number. In case of a priority tie, the atomic numbers of the next attached atoms are considered. The circular arrangement of groups 1, 2, and 3 is examined. If the lowest-priority group (4) is pointing into the plane (dash), a clockwise circle formed by these groups is R and a counterclockwise circle is S. If the lowest-priority group is pointing out of the plane (wedge), a clockwise circle is S and a counterclockwise circle is R.

Organic Extraction Method

Utilizing Densities

Vacuum Distillation

appropriate for compounds that have boiling points greater than 150 Degrees Celsius, which may decompose when heated beyond this temperature. Connection to vacuum decreases pressure of the system and lowers boiling points of the mixture component

Epimers

are diastereomers that differ in configuration at one position, and anomers are a specific type of epimer that differs at the anomeric carbon.

alcohols

are named based on the longest continuous carbon chain containing the hydroxyl group (-OH). The prefix corresponds to the number of carbons in the alkyl chain, and the suffix -ol corresponds to the hydroxyl functional group.

Proton NMR (nuclear magnetic resonance spectroscopy)

detects protons in a molecule when an external magnetic field and radio frequency are applied to a sample. The protons align their magnetic field either with (low-energy alpha spin state) or against (high-energy B spin state) the external magnetic field.

anomers

differ in configuration at the anomeric carbon only which is carbon C2 in a cyclic molcule Alpha refers to down (hydroxyl) and Beta refers to up (hydroxyl)

Shielding vs De-shielding Diagram

electronegative groups deshield

stereospecific reactions

occur when stereoisomers that undergo the same reaction give different stereoisomers of the product. The stereochemistry of the starting material determines the stereochemistry of the product.

Lowering the pH

of the solvent increases the concentration of protons and results in a greater number of multiply charged molecules (z > 1). An increase in multiply charged molecules would therefore result in greater signal intensity for smaller m/z values.

Reduction with LiAlH4

reduces carboxylic acids and esters to primary alcohols LiAlH4 is a strong reducing agent and will reduce carbonyl compounds to alcohols. Aldehydes, esters, and carboxylic acids will be reduced to primary alcohols, and ketones will be reduced to secondary alcohols.

3100 cm^-1

sp2 C-H Stretch (IR Spectra) conjugated to have one double bond and attaches to 3 things, of one which is hydrogen

Ketose

such as fructose the anomeric carbon is at c2

Aldose

such as glucose the anomeric carbon is C1

Reversed Phase High Performance Liquid Chromatography (RP-HPLC)

the stationary phase is a nonpolar compound and the mobile phase is a polar solvent; polar molecules move faster through the column, and nonpolar molecules have longer retention times. Of the materials given, water (polar) would be appropriate for the mobile phase and C-18 alkyl hydrocarbon (nonpolar) would be appropriate for the stationary phase.

3650-3200 cm^-1

O-H Stretching (IR Spectra)

how to determine the structure of an organic molecule from its name:

1. Determine the number of carbon atoms in the parent chain, which is the longest chain containing the highest priority functional group. The prefix of the parent alkane determines the number of carbons, and the suffix describes the high priority functional group. The number prior to the chain name describes the carbon to which the main functional group is attached. 2. Determine the position and identity of each substituent, if any. All substituent names are placed at the beginning of the compound name, together with the number of the carbon to which the substituent is attached.

Fractional Distillation

1. Mixture is heated. 2. Lower boiling compound vapors travel to the fractionating column 3. Lower boiling compound vapors condense 4. Lower boiling compound is collected works best for: compounds that have boiling points that are <25 Degrees Celsius Apart (more difficult so better method for this) Only difference is fractioning column in the primary setup

Mass Spectrometry

1. Sample is ionized and can break apart into fragments (m/z) mass to charge ratio 2. Ions are accelerated toward magnet 3. Ions are deflected according to mass 4. Ions are detected and a plot of ion mass abundance vs. m/z is recorded

1600-1475

C=C double bond stretching (IR Spectra)

1810-1650 cm^-1

C=O stretching (IR Spectra)

Alkene Classification (Z(cis) vs E(trans))

Cis (same side) = Z * sissy = Cis Z Trans (opposite side) = E * tranny = trans-E

Educational Objective for Alkyl Halides and SN1 vs SN2 Rxns

Stereospecific reactions occur when stereoisomers undergo the same reaction and give different stereoisomers of the product. Tertiary alkyl halides readily undergo SN1 reactions, which are not stereospecific because the nucleophile can attack the planar carbocation intermediate from the top or the bottom of the carbocation, forming two stereoisomers. Primary alkyl halides readily undergo SN2 reactions, which are stereospecific because the nucleophile attacks from the opposite side, where the leaving group is eliminated (backside attack).

Hydride reagents, such as LiAlH4 and NaBH4, are common reducing agents and are made of a metal surrounded by one or more hydride ions. The hydride ion acts as a nucleophile and attacks an electrophilic atom. LiAlH4 is a strong reducing agent and will reduce carbonyl compounds to alcohols. Aldehydes, esters, and carboxylic acids will be reduced to primary alcohols, and ketones will be reduced to secondary alcohols.

___________ ____________, such as LiAlH4 and NaBH4, are common reducing agents and are made of a metal surrounded by one or more hydride ions. The hydride ion acts as a nucleophile and attacks an electrophilic atom. LiAlH4 is a strong reducing agent and will reduce carbonyl compounds to alcohols. Aldehydes, esters, and carboxylic acids will be reduced to primary alcohols, and ketones will be reduced to secondary alcohols.

Donors

____________ are hydrogen atoms bonded to an electronegative atom from the second row of the periodic table.

Acceptors

_________________ are electronegative atoms with a lone pair of electrons (eg, oxygen, nitrogen, fluorine).

Transesterification

_________________ is a reaction between an ester and an alcohol in which the ester -OR group is replaced with the alcohol -OR group. __________________ can be either acid-catalyzed or base-catalyzed. The alcohol acts as a nucleophile and attacks the electrophilic carbonyl carbon of the ester, adding a new -OR group to the ester. The original -OR group leaves and is protonated, becoming an alcohol and yielding a new ester.

Stronger intermolecular forces

_________________ require more energy to break, causing molecules with these forces to have a higher boiling point than molecules of similar molecular weight with weaker intermolecular forces.

Diastereomers

a type of stereoisomer, have more than one stereocenter and differ in orientation at some, but not all, stereocenters.

3550-3060 cm^-1

amide N-H Stretching (IR Spectra)

carboxylic acids

are named based on the longest continuous carbon chain containing the carboxylic acid functional group (known as the parent chain). The parent chain is numbered beginning with the carbonyl carbon of the carboxyl group. Substituents on the parent chain are named beginning with the parent chain carbon number it is bonded to, followed by the prefix denoting the number of carbons in the substituent. The substituents are listed in alphabetical order. The parent chain is named last, and for carboxylic acids, the suffix -e of the parent alkane is replaced with -oic acid.

SN1 reaction

are not stereospecific because two isomers are formed - occurs in two steps The first step of an ____________ involves breaking the bond between the leaving group and the adjoining carbon, forming a planar carbocation intermediate. In the second step, the nucleophile can add to the top or bottom of the planar carbocation, so two products form.

hydrogen bonds

are strong intermolecular forces that consist of a donor and acceptor.

inversion of stereochemistry in an SN2 reaction

consequently, when a nucleophile, like the electrons on the Oxygen atom, it strikes the chiral center, which acts as the electrophile, and the leaving group is displaced in one step. The not having of electrons that the OH experiences pulls it to the chiral center for replacement, and this changes the way that it rotates polarized light (this means changes the stereochemistry). so it is replaced with a wedge instead of a dash

ESI MS (electrospray ionization mass spectrometry)

creates ions by protonation of the analyte. The analyte is passed through an electrospray needle that has a potential difference applied with respect to a counterelectrode. This leads to the formation of charged droplets, which are repelled toward the counterelectrode and mass spectrometer upon solvent evaporation.

Reducing Agents

decrease an atom's oxidation state. The reduction of a carbon atom decreases the number of bonds it has to electronegative atoms (including oxygen, nitrogen, and halogens), and increases the number of bonds to less electronegative atoms (typically hydrogen).

separation of enantiomers (RESOLVING AGENT)

enantiomers have many of the same chemical and physical properties, including melting and boiling points, solubility, and polarity, although they differ in the way that they interact with plane-polarized (linear) light. Therefore, separation of enantiomers relies on changing the physical properties of the molecules. This can be accomplished by adding a Resolving Agent (which is a chiral molecule) When a resolving agent is added to a racemic mixture, it reacts with each enantiomer, forming a covalent bond or an ionic salt. Because the resolving agent is chiral, it incorporates a new chiral center into each enantiomer, creating a pair of diastereomers. Diastereomers can be separated from each other because, unlike enantiomers, they have different physical properties. Once the diastereomers are separated, the resolving agent is removed, yielding the original molecules as single enantiomers.

HetteroCyclic amines

in blue distinction between heterocyclic, no bonds other than nitrogen directly attached to ring and further into secondary amine

SN2 reactions

involves strong nucleophile pushing into a compound while displacing LG at same time In contrast, _________________ occur in a single step and the nucleophile always attacks on the side opposite the leaving group (backside attack), causing an inversion at the electrophilic carbon. An _______________ forms only one product.

A Chiral Carbon

is a carbon with four different substituents. The R or S configuration (stereochemistry) of the stereo-center depends on the spatial arrangement of the substituents.

fractional distillation

is a purification technique that separates molecules based on their boiling point, which is dependent on the intermolecular forces holding the molecule together.

High-performance liquid chromatography (HPLC)

is a type of chromatography in which a liquid solvent (mobile phase) carries the sample through a column filled with adsorbent material (stationary phase). The guiding principle for separation is polarity: Molecules with a polarity similar to the stationary phase have longer retention times than molecules with polarities similar to the mobile phase.

"Like dissolves like" (in extraction procedures)

is the driving principle for extraction procedures. During extraction, two immiscible solvents (solvents that will not remain mixed) can be used to separate solutes (dissolved particles) according to differences in polarity. This procedure often entails the addition of an organic solvent to an aqueous mixture. After gentle shaking, hydrophobic solutes such as lipids separate into the organic layer, and polar or charged solutes such as nucleic acids remain in the aqueous layer. During extraction procedures, a molecule's charge or polarity may be modified to increase or decrease its affinity for a particular solvent.

Normal Phase High Performacy Liquid Chromatography (polar stationary phase)

mobile phase consists of a non-polar solution, which is drawn into the column and placed under pressure by the pump a small amount of sample is dissolved in the solution stationary phase contains a polar compound (silica) non-polar compounds interact with the mobile phase more and elude first polar compounds interact more with the stationary phase and elude last Y axis = absorption X axis = retention time is used to separate nonpolar compounds and consists of polar stationary phase and non-polar mobile phase nonpolar mobile phase uses hexanes

Reverse Phase High Performace Liquid Chromatography (nonpolar stationary phase)

more non-polar substances interact with the stationary phase more = longer retention time more polar substances interact less with the stationary phase = shorter retention time used to separate polar compounds and consists of a non-polar stationary phase and a polar mobile phase nonpolar stationary phase uses C18 hydrocarbon polar mobile phase uses water, mathanol, or acetone

Enantiomers

non-superimposable mirror images

Prior to adduct formation, DNA was isolated from a cellular mixture. Membrane lipids were first extracted using an organic solvent, which was then evaporated, and DNA was precipitated from the aqueous layer using cold ethanol and sodium acetate. Which of the following mechanisms allowed for DNA precipitation?

sodium acetate forms ionic bonds with DNA, neutralizing its charge

3300 cm^-1

sp C-H stretch (IR spectra) conjugated to have only H bond

3000 cm^-1

sp3 C-H Stretch (IR spectra) standard hydrogen bonding in tertiary carbon

thin layer chromatography

technique that separates components of a mixture based on polarity and can be used to monitor reactions Stationary Phase: is made of a polar material, usually silica (SiO2). - therefore polar molecules will have a greater affinity for the TLC plate, and travel a smaller distance up the plate than non-polar molecules - Molecules that have UV chromophores, which include double and triple bonds, carbonyls and conjugated systems, can be visualized with UV light

Thin-Layer Chromatography

technique that separates mixture components based on the polarity of the molecules in the mixture. - Remember that molecules with UV chromophores (conjugated systems, double or triple bonds, and carbonyls) the UV light excites the molecule making it visible.

signal intensity

the height of a data peak relative to other peaks, corresponds to the relative quantity of ions at each mass-to-charge ratio m/z. this is in mass spectrometry During electrospray ionization (ESI), particles are charged via protonation within droplets. Ions that have multiple charges have a smaller m/z ratio because the denominator (charge) has increased.