Organic Chemistry Refresher GDNP 6510

Organic Chemistry Refresher

This presentation covers the refresher of organic chemistry.
The presenter is Cora Rabe, for GDNP 6510.

Presentation Objectives

Students will be able to explain the differences between biochemistry and organic chemistry.
Students will be able to recognize the functional groups of organic chemistry.
Students will be able to recall an example of a compound that contains that functional group.
Students will be able to describe the primary chemical bonds.

The Sciences Explained

Biochemistry studies chemical processes in the body. It examines the structures and functions of lipids, proteins, energy production, and DNA.
Organic chemistry is the study of compounds containing carbon. Key organic compounds include carbon, nitrogen, oxygen, halogens, silicone, phosphorus, silicon, and sulfur.
Physics studies matter and its movement through space and related energies.

Organic vs. Inorganic

Organic compounds are typically gases, liquids, or solids with low melting points (<360°C).
Organic compounds are usually insoluble in water but soluble in organic compounds (e.g., diethyl ether, toluene, dichloromethane).
Aqueous solutions of organic compounds don't conduct electricity.
Organic compounds often burn and decompose.
Organic reactions are typically slow.
Inorganic compounds are typically solids with high melting points.
Inorganic compounds are usually soluble in water and insoluble in organic compounds.
Aqueous solutions of inorganic compounds that contain ions conduct electricity.
Inorganic reactions are typically fast.

Elements of the Periodic Table

Hydrogen has 1 proton and 1 electron.
Helium has atomic number 2 (2 protons and 2 electrons).
Lithium has atomic number 3 (3 protons and 3 electrons, but 2 in the core and 1 valence, making it reactive).

The Atom

Atoms are composed of neutrons, protons, and electrons.
Neutrons are neutral and have a weight of 1.
Protons are positive and have a weight of 1.
Electrons are negative and have a weight of 0.

Octet Rule

Atoms strive to have 8 valence electrons.
This arrangement maximizes attraction towards the atomic nucleus while minimizing electron repulsions.

Matter

Matter is anything that has mass and occupies space.
Matter exists in states including solids, liquids, and gases.
lons are atoms or groups of atoms bonded together that have an electrical charge.
Elements consist of only one kind of atom.
Molecules are groups of atoms chemically bonded together; they are electrically neutral.
Compounds are made of more than one kind of atom.
Mixtures consist of different elements or molecules that are not bonded together.

Valence Shell Electron Pair Repulsion (VSEPR)

Some important concepts about bonds in compounds are explained.
Compounds want to achieve the stable electron arrangement.
8 electrons are needed for a complete octet in the outermost shell.
Carbon contains 4 atoms in its outermost shell; shares remaining 4 electrons with other atoms. (Methane is an example).

Covalent vs. Ionic Bonds

Covalent Bonds: Electrons are shared between atoms; typically between non-metals.
Covalent bonds are weak to break; polar and nonpolar; triple bonds are stronger
Covalent bonds are poor conductors.
Ionic Bonds: Electrons are transferred between atoms; typically between metals and nonmetals.
Ionic bonds are strong to break and are easily conducted by water.

Types of Bonds (Single, Double, Triple Bonds)

Different chemical bonding types are illustrated in diagrams.
There are single, double, and triple covalent bonds, along with example compounds.

Electronegativity

Electronegativity is the attraction that an atom has for electrons in a chemical bond. Highly electronegative atoms have a larger ratio of proton-core (positive charge) to electron shells (negative charge).
Strongly electronegative elements (like O, N, F) tend to attract electrons from less electronegative elements (like H, C).
This creates polar molecules with areas of unequal electron distribution (polarity).

Intermolecular Forces

Intermolecular forces are attractions between molecules. Some examples given include:
Hydrogen bonding (strong dipole-dipole attraction)
Dipole-dipole attraction
London forces

Hydrogen, Nitrogen and Oxygen

Hydrogen, nitrogen, and oxygen atoms can either share or lose electrons to complete their outer electron shell(s).
Hydrogen tends to form one bond, nitrogen 3, and oxygen 2.
These atoms tend to strongly attract electrons, creating polar bonds and subsequently polar molecules.

The Element Carbon

Carbon is important and forms a significant foundation for all living things.
Carbon can create many different compounds due to its ability to form four covalent bonds with other atoms.
These bonds often create chains, branched structures, or rings.

Solubility

Solubility is the amount of solute that dissolves in a given amount of solvent.
Saturated solution = maximum solute is dissolved in a solution.
"Like dissolves like" describes substances that are similar in polarity, for example, polar molecules readily dissolve other polar molecules
Temperatures affect solubility
Water is an example of a universal solvent.

Functional Groups

Functional groups are specific groups of atoms within organic molecules that determine many chemical reactions.
The presence of functional groups in molecules will often dictate their unique physical and chemical properties.
The functional groups can be grouped into several classes, with each class having unique physical and chemical properties.

Alkanes, Cycloalkanes, Alkenes, Alkynes & Arenes

Hydrocarbons are compounds that contain only carbon and hydrogen atoms.
Alkanes (saturated) have only single bonds between carbon atoms.
Cycloalkanes are alkanes in ring form.
Alkenes (unsaturated) have at least one double bond between carbon atoms.
Alkynes have at least one triple bond between carbon atoms.
Arenes (aromatic) have a benzene ring structure.

Hydrocarbons

Alkene compounds are more reactive than alkanes, with higher electron densities in double bonds.
Alkenes often appear as monomers or polymers.
Arenes are commonly observed and are stable compounds with a common benzene ring which is a stick-on group. (e.g., phenyl group).

Alkanes and Alkenes

Aliphatic hydrocarbons (long carbon chains) have properties that resemble fats and oils
Lack of polarity- Nonpolar- Insoluble in water

Cycloalkanes

Cycloalkanes are saturated hydrocarbons containing carbon rings.
They are often unstable and react with oxygen, releasing heat and producing carbon dioxide and water.
Some halogenated cycloalkanes are created by the substitution of halogen atoms for hydrogen atoms. This creates alkyl halides (e.g., halothane).

Alcohols

Alcohols are molecules containing a hydroxyl group (-OH) bonded to a tetrahedral carbon.
Alcohols are classified as primary (1°), secondary (2°), or tertiary (3°) based on the number of carbons bonded to the carbon attached to the hydroxyl group.
Alcohols are negatively charged (polar), making them soluble in water (hydrophilic).

Alcohols - Phenyls

Aromatic alcohols that are insoluble (lipophilic substances) in water are called phenols. A phenol is a compound that contains at least one hydroxyl group attached to an aromatic ring (has a benzene ring and a hydroxyl group).
Propofol has 12 carbon atoms.

Amines & Amides

Amines are molecules containing carbon-nitrogen bonds.
An amino group is a nitrogen atom bonded to one, two, three, or four carbons.
A lone pair of electrons results in molecules that are electrically neutral (especially in primary, secondary, and tertiary amines).
Quaternary amines have a positively charged nitrogen atom due to the loss of one electron from the lone pair.
Amides are molecules containing an amino group connected to the carbonyl group.

Amines

Neutral amines can easily cross biological barriers (e.g., blood-brain barrier).
Charged amines (e.g., quaternary amines) cannot easily cross those barriers.
Amine derivatives are commonly used as drugs.

Amides

Amides contain nitrogen atoms bonded to carbonyl groups
Carbonyl groups consist of a carbon atom double-bonded to an oxygen atom
Amides are created by the condensation reaction between a carboxylic acid and an alcohol.

Carboxylic Acids

Carboxylic acids have a carboxyl group (-COOH).
Carboxyl groups consist of a carbonyl group (-C=O) and a hydroxyl group (-OH).
Long-chain carboxylic acids, such as fatty acids, are crucial for energy storage in living organisms.

Carboxylic Acids + Amines = Amides

Amides are products from the reaction or condensation of a carboxylic acid with an amine.
This is a vital biochemical reaction, especially for linking amino acids to form proteins.

Amino Acids

Amino acids are molecules containing amine and carboxylic acid functional groups.
Amino acids connect to each other via a peptide bond (connecting amino acids).
The composition and structure of the amino acid's R group (side chain) significantly impacts the structure, and function of the resulting protein.

Amino Acids to Proteins

Amino acids combine to form proteins.
Bonding amino acids shapes proteins to have primary, secondary, tertiary, and quaternary protein structures.

Aldehydes & Ketones

Both Aldehydes and Ketones contain a carbonyl group
(O=C)
Aldehyde: carbonyl group bonded to a hydrogen
Ketone: carbonyl group bonded to two carbons.

Reactions of Aldehydes & Ketones

Aldehydes and ketone molecules can undergo oxidation and reduction reactions.
Aldehydes and ketone molecules can participate in the condensation reaction. This creates acetal and hemiaetal compounds.

Esters

Esters are a type of carboxylic acid derivative.
The H of the carboxyl group is replaced by a carbon group.
Esters can be formed when carboxylic acids react with alcohols (esterification).
Ester formation involves losing a water molecule via a condensation reaction.

Local Anesthetics

Local anesthetics are classified as either esters or amides.
Local anesthetic structure and properties affect their ability to cross barriers.
Anesthetics' effectiveness hinges on their ability to pass through certain biological barriers.

Ethers

Ethers contain an oxygen atom bonded to two carbon atoms.
Diethyl ether was a very early anesthetic.
Ethers are often polar and can dissolve other molecules.

Halogenated Ethers

These ethers have halogen atoms (e.g., chlorine, fluorine) in their structure.
Usually more stable and non-explosive than other ethers.

Thiols & Sulfides

Thiols are like alcohols but with sulfur instead of oxygen at the functional group. (e.g., an S-H group)
Oxidation of thiols produces a disulfide bond (e.g., S-S bond).
Thiols and sulfides have particular odors like the smell of skunks, rotten eggs to sewage.

Disulfide Bonds

Disulfide bonds are important in the structure and function of proteins.
Oxidation reactions connect sulfur atoms to form disulfide bridges in protein structures (e.g., secondary, tertiary, quaternary structures.

Capsaicin

Capsaicin is a chemical compound found in chili peppers.
The chemical formula and structure are provided.
Capsaicin has an effect on different organic compounds.

Isomers

Isomers are compounds with the same molecular formula but different structures or arrangements of their atoms.

Structural vs. Stereoisomers

The basic difference between structural and stereoisomers is that structural isomers have a different arrangement of atoms, while stereoisomers have the same arrangement but a different orientation of atoms.

Stereocenter (Chiral Center)

A stereocenter (chiral center) is an atom within a molecule which has different substituents attached.
Molecules with chiral centers and their mirror images are called enantiomers.

Enantiomers

Enantiomers are mirror images of each other but not identical.
Compounds with enantiomers often differ in their pharmacological activity.
Many drugs have specific enantiomer activity that can impact their efficacy and/or toxicity.

Enantiomers Continued

50% of drugs on the market are supplied as a racemic mixture (mixture of enantiomers). Enantiomers exhibit different affinities and behaviors within the body (e.g. receptor binding, metabolism, side effects).
Certain reactions are specific to an enantiomer.

Thank You

The slide expresses gratitude and encourages further questions.