Organic Chemistry: Carbon, Lipids, and Isomers

• The lecture introduces organic chemistry, carbon compounds, lipids, and isomers.
• Learning objectives include describing and visualizing organic structures, characterizing hydrocarbon frameworks, classifying structures by isomerism, identifying stereochemical centers, and providing an overview of lipids.

Organic Chemistry Definition

• Organic chemistry was originally defined as the chemistry of living things but expanded to chemistry based mainly on carbon.
• The carbon and hydrogen framework, along with heteroatoms, provides the building blocks of organic compounds.
• Organic chemistry is the chemistry of carbon compounds that form living systems.

Hydrocarbon Frameworks

• Organic compounds are based on hydrocarbon frameworks with embedded heteroatoms (O, N, S).
• Remaining bonds fulfill the octet rule with hydrogen atoms.
• Specific combinations and arrangements of heteroatoms with carbons form functional groups that provide chemical variety and interactions.
• Knowledge of common and stable functional groups helps predict organic compound chemistry.

Drawing Organic Molecules

• Organic structures are drawn as zig-zag chains of atoms, where each vertex represents one carbon.
• Hydrogen atoms and C-H bonds are usually not shown unless important for reactions.
• Zig-zag drawing aims to reproduce actual geometry, important for complex structures like rings.

Carbon Chains

• Carbon chains serve as the basic framework for organic chemistry.
• Alkanes are chains of hydrocarbons linked only by single bonds and can be linear or branched, following the formula CnH2n+2.

Alkane Properties

• Alkanes have weak van der Waals forces, which strengthen with more electrons and larger surfaces.
• They are weakly reactive due to strong C-C and C-H bonds, with high pKa values.
• Branching leads to a large number of possible isomers as alkane size increases.
• Alkyl groups can branch off other organic molecules.

Unsaturated Hydrocarbons

• Alkenes contain at least one C-C double bond, with properties similar to alkanes.
• They are slightly more reactive due to the double bond allowing addition reactions.
• Alkynes contain at least one C-C triple bond, are rarer, and have higher reactivity than alkenes.

Aryl Groups

• Aryl groups are substituents derived from an aromatic ring and are used as a generalization for a large range of different groups.

Functional Groups

• The addition of heteroatoms (O, N, S, P) to hydrocarbons results in functional groups that drive chemical behavior in organic and biological molecules.

Naming Organic Compounds

• IUPAC rules are extensive, with over 1000 pages in the 2013 edition making the process automated for complex molecules.
• Give a molecular structure rather than a name for complicated molecules.
• Naming describes the hydrocarbon framework, substituents, functional groups, and their positions.
• Functional groups are indicated by specific prefixes or suffixes while numbers distinguish group positions.

Characterizing Organic Molecules

• Mass spectrometry provides molecule mass and composition using ionized molecules and fragments.
• X-ray crystallography provides bond lengths and angles but requires more effort.
• NMR spectroscopy relies on electron densities, revealing carbon frameworks and hydrogen environments.
• IR spectroscopy uses resonance with chemical bond vibrations to reveal characteristic bonds and functional groups.

Isomerism

• Isomers are molecules with identical formulas but different 3D structures, existing as constitutional isomers and stereoisomers.
• Constitutional isomers differ in chemical bonding.
• Stereoisomers have identical bonding but differ in spatial arrangement.

Cis-Trans Isomerism

• Arises when restricted bond rotation (alkenes/cyclic systems) leads to distinct isomers denoted as cis (same side) or trans (opposite side).
• Cis-trans isomers have exhibited different interactions leading to significant property changes.
• R/S nomenclature is used when there are two substituents, otherwise E/Z nomenclature for other instances.
• Priorities are the same as for enantiomers, based on Cahn-Ingold-Prelog rules.

Atropisomerism

• Isomers are a result of restricted rotation.
• They can be isolated and distinct at room temperature.

Chirality

• Molecules are chiral, aka cannot be superimposed on their mirror image through translations, rotations, and bond rotations.
• Chiral molecules have non-superimposable mirror images called enantiomers.
• Enantiomers rotate polarized light in opposite directions with identical physical properties.
• Chemical properties differ in chiral environments like biological systems.

Chirality Importance

• Thalidomide scandal: One enantiomer was an effective drug and the other was toxic and caused birth defects.
• A racemic mixture is a mixture of both enantiomers.
• The compound can change to a racemic mixture even with only one enantiomer present.

Optical Activity

• Chiral compounds rotate polarized light.
• A (+) or (-) may be included in the compound name to indicate this behavior, but these do not correlate with the actual nomenclature used to describe enantiomers and the rotation direction cannot be predicted.

Chiral Centers

• Stereocenters in molecules exhibit chirality and are often carbon atoms.
• A chirality center is a stereocenter with four different substituents, typically sp³-hybridized carbons.
• Biological molecules are assigned D and L labels to characterize stereochemistry; a more universal nomenclature uses R and S labels.

CIP Naming Conventions

• Assign priorities to substituents based on atomic numbers.
• For a tie, consider atoms bonded to the substituents until a difference is found.
• Align the molecule to view it with the lowest priority substituent into the paper.
• Follow the path from highest to second-highest to third-highest priority.
• Clockwise configuration is (R) (rectus); anticlockwise is (S) (sinister).

Fischer Projection

• Used for carbohydrates.
• Design to assign stereochemistry and identify enantiomers.

D/L Nomenclature

• The labels refer to the orientation of the final hydroxyl (-OH) or amine (-NH2) group on the (chiral) carbon chain.
• If the group is on the right, it is the D configuration, and if it is on the left, it is the L configuration.

Diastereomers

• Molecules are stereoisomers that are not mirror images of each other.
• Enantiomers must have different configurations at each of their chiral centers, while diastereomers will only differ in some.

Stereochemistry of Sugars

• Naturally occurring sugars are in their D-configuration.
• The chirality pattern on stereocenters distinguishes sugars.

Ring-Chain Tautomerism

• Sugars can form cyclic configurations through prototropy.
• Tautomers are structural isomers that readily interconvert, distinct from resonance structures.

Keto-Enol Tautomerism

• A ketone is a carbonyl group and an enol is a hydroxyl group adjacent to a C-C double bond.
• Enzymes, acids, and bases can catalyze the transition leading to a tautomerism.

Lipids

• Lipids are essential organic molecules insoluble in water, generally hydrophobic or amphiphilic, contain long carbon chains, and/or rings with heteroatoms.
• Glycerolipids consist of fatty acids combined with glycerol, while glycerophospholipids combine long chains with glycerol-3-phosphate, which are the main component of membranes.

Phospholipids Properties

• Polar head, non-polar tail.
• Act as dispersion forces with in hydrophobic tails.

Summary of the lecture

• Organic molecules are analysable as a combination of hydrocarbon framework and functional groups in VSEPR-predicted geometries.
• A single molecular composition may lead to isomers with different constitutions.
• Stereoisomers exist even with identical bonding, differentiated by atom orientation.
• R/S and D/L labelling systems are used for chiral centers in amino acids and sugars.
• Molecules can possess diastereoisomers with distinct properties, and tautoermisation enables chemical transformations between constitutional isomers.