Cis and Trans

• “Initial Tails” and “Final Heads”
• 3 Ways To Make OH A Better Leaving Group
• A Simple Formula For 7 Important Aldehyde/Ketone Reactions
• Acetoacetic
• Acids (Again!)
• Activating and Deactivating
• Actors In Every Acid Base Reaction
• Addition – Elimination
• Addition Pattern 1 – Carbocations
• Addition pattern 2 – 3 membered rings
• Addition Reactions
• Aldehydes And Ketones – Addition
• Alkene Pattern #3 – The “Concerted” Pathway
• Alkyl Rearrangements
• Alkynes – 3 Patterns
• Alkynes: Deprotonation and SN2
• Amines
• Aromaticity: Lone Pairs
• Avoid These Resonance Mistakes
• Best Way To Form Amines
• Bulky Bases
• Carbocation Stability
• Carbocation Stability Revisited
• Carboxylic Acids are Acids
• Chair Flips
• Cis and Trans
• Conformations
• Conjugate Addition
• Curved Arrow Refresher
• Curved Arrows
• Decarboxylation
• Determining Aromaticity
• Diels Alder Reaction – 1
• Dipoles: Polar vs. Covalent Bonding
• E2 Reactions
• Electronegativity Is Greed For Electrons
• Electrophilic Aromatic Substitution – Directing Groups
• Elimination Reactions
• Enantiocats and Diastereocats
• Enolates
• Epoxides – Basic and Acidic
• Evaluating Resonance Forms
• Figuring Out The Fischer
• Find That Which Is Hidden
• Formal Charge
• Frost Circles
• Gabriel Synthesis
• Grignards
• Hofmann Elimination
• How Acidity and Basicity Are Related
• How Are These Molecules Related?
• How Stereochemistry matters
• How To Stabilize Negative Charge
• How To Tell Enantiomers From Diastereomers
• Hybridization
• Hybridization Shortcut
• Hydroboration
• Imines and Enamines
• Importance of Stereochemistry
• Intermolecular Forces
• Intro to Resonance
• Ketones on Acid
• Kinetic Thermodynamic
• Making Alcohols Into Good Leaving Groups
• Markovnikov’s rule
• Mechanisms Like Chords
• Mish Mashamine
• More On The E2
• Newman Projections
• Nucleophiles & Electrophiles
• Nucleophilic Aromatic Substitution
• Nucleophilic Aromatic Substitution 2
• Order of Operations!
• Oxidation And Reduction
• Oxidative Cleavage
• Paped
• Pi Donation
• Pointers on Free Radical Reactions
• Protecting Groups
• Protecting Groups
• Proton Transfer
• Putting it together (1)
• Putting it together (2)
• Putting it together (3)
• Putting the Newman into ACTION
• Reaction Maps
• Rearrangements
• Recognizing Endo and Exo
• Redraw / Modify
• Robinson Annulation
• Robinson Annulation Mech
• Sigma and Pi Bonding
• SN1 vs SN2
• sn1/sn2 – Putting It Together
• sn1/sn2/e1/e2 – Exceptions
• sn1/sn2/e1/e2 – Nucleophile
• sn1/sn2/e1/e2 – Solvent
• sn1/sn2/e1/e2 – Substrate
• sn1/sn2/e1/e2 – Temperature
• Stereochemistry
• Strong Acid Strong Base
• Strong And Weak Oxidants
• Strong and Weak Reductants
• Stronger Donor Wins
• Substitution
• Sugars (2)
• Synthesis (1) – “What’s Different?”
• Synthesis (2) – What Reactions?
• Synthesis (3) – Figuring Out The Order
• Synthesis Part 1
• Synthesis Study Buddy
• Synthesis: Walkthrough of A Sample Problem
• Synthesis: Working Backwards
• t-butyl
• Tautomerism
• The 4 Actors In Every Acid-Base Reaction
  • Conjugation
• The Claisen Condensation
• The E1 Reaction
• The Inflection Point
• The Meso Trap
• The Michael Reaction
• The Nucleophile Adds Twice (to the ester)
• The One-Sentence Summary Of Chemistry
• The Second Most Important Carbonyl Mechanism
• The Single Swap Rule
• The SN1 Reaction
• The SN2 Reaction
• The Wittig Reaction
• Three Exam Tips
• Tips On Building Molecular Orbitals
• Top 10 Skills
• Try The Acid-Base Reaction First
• Two Key Reactions of Enolates
• What makes a good leaving group?
• What Makes A Good Nucleophile?
• What to expect in Org 2
• Work Backwards
• Zaitsev’s Rule

The first is in alkenes. Remember that we can’t rotate Pi bonds? This means that a molecule like 2-butene will have two possible isomers; the isomer where the two methyl groups are on the same side of the double bond is called “cis”, and the isomer where the two methyl groups are on the opposite side are called “trans”. A more generalized system for double bonds involves the Z  – E system.

• Cis – Same – “Zame”
• Trans – Opposite – “Epposite”

The second place where you encounter cis/trans is in cyclic alkanes.

When a molecule forms a ring, that “locks” it to a certain extent. Think of a belt (or better yet, a dog collar).  Before you fasten it together, you can twist it as much as you want. But once you fasten it, there are practical limits to how much you can turn it inside-out. If the radius is too small (or the material too stiff!), it becomes “locked”. You can’t turn it inside out anymore. That describes the situation with the cyclic alkanes we’ll encounter the most here.

So if two groups are on the same side of a ring, we use the same word : cis to describe it. And if they’re on the opposite side, we use the word “trans” to describe it.

To show this though we’ll need new visual terminology to depict how these molecules appear in 3D.

• To show a group pointing OUT of the page, we use a dark line “Wedge”.
• To show a group pointing IN to the page, we use a dashed line “Dash”.

So for 1,2-dimethyl cyclohexane, we can show the following two possibilities.

These two molecules are isomers of each other. We call them “stereoisomers” because they have the same connectivity but differ in the arrangement of their arrangement in space.

Thanks for reading! James

P.S. Subtle extra point. There’s a lot of confusion between the terms “cis” and “syn” and “trans” and “anti”. The difference is subtle: “cis” and “trans” implies that the orientation of the two groups is locked; you can’t convert cis to trans through rotation. The terms “syn” and “anti” imply similar relationships to “cis” and “trans”, but can also be applied to systems which are not locked. For example in certain Newman projections we can convert a “syn” relationship to an “anti” one through bond rotation.