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9 Nomenclature Conventions To Know
Last updated: January 23rd, 2024 |
Chemical nomenclature can be frustrating to learn. It’s a series of conventions which have been patched together over a long period of time, some of which date back to the 19th century. The language contains archaic terms that are past their useful prime, but are lodged deeply in the language of chemistry and almost impossible to excise at this point. The point of this article is to go beyond the common terms cis, trans, (E,Z), (S,R) – which are an absolute must to know – to point out some of the less frequently encountered aspects of nomenclature which might make you furrow your brow and say – “what does that mean?”
1. Bracket notation.
- When it’s used: In condensed formulas.
- What it means: Signifies that a substituent is attached directly to the preceding carbon.
- Example: CH3C(O)CH2CH3 (2-butanone)
- Why it’s useful: Without the bracket, the structure would be written CH3COCH2CH3, which might be confused for an ether. The bracket makes it more clear that it’s a ketone.
- Notes: Although not exactly obscure, it’s an aspect of nomenclature that can lead to confusion.
2. n-, s-, and t-
- When it’s used: for short chain alkanes and alcohols.
- What it means: n- means “normal” – an unbranched chain with the functional group (if present) on the 1-position. s– means “secondary”, t– means “tert“.
- Why it’s useful: Just a shorthand way of describing different structural isomers.
- Notes: n-hexane is another frequently encountered name, which simply represents a linear six-carbon chain. “Hexanes”, which you might see in the lab, refers to a mixture of different (branched) isomers of hexane.(it’s purified by distillation, and the isomers have very similar boiling points, so it’s sold as “hexanes”. Pure n-hexane is more expensive because separating it from its isomers is a royal pain).
3. The N- prefix
- When it’s used: for amines and amides.
- What it means: The N– signifies that the substitutent is connected to the nitrogen.
- Example: N-methyl butylamine, N,N-dimethylformamide.
- Why it’s useful: it removes ambiguity. “Methyl butylamine”, for instance, could refer to an isomer where the methyl group is on the carbon chain.
- Notes; when different substituents are present on the nitrogen, the terminology is N-(substituent),N-(substituent), for instance N-methyl,N-ethylbutylamine.
4. L and D
- When it’s used: for sugars and amino acids.
- What it means: It goes back to Emil Fischer, who designated the two enantiomers of glyceraldehyde (the simplest sugar) L-glyceraldehyde and D-glyceraldehyde. At a time (1890) where techniques for determining absolute structure were not available, he GUESSED(!) that structure of the leveratory (left-rotating) and dextrarotatory (right-rotating) structures of glyceraldehyde was as depicted in the Fischer projection, and gave them the prefixes L and D respectively. Thankfully, when X-ray crystallography was developed, it was found that his guess was correct. In L-sugars, the oxygen on the carbon second from the end is on the left hand side in the Fischer projection. In D-sugars, the oxygen is on the right-hand side.
- Why it’s useful: It was originally used to correlate the absolute structures of sugars to the two glyceraldehydes. It is no longer useful for this purpose, but like the appendix, it hangs around anyway. Like the appendix, it only seems to get noticed when it causes problems.
- Notes: This notation causes a lot of confusion. Just because something is “D” does not mean it rotates polarized light to the right and vice versa [that is the function of (+)- and (–)]. For example D-fructose rotates polarized light to the left (–). Furthermore, any correlation between L/D and S/R is coincidental. The 20 essential amino acids in the body are L-amino acids. They are all (S) except for cysteine, which is (R) (due to the sulfur having higher priority in the Cahn-Ingold-Prelog rules). Racemates are written as DL (for instance, DL-glucose is the racemic mixture).
5. (+) and (–)
- When it’s used: for any optically active compound
- What it means: (+) and (–) refer to the direction in which pure enantiomers of this compound rotate plane-polarized light. (+)-indicates clockwise rotation, while (–)-indicates counterclockwise rotation.
- Example: (+)-glucose, (–)-cysteine
- Why it’s useful: it depicts the direction of optical rotation.
- Notes: Racemic mixtures are referred to as (+/–), e.g. (+/–)-fructose
6. Vicinal and Geminal (vic– and gem-)
- When it’s used: often used in NMR to depict the relationships between hydrogens, also used to describe certain types of products (e.g. bromination produces vic-dibromides).
- What it means: Vicinal refers to two functional groups on adjacent carbons. Geminal refers to two functional groups on the same carbon.
- Why it’s useful: Instead of saying “the protons are on adjacent carbons” or “the protons are on the same carbons”, you can say “the protons are vicinal” or “the protons are geminal”.
- Notes: remember “gem” like “Gemini”, the constellation and astrological sign, meaning “twins”.
7. Methyl, methylene, methine
- When it’s used: most commonly in referring to protons in NMR
- What it means: methyl protons are on a primary carbon (CH3). Methylene protons are on a secondary carbon (CH2). Methine protons are on a tertiary carbon (CH).
- Why it’s useful: In the case of methine, useful shorthand for saying “proton on a tertiary carbon”.
8. Alpha and beta (α/β)
- When it’s used: Predominantly seen in naming sugars. Also used for steroids.
- What it means: When the sugar is drawn in the orientation as shown (carbons 1 through 5 follow a clockwise path), if the anomeric oxygen is UP (equatorial) it is “beta”, and if it is “down” it is alpha. [EDIT: as Bruce notes, this is incomplete and works only for D-sugars. More properly, a sugar is “alpha” if the C-1 OH and the substituent on the penultimate carbon (the CH2OH attached to C5) are on opposite sides of the ring, and “beta” if those two substituents are on the same side. See The Big Damn Post of Sugar Nomenclature for a more thorough description. ]
- Why it’s useful: Useful shorthand for describing the orientation of the anomeric oxygen which can be crucial in biochemistry. Cellulose and starch differ only in how the glucose subunits are linked together. We can digest starch (α-linked) but not cellulose (β-linked)
- Notes: The sugar has to be drawn in this specific orientation in order to apply α,β (it is a convention).
9. Erythro and threo
- When it’s used: Kind of old-fashioned, but indicates a diastereomeric relationship between two compounds with adjacent stereocenters.
- What it means: Erythrose and threose are the 4-carbon aldoses and they are diastereomers. In erythrose, a the oxygens are oriented on the same side in the Fischer projection. In threose, they are oriented trans. The erythro- and threo– prefixes generalize this relationship to other diastereomers.
- Why it’s useful. To be honest, if you’re not going beyond sophomore organic chemistry, it’s probably not all that useful.
Questions, comments, anything missing – as always, I want to hear about it.
00 General Chemistry Review
01 Bonding, Structure, and Resonance
- How Do We Know Methane (CH4) Is Tetrahedral?
- Hybrid Orbitals and Hybridization
- How To Determine Hybridization: A Shortcut
- Orbital Hybridization And Bond Strengths
- Sigma bonds come in six varieties: Pi bonds come in one
- A Key Skill: How to Calculate Formal Charge
- The Four Intermolecular Forces and How They Affect Boiling Points
- 3 Trends That Affect Boiling Points
- How To Use Electronegativity To Determine Electron Density (and why NOT to trust formal charge)
- Introduction to Resonance
- How To Use Curved Arrows To Interchange Resonance Forms
- Evaluating Resonance Forms (1) - The Rule of Least Charges
- How To Find The Best Resonance Structure By Applying Electronegativity
- Evaluating Resonance Structures With Negative Charges
- Evaluating Resonance Structures With Positive Charge
- Exploring Resonance: Pi-Donation
- Exploring Resonance: Pi-acceptors
- In Summary: Evaluating Resonance Structures
- Drawing Resonance Structures: 3 Common Mistakes To Avoid
- How to apply electronegativity and resonance to understand reactivity
- Bond Hybridization Practice
- Structure and Bonding Practice Quizzes
- Resonance Structures Practice
02 Acid Base Reactions
- Introduction to Acid-Base Reactions
- Acid Base Reactions In Organic Chemistry
- The Stronger The Acid, The Weaker The Conjugate Base
- Walkthrough of Acid-Base Reactions (3) - Acidity Trends
- Five Key Factors That Influence Acidity
- Acid-Base Reactions: Introducing Ka and pKa
- How to Use a pKa Table
- The pKa Table Is Your Friend
- A Handy Rule of Thumb for Acid-Base Reactions
- Acid Base Reactions Are Fast
- pKa Values Span 60 Orders Of Magnitude
- How Protonation and Deprotonation Affect Reactivity
- Acid Base Practice Problems
03 Alkanes and Nomenclature
- Meet the (Most Important) Functional Groups
- Condensed Formulas: Deciphering What the Brackets Mean
- Hidden Hydrogens, Hidden Lone Pairs, Hidden Counterions
- Don't Be Futyl, Learn The Butyls
- Primary, Secondary, Tertiary, Quaternary In Organic Chemistry
- Branching, and Its Affect On Melting and Boiling Points
- The Many, Many Ways of Drawing Butane
- Wedge And Dash Convention For Tetrahedral Carbon
- Common Mistakes in Organic Chemistry: Pentavalent Carbon
- Table of Functional Group Priorities for Nomenclature
- Summary Sheet - Alkane Nomenclature
- Organic Chemistry IUPAC Nomenclature Demystified With A Simple Puzzle Piece Approach
- Boiling Point Quizzes
- Organic Chemistry Nomenclature Quizzes
04 Conformations and Cycloalkanes
- Staggered vs Eclipsed Conformations of Ethane
- Conformational Isomers of Propane
- Newman Projection of Butane (and Gauche Conformation)
- Introduction to Cycloalkanes (1)
- Geometric Isomers In Small Rings: Cis And Trans Cycloalkanes
- Calculation of Ring Strain In Cycloalkanes
- Cycloalkanes - Ring Strain In Cyclopropane And Cyclobutane
- Cyclohexane Conformations
- Cyclohexane Chair Conformation: An Aerial Tour
- How To Draw The Cyclohexane Chair Conformation
- The Cyclohexane Chair Flip
- The Cyclohexane Chair Flip - Energy Diagram
- Substituted Cyclohexanes - Axial vs Equatorial
- Ranking The Bulkiness Of Substituents On Cyclohexanes: "A-Values"
- Cyclohexane Chair Conformation Stability: Which One Is Lower Energy?
- Fused Rings - Cis-Decalin and Trans-Decalin
- Naming Bicyclic Compounds - Fused, Bridged, and Spiro
- Bredt's Rule (And Summary of Cycloalkanes)
- Newman Projection Practice
- Cycloalkanes Practice Problems
05 A Primer On Organic Reactions
- The Most Important Question To Ask When Learning a New Reaction
- Learning New Reactions: How Do The Electrons Move?
- The Third Most Important Question to Ask When Learning A New Reaction
- 7 Factors that stabilize negative charge in organic chemistry
- 7 Factors That Stabilize Positive Charge in Organic Chemistry
- Nucleophiles and Electrophiles
- Curved Arrows (for reactions)
- Curved Arrows (2): Initial Tails and Final Heads
- Nucleophilicity vs. Basicity
- The Three Classes of Nucleophiles
- What Makes A Good Nucleophile?
- What makes a good leaving group?
- 3 Factors That Stabilize Carbocations
- Equilibrium and Energy Relationships
- What's a Transition State?
- Hammond's Postulate
- Learning Organic Chemistry Reactions: A Checklist (PDF)
- Introduction to Free Radical Substitution Reactions
- Introduction to Oxidative Cleavage Reactions
06 Free Radical Reactions
- Bond Dissociation Energies = Homolytic Cleavage
- Free Radical Reactions
- 3 Factors That Stabilize Free Radicals
- What Factors Destabilize Free Radicals?
- Bond Strengths And Radical Stability
- Free Radical Initiation: Why Is "Light" Or "Heat" Required?
- Initiation, Propagation, Termination
- Monochlorination Products Of Propane, Pentane, And Other Alkanes
- Selectivity In Free Radical Reactions
- Selectivity in Free Radical Reactions: Bromination vs. Chlorination
- Halogenation At Tiffany's
- Allylic Bromination
- Bonus Topic: Allylic Rearrangements
- In Summary: Free Radicals
- Synthesis (2) - Reactions of Alkanes
- Free Radicals Practice Quizzes
07 Stereochemistry and Chirality
- Types of Isomers: Constitutional Isomers, Stereoisomers, Enantiomers, and Diastereomers
- How To Draw The Enantiomer Of A Chiral Molecule
- How To Draw A Bond Rotation
- Introduction to Assigning (R) and (S): The Cahn-Ingold-Prelog Rules
- Assigning Cahn-Ingold-Prelog (CIP) Priorities (2) - The Method of Dots
- Enantiomers vs Diastereomers vs The Same? Two Methods For Solving Problems
- Assigning R/S To Newman Projections (And Converting Newman To Line Diagrams)
- How To Determine R and S Configurations On A Fischer Projection
- The Meso Trap
- Optical Rotation, Optical Activity, and Specific Rotation
- Optical Purity and Enantiomeric Excess
- What's a Racemic Mixture?
- Chiral Allenes And Chiral Axes
- Stereochemistry Practice Problems and Quizzes
08 Substitution Reactions
- Introduction to Nucleophilic Substitution Reactions
- Walkthrough of Substitution Reactions (1) - Introduction
- Two Types of Nucleophilic Substitution Reactions
- The SN2 Mechanism
- Why the SN2 Reaction Is Powerful
- The SN1 Mechanism
- The Conjugate Acid Is A Better Leaving Group
- Comparing the SN1 and SN2 Reactions
- Polar Protic? Polar Aprotic? Nonpolar? All About Solvents
- Steric Hindrance is Like a Fat Goalie
- Common Blind Spot: Intramolecular Reactions
- The Conjugate Base is Always a Stronger Nucleophile
- Substitution Practice - SN1
- Substitution Practice - SN2
09 Elimination Reactions
- Elimination Reactions (1): Introduction And The Key Pattern
- Elimination Reactions (2): The Zaitsev Rule
- Elimination Reactions Are Favored By Heat
- Two Elimination Reaction Patterns
- The E1 Reaction
- The E2 Mechanism
- E1 vs E2: Comparing the E1 and E2 Reactions
- Antiperiplanar Relationships: The E2 Reaction and Cyclohexane Rings
- Bulky Bases in Elimination Reactions
- Comparing the E1 vs SN1 Reactions
- Elimination (E1) Reactions With Rearrangements
- E1cB - Elimination (Unimolecular) Conjugate Base
- Elimination (E1) Practice Problems And Solutions
- Elimination (E2) Practice Problems and Solutions
10 Rearrangements
11 SN1/SN2/E1/E2 Decision
- Identifying Where Substitution and Elimination Reactions Happen
- Deciding SN1/SN2/E1/E2 (1) - The Substrate
- Deciding SN1/SN2/E1/E2 (2) - The Nucleophile/Base
- SN1 vs E1 and SN2 vs E2 : The Temperature
- Deciding SN1/SN2/E1/E2 - The Solvent
- Wrapup: The Key Factors For Determining SN1/SN2/E1/E2
- Alkyl Halide Reaction Map And Summary
- SN1 SN2 E1 E2 Practice Problems
12 Alkene Reactions
- E and Z Notation For Alkenes (+ Cis/Trans)
- Alkene Stability
- Alkene Addition Reactions: "Regioselectivity" and "Stereoselectivity" (Syn/Anti)
- Stereoselective and Stereospecific Reactions
- Hydrohalogenation of Alkenes and Markovnikov's Rule
- Hydration of Alkenes With Aqueous Acid
- Rearrangements in Alkene Addition Reactions
- Halogenation of Alkenes and Halohydrin Formation
- Oxymercuration Demercuration of Alkenes
- Hydroboration Oxidation of Alkenes
- m-CPBA (meta-chloroperoxybenzoic acid)
- OsO4 (Osmium Tetroxide) for Dihydroxylation of Alkenes
- Palladium on Carbon (Pd/C) for Catalytic Hydrogenation of Alkenes
- Cyclopropanation of Alkenes
- A Fourth Alkene Addition Pattern - Free Radical Addition
- Alkene Reactions: Ozonolysis
- Summary: Three Key Families Of Alkene Reaction Mechanisms
- Synthesis (4) - Alkene Reaction Map, Including Alkyl Halide Reactions
- Alkene Reactions Practice Problems
13 Alkyne Reactions
- Acetylides from Alkynes, And Substitution Reactions of Acetylides
- Partial Reduction of Alkynes With Lindlar's Catalyst
- Partial Reduction of Alkynes With Na/NH3 To Obtain Trans Alkenes
- Alkyne Hydroboration With "R2BH"
- Hydration and Oxymercuration of Alkynes
- Hydrohalogenation of Alkynes
- Alkyne Halogenation: Bromination, Chlorination, and Iodination of Alkynes
- Alkyne Reactions - The "Concerted" Pathway
- Alkenes To Alkynes Via Halogenation And Elimination Reactions
- Alkynes Are A Blank Canvas
- Synthesis (5) - Reactions of Alkynes
- Alkyne Reactions Practice Problems With Answers
14 Alcohols, Epoxides and Ethers
- Alcohols - Nomenclature and Properties
- Alcohols Can Act As Acids Or Bases (And Why It Matters)
- Alcohols - Acidity and Basicity
- The Williamson Ether Synthesis
- Ethers From Alkenes, Tertiary Alkyl Halides and Alkoxymercuration
- Alcohols To Ethers via Acid Catalysis
- Cleavage Of Ethers With Acid
- Epoxides - The Outlier Of The Ether Family
- Opening of Epoxides With Acid
- Epoxide Ring Opening With Base
- Making Alkyl Halides From Alcohols
- Tosylates And Mesylates
- PBr3 and SOCl2
- Elimination Reactions of Alcohols
- Elimination of Alcohols To Alkenes With POCl3
- Alcohol Oxidation: "Strong" and "Weak" Oxidants
- Demystifying The Mechanisms of Alcohol Oxidations
- Protecting Groups For Alcohols
- Thiols And Thioethers
- Calculating the oxidation state of a carbon
- Oxidation and Reduction in Organic Chemistry
- Oxidation Ladders
- SOCl2 Mechanism For Alcohols To Alkyl Halides: SN2 versus SNi
- Alcohol Reactions Roadmap (PDF)
- Alcohol Reaction Practice Problems
- Epoxide Reaction Quizzes
- Oxidation and Reduction Practice Quizzes
15 Organometallics
- What's An Organometallic?
- Formation of Grignard and Organolithium Reagents
- Organometallics Are Strong Bases
- Reactions of Grignard Reagents
- Protecting Groups In Grignard Reactions
- Synthesis Problems Involving Grignard Reagents
- Grignard Reactions And Synthesis (2)
- Organocuprates (Gilman Reagents): How They're Made
- Gilman Reagents (Organocuprates): What They're Used For
- The Heck, Suzuki, and Olefin Metathesis Reactions (And Why They Don't Belong In Most Introductory Organic Chemistry Courses)
- Reaction Map: Reactions of Organometallics
- Grignard Practice Problems
16 Spectroscopy
- Degrees of Unsaturation (or IHD, Index of Hydrogen Deficiency)
- Conjugation And Color (+ How Bleach Works)
- Introduction To UV-Vis Spectroscopy
- UV-Vis Spectroscopy: Absorbance of Carbonyls
- UV-Vis Spectroscopy: Practice Questions
- Bond Vibrations, Infrared Spectroscopy, and the "Ball and Spring" Model
- Infrared Spectroscopy: A Quick Primer On Interpreting Spectra
- IR Spectroscopy: 4 Practice Problems
- 1H NMR: How Many Signals?
- Homotopic, Enantiotopic, Diastereotopic
- Diastereotopic Protons in 1H NMR Spectroscopy: Examples
- C13 NMR - How Many Signals
- Liquid Gold: Pheromones In Doe Urine
- Natural Product Isolation (1) - Extraction
- Natural Product Isolation (2) - Purification Techniques, An Overview
- Structure Determination Case Study: Deer Tarsal Gland Pheromone
17 Dienes and MO Theory
- What To Expect In Organic Chemistry 2
- Are these molecules conjugated?
- Conjugation And Resonance In Organic Chemistry
- Bonding And Antibonding Pi Orbitals
- Molecular Orbitals of The Allyl Cation, Allyl Radical, and Allyl Anion
- Pi Molecular Orbitals of Butadiene
- Reactions of Dienes: 1,2 and 1,4 Addition
- Thermodynamic and Kinetic Products
- More On 1,2 and 1,4 Additions To Dienes
- s-cis and s-trans
- The Diels-Alder Reaction
- Cyclic Dienes and Dienophiles in the Diels-Alder Reaction
- Stereochemistry of the Diels-Alder Reaction
- Exo vs Endo Products In The Diels Alder: How To Tell Them Apart
- HOMO and LUMO In the Diels Alder Reaction
- Why Are Endo vs Exo Products Favored in the Diels-Alder Reaction?
- Diels-Alder Reaction: Kinetic and Thermodynamic Control
- The Retro Diels-Alder Reaction
- The Intramolecular Diels Alder Reaction
- Regiochemistry In The Diels-Alder Reaction
- The Cope and Claisen Rearrangements
- Electrocyclic Reactions
- Electrocyclic Ring Opening And Closure (2) - Six (or Eight) Pi Electrons
- Diels Alder Practice Problems
- Molecular Orbital Theory Practice
18 Aromaticity
- Introduction To Aromaticity
- Rules For Aromaticity
- Huckel's Rule: What Does 4n+2 Mean?
- Aromatic, Non-Aromatic, or Antiaromatic? Some Practice Problems
- Antiaromatic Compounds and Antiaromaticity
- The Pi Molecular Orbitals of Benzene
- The Pi Molecular Orbitals of Cyclobutadiene
- Frost Circles
- Aromaticity Practice Quizzes
19 Reactions of Aromatic Molecules
- Electrophilic Aromatic Substitution: Introduction
- Activating and Deactivating Groups In Electrophilic Aromatic Substitution
- Electrophilic Aromatic Substitution - The Mechanism
- Ortho-, Para- and Meta- Directors in Electrophilic Aromatic Substitution
- Understanding Ortho, Para, and Meta Directors
- Why are halogens ortho- para- directors?
- Disubstituted Benzenes: The Strongest Electron-Donor "Wins"
- Electrophilic Aromatic Substitutions (1) - Halogenation of Benzene
- Electrophilic Aromatic Substitutions (2) - Nitration and Sulfonation
- EAS Reactions (3) - Friedel-Crafts Acylation and Friedel-Crafts Alkylation
- Intramolecular Friedel-Crafts Reactions
- Nucleophilic Aromatic Substitution (NAS)
- Nucleophilic Aromatic Substitution (2) - The Benzyne Mechanism
- Reactions on the "Benzylic" Carbon: Bromination And Oxidation
- The Wolff-Kishner, Clemmensen, And Other Carbonyl Reductions
- More Reactions on the Aromatic Sidechain: Reduction of Nitro Groups and the Baeyer Villiger
- Aromatic Synthesis (1) - "Order Of Operations"
- Synthesis of Benzene Derivatives (2) - Polarity Reversal
- Aromatic Synthesis (3) - Sulfonyl Blocking Groups
- Birch Reduction
- Synthesis (7): Reaction Map of Benzene and Related Aromatic Compounds
- Aromatic Reactions and Synthesis Practice
- Electrophilic Aromatic Substitution Practice Problems
20 Aldehydes and Ketones
- What's The Alpha Carbon In Carbonyl Compounds?
- Nucleophilic Addition To Carbonyls
- Aldehydes and Ketones: 14 Reactions With The Same Mechanism
- Sodium Borohydride (NaBH4) Reduction of Aldehydes and Ketones
- Grignard Reagents For Addition To Aldehydes and Ketones
- Wittig Reaction
- Hydrates, Hemiacetals, and Acetals
- Imines - Properties, Formation, Reactions, and Mechanisms
- All About Enamines
- Breaking Down Carbonyl Reaction Mechanisms: Reactions of Anionic Nucleophiles (Part 2)
- Aldehydes Ketones Reaction Practice
21 Carboxylic Acid Derivatives
- Nucleophilic Acyl Substitution (With Negatively Charged Nucleophiles)
- Addition-Elimination Mechanisms With Neutral Nucleophiles (Including Acid Catalysis)
- Basic Hydrolysis of Esters - Saponification
- Transesterification
- Proton Transfer
- Fischer Esterification - Carboxylic Acid to Ester Under Acidic Conditions
- Lithium Aluminum Hydride (LiAlH4) For Reduction of Carboxylic Acid Derivatives
- LiAlH[Ot-Bu]3 For The Reduction of Acid Halides To Aldehydes
- Di-isobutyl Aluminum Hydride (DIBAL) For The Partial Reduction of Esters and Nitriles
- Amide Hydrolysis
- Thionyl Chloride (SOCl2)
- Diazomethane (CH2N2)
- Carbonyl Chemistry: Learn Six Mechanisms For the Price Of One
- Making Music With Mechanisms (PADPED)
- Carboxylic Acid Derivatives Practice Questions
22 Enols and Enolates
- Keto-Enol Tautomerism
- Enolates - Formation, Stability, and Simple Reactions
- Kinetic Versus Thermodynamic Enolates
- Aldol Addition and Condensation Reactions
- Reactions of Enols - Acid-Catalyzed Aldol, Halogenation, and Mannich Reactions
- Claisen Condensation and Dieckmann Condensation
- Decarboxylation
- The Malonic Ester and Acetoacetic Ester Synthesis
- The Michael Addition Reaction and Conjugate Addition
- The Robinson Annulation
- Haloform Reaction
- The Hell–Volhard–Zelinsky Reaction
- Enols and Enolates Practice Quizzes
23 Amines
- The Amide Functional Group: Properties, Synthesis, and Nomenclature
- Basicity of Amines And pKaH
- 5 Key Basicity Trends of Amines
- The Mesomeric Effect And Aromatic Amines
- Nucleophilicity of Amines
- Alkylation of Amines (Sucks!)
- Reductive Amination
- The Gabriel Synthesis
- Some Reactions of Azides
- The Hofmann Elimination
- The Hofmann and Curtius Rearrangements
- The Cope Elimination
- Protecting Groups for Amines - Carbamates
- The Strecker Synthesis of Amino Acids
- Introduction to Peptide Synthesis
- Reactions of Diazonium Salts: Sandmeyer and Related Reactions
- Amine Practice Questions
24 Carbohydrates
- D and L Notation For Sugars
- Pyranoses and Furanoses: Ring-Chain Tautomerism In Sugars
- What is Mutarotation?
- Reducing Sugars
- The Big Damn Post Of Carbohydrate-Related Chemistry Definitions
- The Haworth Projection
- Converting a Fischer Projection To A Haworth (And Vice Versa)
- Reactions of Sugars: Glycosylation and Protection
- The Ruff Degradation and Kiliani-Fischer Synthesis
- Isoelectric Points of Amino Acids (and How To Calculate Them)
- Carbohydrates Practice
- Amino Acid Quizzes
25 Fun and Miscellaneous
- A Gallery of Some Interesting Molecules From Nature
- Screw Organic Chemistry, I'm Just Going To Write About Cats
- On Cats, Part 1: Conformations and Configurations
- On Cats, Part 2: Cat Line Diagrams
- On Cats, Part 4: Enantiocats
- On Cats, Part 6: Stereocenters
- Organic Chemistry Is Shit
- The Organic Chemistry Behind "The Pill"
- Maybe they should call them, "Formal Wins" ?
- Why Do Organic Chemists Use Kilocalories?
- The Principle of Least Effort
- Organic Chemistry GIFS - Resonance Forms
- Reproducibility In Organic Chemistry
- What Holds The Nucleus Together?
- How Reactions Are Like Music
- Organic Chemistry and the New MCAT
26 Organic Chemistry Tips and Tricks
- Common Mistakes: Formal Charges Can Mislead
- Partial Charges Give Clues About Electron Flow
- Draw The Ugly Version First
- Organic Chemistry Study Tips: Learn the Trends
- The 8 Types of Arrows In Organic Chemistry, Explained
- Top 10 Skills To Master Before An Organic Chemistry 2 Final
- Common Mistakes with Carbonyls: Carboxylic Acids... Are Acids!
- Planning Organic Synthesis With "Reaction Maps"
- Alkene Addition Pattern #1: The "Carbocation Pathway"
- Alkene Addition Pattern #2: The "Three-Membered Ring" Pathway
- Alkene Addition Pattern #3: The "Concerted" Pathway
- Number Your Carbons!
- The 4 Major Classes of Reactions in Org 1
- How (and why) electrons flow
- Grossman's Rule
- Three Exam Tips
- A 3-Step Method For Thinking Through Synthesis Problems
- Putting It Together
- Putting Diels-Alder Products in Perspective
- The Ups and Downs of Cyclohexanes
- The Most Annoying Exceptions in Org 1 (Part 1)
- The Most Annoying Exceptions in Org 1 (Part 2)
- The Marriage May Be Bad, But the Divorce Still Costs Money
- 9 Nomenclature Conventions To Know
- Nucleophile attacks Electrophile
27 Case Studies of Successful O-Chem Students
- Success Stories: How Corina Got The The "Hard" Professor - And Got An A+ Anyway
- How Helena Aced Organic Chemistry
- From a "Drop" To B+ in Org 2 – How A Hard Working Student Turned It Around
- How Serge Aced Organic Chemistry
- Success Stories: How Zach Aced Organic Chemistry 1
- Success Stories: How Kari Went From C– to B+
- How Esther Bounced Back From a "C" To Get A's In Organic Chemistry 1 And 2
- How Tyrell Got The Highest Grade In Her Organic Chemistry Course
- This Is Why Students Use Flashcards
- Success Stories: How Stu Aced Organic Chemistry
- How John Pulled Up His Organic Chemistry Exam Grades
- Success Stories: How Nathan Aced Organic Chemistry (Without It Taking Over His Life)
- How Chris Aced Org 1 and Org 2
- Interview: How Jay Got an A+ In Organic Chemistry
- How to Do Well in Organic Chemistry: One Student's Advice
- "America's Top TA" Shares His Secrets For Teaching O-Chem
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Please suggest me a book or a website to learn nomenclature of polycyclic compound with substituent
Bite the bullet and read the IUPAC blue book?
Very helpful resource
A question:
I am helping a non-native English speaker with a “manure” problem.
I think this is error but cannot find the answer google-monkeying around:
the 2,936-2,956 cm-1 peak is the C-H stretching vibration of aliphatic methyl, methylene, and methylene
==
They correspond to “H-C-, H-C=, H-C≡”; but i don’t know how to express the “H-C≡” in English.
Hi Steve – A tertiary carbon bonded to hydrogen is called, “methine”
Hi…
Could you please explain the meaning of using a ‘dash’ over the repeated term as in, p,p’-dihydroxybenzophenone,
That p,p’ poses me a problem…
Benzophenone has two phenyl groups, which we can abbreviate by Ph. To differentiate them, one can call one of them Ph and the other Ph prime (abbreviated Ph’). For dihydroxybenzophenone where there is an OH group para on the Ph group and also an OH group para on the Ph’ (Ph prime) we therefore say, “p,p’-dihydroxybenzophenone)
It’s superfentabulous resource for ORGANIC CHEMISTRY.
JAMES, you and this website are amazing.
It very fun and amazing to read organic chemistry in this website.
THANK YOU
Awesome site. Thank you! But your rule #8 (alpha vs. beta) only applies to D-sugars. It is opposite for L-sugars.
Thanks Bruce – fixed!
In section 4 on L- and D- enantiomers it seems that gluteraldehyde has been used instead of glucose.
? Gluteraldehyde is a completely different molecule – a dialdehyde lacking any hydroxy groups…
Hi, I just wanted to agree with the above praise.
Also, don’t discount the value of number 9 (erythro- and threo-) because that’s what brought me here. I came upon
l-erythro-3,5-diaminohexanoate in a paper and needed to know what it is. Sure, I can google it but I also wanted to understand it. Thanks for the help!
Your articles are life-savers for organic chemistry students like me. Thank you!
Glad to hear it Cassandra. Thank you.
This is a fantastic site! I was trying to find our what N meant in the compound N-methyl D-aspartate. It has been 50 years since I took organic chem and could not remember. I did remember what the D stood for. Thanks
Elaine – thanks for letting me know! Glad the site can be of service – James
Could you help me by explaining the the use of alpha in the case of morphine’s IUPAC?
(5α,6α)-17-Methyl-7,8-didehydro-4,5-epoxymorphinan-3,6-diol
I’m understanding that the numbers within are identifying the location in the structure in which these can be found but I’m still unsure about the part in parenthesis.
Hi
(5α,6α)-17-Methyl-7,8-didehydro-4,5-epoxymorphinan-3,6-diol
I’m understanding that the numbers within are identifying the location in the structure in which these can be found but I’m still unsure about the part in parenthesis.
Alpha and beta are relatively old terms for denoting the orientation of atoms with respect to the plane of the ring (stereochemistry). It’s common in steroids and sugars (e.g. alpha-glycoside or beta-glycoside)
http://science.uvu.edu/ochem/index.php/alphabetical/a-b/alpha-anomer/
Alpha means the substituents are on the “bottom” plane of the ring, but at this moment I can’t find out how which plane of the ring is defined as the “top” and “bottom” .
If the stereochemistry of the alcohol on 6 was flipped, it would be labelled (5a, 6B)-17-Methyl…..
Hope this helps – James
This is very helpful. By the way, when there’s an “A” beside a number in the chemical name, what does it intepret?
For example, mono-6A-ammonium-6A-deoxy-CD chloride.
Sounds like you’re describing a tetracycline or similar cyclic compound. In complex ring systems there are weird IUPAC nomenclature conventions that I confess I haven’t tried to understand very much. Sorry, I don’t know.
I often see the “prime” symbol after a letter or number in the notation describing an organic molecule. For example, 2′-F, 2′-C-methyluridine-5′-monophosphate . I’m guessing the F means floro, but I am clueless about the primes. Help!
Hello!, love your site, btw.
I’m trying to figure out what the ” R* ” reference is in the following synonym for Endrin aldehyde:
1,2,4-Methenocyclopenta(cd)pentalene-5-carboxaldehyde, 2,2a,3,3,4,7-hexachlorodecahydro-, (1alpha,2beta,2abeta,4beta,4abeta,5beta,6abeta,6bbeta,7R*)-;
It’s some bit of more obscure meta-info , but I can’t find in referenced anywhere…can you help??
thanks!
The presence of identical unsubstituted radicals is indicated by the appropriate multiplying prefix di-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca, etc.
The presence of identical radicals each substituted in the same way may be indicated by the appropriate multiplying prefix bis-, tris-, tetrakis-, pentakis-, etc. The complete expression denoting such a side chain may be enclosed in parentheses or the carbon atoms in side chains may be indicated by primed numbers.
Ref: http://www.acdlabs.com/iupac/nomenclature/79/r79_36.htm
Dear James,
At the IUPAC system, the correct nomenclature of 2-butanol is butan-2-ol. The number of function’s position have to precede it.
Thanks
The purpose of nomenclature is to provide a unique, non-ambiguous way of translating a name to a structure. 2-butanol satisfies this criterion. It is also easier to say. The nomenclature system exists to serve us, not the other way around.
Hi, you mentioned that alpha and beta are used in naming sugars and that they are also used for steroids. What about terpenes? Can you tell me what alpha-myrcene is indicating as opposed to beta-myrcene? Thank
What’s the “O” mean in 4-O-methylhonokiol?
It’s saying that the oxygen has a methyl group attached. Kind of a weird way of naming it, you don’t see this very often. It’s more often seen with amines (e.g. N-methylformamide)
Another nice piece of clarification!
I would suggest that you add another notation used in organic chemistry conversations and contrasted with your number 8. That would be the use of Greek characters to refer to carbons counted from a functional group. For example, α,β-diketones, β-amino acids, β-keto esters, etc.
Great suggestion. Thanks!
Great list! You know what would be helpful for readers like me is you have an ability to export these posts into pdf files to print out, or at least have some ability to easily print out these posts. Maybe there is one present on this blog, but I couldn’t find it. I know there must be a plugin for wordpress that allows this.
You can try clicking on the post and then Print – you should get an option to Print as PDF, and there you go.
This may be system dependent, however. It works OK on my home PC and office one, but not on the one in the library. Perhaps you need something like ghostscript or similar installed?
I think many times chemists forget that you don’t know little terms and never think to explain them. This leaves students that are probably way too attention-detailed for their own good to have trip up a lot on things that could have easily been explained but never were. This page has solved multiple problems of mine that I either never understood or had to search a lot to find. Should be at the first of every nomenclature chapter of every ochem book! :)
Thanks!
Thanks! That’s the goal… to try and make summaries of things that haven’t been summarized before.
wow – this is a fantastic resource. what astonishes me is that i’ve not seen anything like it until now (not in a textbook or website).
thank you!
sue