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Hidden Hydrogens, Hidden Lone Pairs, Hidden Counterions
Last updated: December 13th, 2022 |
Hidden Hydrogens, Lone Pairs, and Counter-Ions
Time is precious. Drawing the full structures of chemical formulae out takes time.
Shaving an extra 10-20 seconds here or there might not sound like a lot to you, but you might be surprised by what people will do to take 5 seconds of boredom off their journey. (See article: The Power of Laziness)
The point is, corners will get cut and shortcuts are inevitable. This post is about the shortcuts you have to know about when looking at chemical structures.
There are 3 common types of shortcuts that organic chemists make when drawing structures. They will omit drawing the following:
- hydrogen atoms
- lone pairs
- counter-ions
The key is learning to recognize the things that “you’re just supposed to know are there”.
1. Hidden hydrogens
Line drawings are the chemists’ method of choice for depicting structures. And it’s not hard to see why: they’re a snap to draw. Why? Because we omit drawing in all the pesky little hydrogens!
The key thing in recognizing hidden hydrogens is that wherever you see less than 4 bonds to carbon, that carbon is going to have hydrogens attached such that there’s a full octet. Here are some examples.
2. Hidden lone pairs
Lone pairs are often not drawn on structures either. Again, this is a time-saving measure, but also they tend to get in the way and clutter up the structure. Like hydrogens, you’re “just supposed to know that they’re there”.
How do you know how many to draw? If you understand formal charge, this should be a snap.
(For more on formal charges, see: How To Calcluate Formal Charge)
The atom that causes the most confusion on this point is probably carbon when it is drawn with a negative charge: the negative charge implies the existence of a lone pair.
This also comes up in reactions. Using the curved arrow notation, you’ll often see the tail of an arrow coming from a negative charge on a given atom. You’re just supposed to know that the negative charge represents a pair of electrons on the atom.
Finally, if you see a positive charge on carbon, you’re supposed to know that not only are there zero lone pairs on the carbon, there are only 3 bonds.
3. Hidden Counter-ions
The subject of counterions also causes a lot of confusion. Students coming out of gen chem where they have had to balance these massive redox equations often get confused when they notice their instructor (or the textbook) not balancing charges anymore. It’s a signal that “suddenly the charges aren’t that important”, or even worse, they aren’t there.
The charge IS there, it just hasn’t been drawn in.
Charge is always conserved, and balanced: the presence of a charge implies the existence of an equal and opposite charge somewhere else. Always.
The reason why the balancing ions are often left off, I think, is not due to simple laziness but also for a desire to avoid confusion by focusing on specifics. It’s a bit of a Catch-22.
- If the counterion is omitted, one risks confusing the students by implying that the charges are unbalanced.
- However, if one puts in a specific counterion such as Cl(-) , then one will have to eventually explain that Cl(-) is not crucial to the reaction and any number of other counterions would work just as well.
My compromise is to use X(-) or M(+) for this purpose. The exact counterion for a given reaction will depend on how the ion is made in the first place.
4. Hidden Charges
A related issue is not hidden counterions but hidden charges. Specifically, ionic compounds.
Again, it’s easier to just omit drawing in charges rather than drawing them in.
A classic example is NaOH. From general chemistry, it’s well understood that NaOH is an ionic compound and is better represented as Na(+)OH(-). However often times the charges will be omitted.
Hopefully now you’ll have a better idea of the things that you’re “just supposed to know are there”.
Notes
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05 A Primer On Organic Reactions
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06 Free Radical Reactions
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07 Stereochemistry and Chirality
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08 Substitution Reactions
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11 SN1/SN2/E1/E2 Decision
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- PBr3 and SOCl2
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- Demystifying The Mechanisms of Alcohol Oxidations
- Protecting Groups For Alcohols
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- Calculating the oxidation state of a carbon
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- Oxidation Ladders
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16 Spectroscopy
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17 Dienes and MO Theory
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- 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
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- Thermodynamic and Kinetic Products
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- s-cis and s-trans
- The Diels-Alder Reaction
- Cyclic Dienes and Dienophiles in the Diels-Alder Reaction
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- HOMO and LUMO In the Diels Alder Reaction
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- Diels-Alder Reaction: Kinetic and Thermodynamic Control
- The Retro Diels-Alder Reaction
- The Intramolecular Diels Alder Reaction
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- The Cope and Claisen Rearrangements
- Electrocyclic Reactions
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18 Aromaticity
- Introduction To Aromaticity
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- The Pi Molecular Orbitals of Cyclobutadiene
- Frost Circles
- Aromaticity Practice Quizzes
19 Reactions of Aromatic Molecules
- Electrophilic Aromatic Substitution: Introduction
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- 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
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- The Michael Addition Reaction and Conjugate Addition
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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
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- 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
- "Organic Chemistry Is Like..." - A Few Metaphors
- How To Do Well In Organic Chemistry: Advice From A Tutor
- Guest post: "I went from being afraid of tests to actually looking forward to them".
Hi James,
I really like your site, it is very informative. However, I didnt notice any topics on hydrogen bonding and I was wondering if you could try answering my somewhat peculiar question. Is it possible to get a hydrogen bonding between a hydroxy (R-OH) group and alkoxide (R-O-) group if pKa values of both are somewhat similar or if they differ greatly? or do we get a simple proton transfer reaction?
To be more specific, I have a material which has alkoxide functionality on the surface and I am wondering if an alcohol (phenol) could form a stronger H-bond in comparison to the material with hydroxyl functionality?
Cheers
Thanks for the kind words. The resonance structure rule is Meier’s rule, named after my colleague Mark Meier, who says, “When in doubt, draw in all the lone pairs, and then draw resonance structures until the cows come home.” The “cows come home” part is very important.
4th! on Grossman’s rule. A very useful thought, early in the book.
[I bumped into him at NOS 2003 literally. I excused myself, looked at his name tag and said, “I have your book — it’s great!” He’s terribly modest.]
3rd for Grossman’s rule and the resonance rule in his book (I don’t know if he attributes it to himself or someone else):
The 2nd best resonance structure usually defines a molecules reactivity.
-It explains Markovnikov’s rule, Electrophilic Aromatic Substitution, enolate chemistry…
Grossmans rule is super useful. It also helps prevent that accidental dropping of carbons. Whenever I tutor I always encourage addingin everything to help avoiding mistakes.
since 2 people have mentioned it I’ll have to do a post on Grossman’s rule. thanks for the input.
With regards to hidden hydrogens, don’t forget “Grossman’s Rule” (named by Robert Grossman in his “Art of Writing Reasonable Organic Reaction Mechanisms” book) which basicallys says “When you’re stuck, draw in the implicit hydrogens near the reactive sites”.
It’s amazingly effective, especially when students first encounter acid mediated reactions (like 1,2-shifts) where they may forget there’s a hydrogen that can move.
that *is* effective, thanks for bringing it to my attention. I have the Grossman book but don’t recall the rule. Thanks!
Nice overview. Now, I think the challenge with respect to lone pairs lies in the various coordinate systems for particularly S and P… PH3 has how many lone pairs, and how many has H2S. Or that R2S=O has a lone pair. That is less known. What about phosphors and sulphurs with more neighbors. This atom typing is one source of pain in the cheminformatics software, the Chemistry Development Kit (and others too, of course).