Organic chemistry exam helper introduction to organic chemistry

The frequent practice of organic chemistry reactions will help you pass, or evenace, an organic chemistry exam.. Fundamentally, the chemistry of non-living reactions, the chemistry of or

Organic Chemistry Exam Helper Introduction to Organic Chemistry

By Matthew Pasek, Ph.D.

freeradicalconsulting@gmail.com

This book is part of a series of organic chemistry study guides It focuses on theintroductory material covered by organic chemistry classes: a general overview,details of bonding, molecular formulae, acids and bases, hybridization,

nomenclature, and conformations Most important to the student of organicchemistry are the quizzes at the end These quizzes allow you to test your

knowledge of key concepts With organic chemistry, practice makes perfect The frequent practice of organic chemistry reactions will help you pass, or evenace, an organic chemistry exam

The subjects covered in this book are the introductory materials of organic

chemistry Each organic chemistry class is different: some will emphasize

specific characteristics not included here, others will be sticklers for certainaspects of organic chemistry (typically if that’s the professor’s area of focus) andmay not use the same suite as those shown here, and still others will focus on abare minimum set of concepts, due either to time constraints or pedagogicalconcerns This guide is meant to supplement, and not replace, attending theorganic chemistry course

I am a professor of geochemistry and not an organic chemist However, theorganic chemistry fundamentals are an important part of any chemist’s training,and I learned organic chemistry left and right for my own research and for mygrants I’ve tutored many students in this subject, but it is possible for there to

be errors in these questions as I am not an organic chemist by profession

Figures here were drawn using ACD lab’s ChemSketch program This program

is great for drawing organic molecules Other sketches are done by hand or withpower point

Chemistry is the science of the electron Organic chemistry is a branch of

chemistry Organic chemistry is the chemistry of the element carbon, glibly put.Nearly all (but NOT all) carbon compounds are organic compounds Organicchemistry arose out of a search for a difference between “alive” and “not alive” Such a search involved a concept called “vitalism”, the belief that there wassomething fundamentally different between the molecules of life and those thatwere formed by non-life Well, it turns out there isn’t really any major

difference Aside from a bit more radiocarbon in living things (because theyactively exchange carbon with the atmosphere, unlike most non-living

biologic reactions is the same Fundamentally, the chemistry of non-living

reactions), the chemistry of organic compounds made by life or by man and non-carbon compounds is identical to living carbon compounds

The glib definition of “organic chemistry = carbon chemistry” does need somecaveats, however For instance, many geologists study a rock called limestone Limestone is mostly composed of a mineral called calcite, which has a formula

general, is not considered to be organic, since it forms by non-biologic

processes

Similarly, several other simple compounds are not considered to be organic These include hydrogen cyanide (HCN), which forms several inorganic salts,and diamond and graphite, which are both carbon minerals, and silicon carbide(SiC) and iron carbide, which are minerals

A more exhaustive definition of organic is that the carbon atoms of the moleculeshould be covalently bound to either hydrogen or carbon (and preferentiallyhydrogen at some point in the structure) Carbon that forms ionic bonds andmetallic bonds is typically not considered organic Similarly, graphite and

diamond are essentially pure carbon, and aren’t considered organic

Naturally there’s a fair bit of fuzziness with determining whether a carbon-containing compound is organic or not Some don’t feel that formaldehyde is anorganic compound, whereas to others it obviously is The same is true for HCN,which we identified as inorganic Some scientists argue it is better described asorganic In the end, most of the cases at the intersection are intuitive As long as

Note that organic has nothing to do with “coming from nature”, so there’s a vastdifference between organic chemistry and the organic food that you might buy atWhole Foods or Trader Joe’s Organic in chemistry provides no real discerningvalue as to its origin, or its inherent “health”

A common way of representing bonding in molecules is through a Lewis dotstructure Lewis dot structures were first used by a chemist Gilbert Lewis, whodesigned these diagrams to show how electrons were shared or not (not involved

in a bond) between different atoms in a bond or molecule

You can calculate a “formal charge” of a molecule by:

the number of electrons participating in bonds

to simplify some of this by drawing bonding electrons as a line, instead of dots Two lines show there’s a double bond, and three show there’s a triple bond Electrons that don’t participate in bonds are still shown explicitly in a Lewis dotstructure

Identify which of these is an organic compound

Next problem?

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Watch out for Texas Carbons!

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This foray into molecular formulae give us chance to broach a new topic: theidea of saturation number or degree of unsaturation

An organic compound is considered saturated if it is a linear molecule, without

rings or double/triple bonds It may have branching side chains and still be

considered saturated Calculating the degree of unsaturation tells you

immediately a few key clues about the structure of an organic molecule: howmany double/triple bonds and rings there are The calculation is:

double bonds present However, a C=O bond does increase the degree of

unsaturation by one

Five examples of degrees of saturation and molecular structures are given below

Calculate the degree of unsaturation to see how many double and triple bondsare in a molecule, and how many rings are in it This will give you a quick guess

as to whether a molecular formula and a structure are related to each other,

especially when turning a molecular formula into a structure

drawings contribute to the actual structure, called a resonance hybrid This sharing of electrons is called delocalization

When drawing resonance structures, the only things that change between

different structures is the distribution of bonds and electrons Atoms do notmove in resonance, only electrons This means that if you have to move a Hatom to make a structure work, the new structure is not an alternative resonancestructure!

The ability of a molecule to delocalize electrons also stabilizes the molecule This means that if there are multiple resonances possible, the molecule tends to

be more stable (lower in potential energy) than might be expected in the absence

of resonance The best example of this is benzene, which has three double

bonds, and is more stable than would be expected for an unsaturated organicmolecule

Resonance structures don’t move atoms!

The molecule pyruvate participates in biochemical reactions A second formcalled an “enol” form is shown next to pyruvate

Which of the following is true?

A) These structures are resonance structures and have the same degree ofunsaturation

B) These structures are not resonance structures and have different degrees ofunsaturation

C) The structures are resonance structures and have different degrees ofunsaturation

D) The structure are not resonance structures and have the same degree ofunsaturation

Go back to section

When drawing larger and larger molecular diagrams, it can quickly becometiresome filling in and writing out each carbon As a result, most organic

structure Methyl groups are usually spelled out if the methyl is on a heteroatom

Lone pairs of electrons may be shown, if they are important to the structure, orthe reactivity of the molecule For this reason, most of the time the lone pairsare omitted on halogen atoms, as they don’t usually do much in the way of

reactions

Skeletal drawings are faster than most other molecular representations

Assume there are as many H atoms as needed to make the atom saturated, unlessthere’s an explicit double or triple bond

CENTIPEDE!!!!

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Why are organic chemistry molecules shaped the way they are? This ends uphaving to do with an idea called orbital hybridization Recall again from GenChem 2 the less-than-fun activity of breaking down the electron configuration of

structure of atoms, specifically the orbitals electrons fall in Carbon has s and porbitals

Molecules are characterized by bonds More specifically, organic moleculeshave bonds that are hybrids of the s and p orbitals When s and p orbitals mix,you can either have a mix of 1:1 s:p, 1:2 s:p, or 1:3 s:p, because there is one sorbital, and up to 3 p orbitals that can mix to form a bond When these orbitals

hybridization These p orbitals participate in bonding, linking to form bonds These bonds are quite important to organic chemical structures.

KEY POINTS AND HINTS:

The quick of it- if a carbon is bonded to two things, it’s sp and linear Three

Pi bonds are not a form of hybridization, but instead are the merging of the pshells of two atoms

always obvious when you look at molecular structures The Lewis definitionencompasses the other two definitions quite well

The question you need to view organic chemistry through is, “How willing toleave a molecule is a proton on an organic compound? The answer will rangefrom “very” to “not at all” Recall again that when an acid leaves its molecule, it

Even less acidic (H on OH)

Note that for alcohols, as the OH occurs on more substituted carbon atoms (lessH-atoms bound to it), the alcohol becomes more acidic

Note that the basicity of the conjugate bases goes in the opposite direct: the lessacidic a molecule, the more basic its conjugate base is if it does happen to lose aproton!

The basicity of a molecule can be determined by adding a proton to the

molecule, and seeing if the new structure is more stable than the one base If so,then the base is probably stronger than others

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One of the most difficult parts of organic chemistry is the transformation ofdrawings on paper of molecules into something more representative of reality This is why most organic chemistry courses also require you to buy a molecularmodeling kit: it is often easier to see a molecule in hand than on paper

Much of organic chemistry isn’t well represented in 2D, unless there’s an

This is especially true of stereochemistry, and chiral centers You will almostcertainly need a model molecule to figure out the handedness in a chiral

molecule Might as well start using those models now!

Bonds in three dimensions tend to be shown with wedge bonds Solid bondsimply the atom is coming out of the screen (bond 2 below), whereas dashedbonds imply the atom is going into the screen (bond 1), and the standard

unwedged lines represent atoms within the plane of the paper (C, 3, and 4) Ingeneral, three dimensional drawings are not necessary for those molecules thathave two atoms/functional groups attached that are identical 3D representationsare critical for understanding stereochemistry, however Chiral centers are bestrepresented by 3D structures, and are discussed in a subsequent study guide

KEY POINTS AND HINTS:

You’ll get a lot more practice in this during conformations and stereochemistry

KEY POINTS AND HINTS:

When in doubt, determine the molecular formula If they differ, then they’re notisomers

As touched upon in section 10, stereoisomers are a variety of isomers that

describe molecules with different structures but the same molecular formula More specifically, stereoisomers describe molecules that differ only with respect

to how their bonds are oriented in space In other words, the connections

between each set of carbons is identical, but they differ in direction See theexample below

carbon is bound to the same sequence of other carbons Thus these two isomersare stereoisomers Stereoisomers are defined by where the bigger (or heavier-more in the next volume of this guide) functional groups are across their doublebond If the two bigger functional groups are on the same side of the molecule,

that is called a cis-isomer, or sometimes “z-“ (German for zusammen, or

“together”) If the two bigger functional groups are across from each other, that

is considered a trans-isomer, or “e-“ (German for entgegen, or “opposite”)

Sadly the e/z isomers are the opposite of their letters: E is on the opposite side,and Z is on the same side Just remember that organic chemistry can be

confusing, and that’s why the e/z nomenclature is the opposite of what the letterslook like

KEY POINTS AND HINTS:

Stereoisomers are like conformation isomers, if you break down the molecule to

Stereoisomers for alkenes change physical properties, but for alkanes don’tchange as much

Intermolecular forces are those forces between separate molecules Think of an

interstate (in the US) These roads nominally take you across at least two states,sometimes more (and occasionally less- there are interstates in Hawaii! Let’s

halogen, though C-I bonds are weaker than C-F, C-Cl, and C-Br N-H and O-Hbonds have a strong dipole One of the strongest commonly encountered organicdipole moments is a C-N triple bond

electrons didn’t move around This effect is also known as the London

Dispersion Force It is more important for big molecules than for small

molecules, as it’s easier to induce a dipole somewhere on a big (or long)

molecule than on a smaller molecule The effect of these forces is that manymolecules stick together more than would be predicted by their weight alone

KEY POINTS AND HINTS:

Functional groups heavily influence molecular forces, especially those that haveoxygen

Would you expect a symmetric cis- or a trans- alkene to have a stronger dipolemoment? Would such an alkene have a higher or lower boiling point than theopposite stereoisomer?

A) The cis-isomer would have a stronger dipole moment, and a lower boilingpoint than trans

B) The cis-isomer would have a stronger dipole moment, and a higher boilingpoint than trans

C) The trans-isomer would have a stronger dipole moment, and a lower boilingpoint than cis

D) The trans-isomer would have a stronger dipole moment, and a higher boilingpoint than cis

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Hydrogen bonds are a special variety of intermolecular forces, mainly becausethey are so common (because hydrogen is so common) They are stronger thanmost other Van der Waals forces, and have energies that reach a few kcal/mol inbond strength The hydrogen bond has characteristics of both a bond and anintermolecular force, as it’s energy is between these two

Hydrogen bonds occur when an H atom is attached to a strongly electronegativeatom, such as O or N Hydrogen bonding does not occur with C-H bonds The

H on an OH or NH group will usually seek to bond to a free electron pair,

typically also on an O or N Hydrogen bonds make water into the ideal solventand make many compounds highly soluble in water, such as alcohols

KEY POINTS AND HINTS:

Hydrogen bonds feature most prominently when there are oxygen and nitrogenatoms around