Organic Chemistry...yeah :(

My way of taking notes and hopefully making me kick ass in this class...impress dem professors.

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Conformations

Molecules are not inanimate objects. They can twist and bends into all kinds of shapes. 

Why is knowing how individual molecules can twist is important:because there are certain activities that can can be performed only in specific conformations. 

There are comfortable positions (low energy) while other positions are uncomfortable (high energy) .

The various positions available to a molecule is called CONFORMATIONS.

**Molecules cannot undergo some reactions from certain conformations. 

There are two important drawing styles that show conformations and give us the power to predict what conformations are available to different types of molecules: Newman projections and chair conformations

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Nomenclature of Organic Compounds

IUPAC Nomenclature Rules:

There are five parts to every name: stereoisomerism, substituents, parent, unsaturation, functional group. You name them by first stereoisomerism and then end with the functional group.

Stereoisomerism: indicates whether double bonds are cis/trans or E/Z, and indicates stereocenters (R,S), which we will cover in the chapter on configuration.

2. Substituents: are groups coming off the main chain.

3. Parent: is the main chain

4. Unsaturation: identifies if there are any double or triple bonds

5. Functional group: the functional group after which the compound is named.

FUNCTIONAL GROUP: 

Functional group: refers to specific arrangements of atoms that have certain characteristics for reactivity. 

**if there is no functional group then we put an e at the end of the name

UNSATURATION:

Many molecules have double or triple bonds, often called "unsaturation" because a compound with a double or triple bond has less hydrogen than it would have without the double or triple bond. 

Single bond (alkane): use "an"

double bond (alkene): use "en"

triple bond (alkyne): use "yn" 

**if there are two double bonds in a compound, then the unsaturation is "dien". Three double bonds is "trien". Two triple bonds "diyn" and three triple bonds:  "triyn". 

For multiple bonds, we use the following terms:

di = 2 

tri = 3

tetra = 4

penta = 5

hexa = 6

**double bonds get listed first : triendiyne

PARENT: 

When naming the parent of the compound, we are looking for the chain of carbon atoms that is gong to be the root of our name. Everything else in the compound is connected to that chain at a specific location, designated by numbers. 

Number of Carbons atoms = parent name

1 carbon - meth

2 carbon = eth

3 carbon = prop

4 carbon = but

5 carbon = pent

6 carbon = hex

7 carbon = hept

8 carbon = oct

9 carbon = non

10 carbon = dec

**If the carbon atoms are in a ring then we add the term: cyclo 

Tricky part is determining which chain to use! To determine which chain to use: it should be the long chain, making sure to include the following groups in order: 

Functional group

double bond 

triple bond

**The functional group that gets priority needs to be in our parent chain.

**IF there are no functional groups, no double bonds, and no triple bonds, then we simply choose the longest chain possible.  

NAMING SUBSTITUENTS

Once we have identified the functional group and the parent chain, then everything else connected to the parent chain is called a substituent. 

Alkyl Substituents:

1 carbon = methyl (on the parent carbon CH3, Me or one single line)

2 carbon = ethyl  (on the parent carbon CH2CH3, Et, or 2 lines)

3 carbon = propyl (  on the parent carbon three link, or Pr)

**the 3 carbon atoms attached to the middle carbon --> isopropyl (branched substituent) 

4 carbon = butyl

(branched 4 carbons is called tert-butyl)

5 carbon = pentyl

6 carbon = hexyl

7 carbon = heptyl

8 carbon = octyl

9 carbon = nonyl

10 carbon = decyl

Halogens: are named substituents in the following way: fluoro, chloro, bromo, iodo. If there are multiple substituents then us prefixes: di , tir, tetra, penta, and hexa

Steps: identify all the groups that would be considered substituents 2) locate the functional group that gets priority then check to see if there are double or triple bonds then determine the parent chain.

STEREOISOMERISM

Stereoisomerism is the first part of every name. It identifies the configuration of any double bonds or stereocenters. If there are no double bonds or stereocenters in the molecules, then you don't need to worry about this part of the name. 

Single bonds can rotate freely but double bonds cannot rotate freely. 

There are two ways to arrange the atoms in space in dealing with double bonds: cis or trans. 

To name a double bond as being cis or trans, you need to have identical groups on either side of the double bond that can be compared to each other. 

On the same side = cis

On opposite sides = trans

**Cis/Trans nomenclature can be used only when we have two identical groups. 

NUMBERING

To number the parent chain properly, we begin with the same hierarchy that we used when choosing the parent in the first place:

Functional group

Double Bond

Triple Bond

*If there is a functional group, then number the parent chain so that the functional group gets the lower number. 

*If there is no functional group, then number the chain so that the double bond gets the lower number

*If there is no functional group or double bond, then number the chain so that the triple bond gets the lower number.

*If there is no functional group, double bond, or triple bond, then we should number the chain so that the substituent has the lower number.

*If there is no more than one substituent on the parent chain, then we should number the chain so that the substituents get the lowest number possible. 

**Stereocenters will be discussed later.

How To Apply the NUMBERS

Parent chain has been chosen:

Functional Group: gets placed directly in front of the suffix. Ex: hexan-2-ol

if the functional group appears at one then there is no need for a number...(ex: hexanol)

If there is no other numbers it is ok to place the number at the beginning (ex: 2-hexanol is the same as hexan-2-ol

Unsaturation: For double and tirple bonds, the number indicates the lower number of the two carbon atoms. (ex: dobule bond is between C2 and C2 then we use C2 --> hex-2-ene or 2-hexene). same for triple

If there is two double bonds in the molecule, then we must indicate both numbers (ex: hexa-2,4-diene or 2,4 hexadiene) Every double and triple bond must be numbered. 

Substituents: the number of substituents goes immediately in fron of the substituent: 2-chlorohexane. This does not change if there are double bonds, triple bonds, or functional groups. 

*If there are multiple substituents, then every substituent must be numbered. 2,3-diclorohexane

*If there are multiple substituents of different types, then we must alphabetize the substituents in the name. 2-chloro-3-ethyl-2,4-difluoro-4-methlynonane

Stereoisomerism: if there are nay double bonds, we place the term cis or trans at the beginning of the name. If there is more than one double bond, then we need to indicate cis or trans for each double bond, and we must number accordingly. If there are any stereocenters, (2R,4S). Stereocenters are palced in parentheses. 

STEPS: 

1. Look for a functional group

2. Look for saturation

3. Name the parent

4. Look for substituents

5. Look for stereoisomerism 

COMMON NAMES

IUPAC Name: 

Methanoic acid --> Formic Acid (common name)

Methanal --> formaldehyde

Ethene --> ethylene

Ethanoic Acid --> acetic acid

Ethanal --> acetaldyhyde

Ethyne --> acetylene

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Geometry

Orbitals and Hybridization States:

A bond is formed when an electron of one atom overlaps with an electron of another atom. The two electrons are shared between both atoms, and we call that a bond. Since electrons exist in regions of space called orbitals, then what we really need to know is; what are the locations and angles of the orbitals around every atom?

Two simple orbitals: s and p orbitals. S orbitals are spherical and p orbitals have two lobes (one front lobe and one back lobe). 

Atoms in the second row (such as C, N, O, and F) have one s orbital and three p orbitals in the valence shell. These orbitals are usually mixed together to give us hybridized orbitals (sp^3, sp^2, and sp). We get these orbitals by mixing the properties of s and p orbitals. When we mix s and p orbitals we get two equivalent orbitals that look the same. The two new orbital have a different shape from the original two orbitals. This new shape is somewhat of an average of the two original shapes. If we start with three orbitals (two p and one s) then we mix them together and end up with three orbitals that look all the same. All three new orbitals have the average properties of the original three orbitals. The three new orbitials (since they came from one s and two p orbitals) are call sp^2 orbitals.  Similarly when you combine three p orbitals and one s orbital, you get four equivalent sp^3 orbitals. 

The hybridization state of an atom describes the type of hybridized atomic orbitals (sp^3, sp^3, or sp) that contain valence electrons. Each hybridized orbital can be used either to form a bond with another atom or to hold a lone pair. 

HOW TO DETERMINE HYBRIDIZATION:

**Just add the number of bonded atoms to the number of lone pairs. The number you get tell you how many hybridized orbitals you need according to the following:

If the sum is 4, then you have 4 sp^3 orbitals.

If the sum is 3, then you have 3 sp^2 orbitals and one p orbital

If the sum is 3, then you have two sp orbitals and two p orbitals 

GEOMETRY:

Now that we know how to determine hybridization states, we need to know the geometry of each of the three hybridization states. One simple theory explains it all.

VSEPER: Valence shell electron pair repulsion theory: all orbitals containing electrons in the outermost shell (the valence shell)  want to get as far apart from each other as possible. 

sp^3 = tetrahedral

sp^2 = trigonal planar

sp = linear

sp^3 with 0 lone pairs = tetrahedral

sp^3 with one lone pair = trigonal pyramidal

sp^3 with 2 lone pairs = bent

sp^2 with 0 lone pairs = trigonal planar

sp^2 with 1 lone pair = bent

sp with 0 lone paris = linear

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Acid- Base Reactions :::NO FINISHED YET::::

Simple Equation:

HA --><-- H+ + A-    

HA = acid

A- = Conjugage base

HA is an acid by virtue of the fact that it has a proton (H+) to give A-.

A- is a base by virtue of fact that it wants to take its proton back

**Acids give protons and bases take protons

Strong acid is indicated by whether how easily HA is willing to give up it proton. If it is not willing to give up its proton then it is a weak acid.

To determine whether HA is willing to give up its proton or not we can look at the conjugate base.

The conjugate base has a negative charge but in determining where HA is a strong acid or weak acid we need to see how stable the conjugate base. If that charge is then HA is willing to give up the proton and HA will be a strong acid. If the charge is not stable then HA will not be willing to give up its proton and HA will be a weak acid.

NEED TO UNDERSTAND WHAT FACTORS STABILIZES CHARES AND WHAT FACTORS DESTABILIZES CHARGES.

Factor 1: What atom is the charge on:

Ask yourself what atom is the charge on. There are two important trends: electronegativity (for comparing atoms in the same row) and size (for comparing atoms in the same column). The first factor (comparing atoms in the same row) is a much stronger effect. In other words, the difference in stability between C- and F- is much greater than the difference in stability between I- and F-. 

Factor 2: Resonance

Charge is stuck on one atom: LOCALIZED

A charge that is spread over more than one atom: DELOCALIZED

**A delocalized negative charge is more stable than a localized charge. 

Resonance (which delocalizes a negative charge) is a stabilizing factor. 

Comparing two compounds that are both resonance stabilized:

Rule 1: The more delocalized the better. A charge spread over four atoms gives a more stable compound than a charge spread over two atoms, but

Rule 2: one oxygen is better than many carbon atoms. 

**the more acidic proton is that one that leaves to give the more stable conjugate base. 

Factor 3: Induction 

Electronegativity measures the affinity of an atom for electrons, so what happens when you have two atoms of different electronegativity connected to each other? In a carbon - oxygen bond, oxygen has a larger electronegativity than carbon. So the electrons that are shared between the two are pulled more strongly by oxygen than carbon. This creates a difference in the electron density on the two atoms- the oxygen becomes more electron rich and the carbon becomes electron poor. This "pulling" of electron density if called induction. 

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Which Resonance Structure is more important.

Two Rules for Determining which Resonance Structure is more Important.

1.Minimize charges: The best structure is one without any charges. It's OK to have two charges but should avoid to have more than two charges.

**Nitrogen is an exception: When counting charges two charges is ok because we cannot draw the nitro group without charges. Thus the two charges of a nitro group don't really count when we are counting charges. 

2. Electronegative atoms (such as N, O, Cl, etc.) can bear a positive charge but only if they possess an octet of electrons. 

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Resonance Structures: Recognizing Patterns

1. A lone pair next to a pi bond.

2. A lone pair next to a positive charge

3.A pi bond net to a positive charge.

4.A pi bond between two atom. where one of those atoms is electronegative.

5. Pi bonds going all the way around a ring.

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Resonance: Step by Step

1. Can we convert any lone pairs into pi bonds?

2.Can we convert and pi bonds into lone pairs?

3.Can we convert pi bonds into pit bonds?

**Double and Triple bonds are pi bonds

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The Two Commandments: Resonance

1. Thou shall not break a single bond

2.Thou shall no exceed an octet for second-row elements.