More Organic Reactions

• Electrophilic Addition to Unsaturated Carbons

A carbon—carbon double or triple bond undergoes an addition reaction bonding a new atom or group of atoms to each of the carbons of the original multiple bond. One of the groups that adds to the multiple (π) bond is an electrophile, the other is a nucleophile. As an addition to a carbon—carbon multiple bond proceeds, the electrophile adds to the less highly substituted carbon, and the nucleophile adds to the more highly substituted carbon. This direction of adding is called Markovnikov's rule.

Hydrogen halides add to the π bonds of alkenes and alkynes to form organohalogen compounds. In a polar-protic solvent this reaction proceeds through a carbocation. In a polar-aprotic solvent the reaction proceeds through an AdE3 mechanism.

An acid-catalyzed addition of water is an AdE2 reaction and proceeds via a carbocation.

The oxymercuration reaction proceeds through an AdE2 reaction via a cyclic mercurinium ion intermediate. Nucleophilic substitution by water followed by reduction with NaBH4 produces an alcohol with net anti addition. The reaction is both stereospecific and regiospecific.

Hydroboration is a stereospecific and regiospecific syn addition to an alkene forming an organoborane. The organoborane can be oxidized to form an alcohol. The alcohol is the anti-Markovnikov product.

Halogens add to alkenes to form vicinal dihalides. For bromine, the reaction proceeds stereospecifically via a three-membered ring bromonium ion. With chlorine, the reaction is less stereospecific. The reaction does not work well with iodine. In a water solvent, the water competes with the bromine nucleophile and reacts with the bromonium ion to form a halohydrin product.

Catalytic hydrogenation reduces a multiple bond by adding hydrogen to the π bond. Catalysts such as platinum, palladium, or nickel are the most common ones in use. Hydrogen adds to the multiple bond to form an alkane.

• Aliphatic Nucleophilic Substitution

An sp3 hybridized carbon undergoes nucleophilic substitution if it has a bond to an atom more electronegative than itself. Nucleophilic substitution at a saturated carbon atom follows one of two mechanisms. In the first mechanism, the leaving group departs before the nucleophile arrives. This is the SN1 mechanism. In the second mechanism, the leaving group departs as the nucleophile arrives. This is the SN2 mechanism. The rate for an SN1 mechanism depends only on the concentration of the substrate. Thus, an SN1 reaction follows first order kinetics and proceeds through a carbocation intermediate. The rate for an SN2 mechanism depends on the concentrations of both the nucleophile and the substrate. Thus, an SN2 reaction follows second order kinetics and is a concerted reaction. Because the SN1 mechanism has a symmetrical carbocation intermediate, it loses all stereochemical information in the reaction. The reaction proceeds with racemization of configuration. In the SN2 reaction, the nucleophile approaches from “behind” the leaving group resulting in an inversion of the configuration of the carbon in the substrate. In the inversion of configuration of the SN2 mechanism, the product has the opposite configuration of the starting material.

Nucleophiles and leaving groups are both bases. Usually, the leaving group is a weaker base than the nucleophile. Most good nucleophiles are soft bases. Reactions with both high solvent polarity and the ability of the solvent to solvate both the carbocation and the nucleophile promote SN1 reaction pathways. Low solvent polarity that does not stabilize carbocation formation promotes SN2 reaction pathways.

Halide nucleophiles react via either the SN1 or the SN2 mechanism depending on the substrate and reaction conditions.

Water and alcohols are good nucleophiles for solvolysis reactions. Their conjugate bases are good nucleophiles as well, but they tend to promote elimination reactions as side reactions to substitution reactions.

Organic Reactions

Organic reactions may be classified according to net result and mechanism.

Based on net result, the types of reactions are:

1. Substitution - an incoming atom or group of atoms replaces a leaving atom or group of atoms

AB + CD → AC + BD

a. Nucleophilic Substitution - an atom or group of atoms in a molecule is replaced by a nucleophile

i. SN1 or Unimolecular Nucelophilic Substitution

ii. SN2 or Bimolecular Nuceleophilic Substitution

b. Electrophilic Substitution - an electrophile attacks the carbanion of the substrate substitutiong one of the hydrogens or other groups

2. Addition - a molecule adds across a pi bond

A + B → C

3. Elimination - one molecule is lost to give a pi bond

AB → A + B

4. Rearrangement - constitutional change in carbon skeleton

Based on mechanism, reaction types are:

1. Polar Reactions - involves heterolytic bond cleavage (heterolytic - uneven breakage: all electrons go to one atom)

2. Radical Reactions - involves homolytic bond cleavage (homolytic - even breakage: one electron goes to each atom)

Chirality

A chiral molecule has no internal plane of symmetry and has a non-superimposable mirror image. No matter how you turn it, it will never be the same as its mirror image. On the contrary, achiral molecules have identical and superimposable mirror images.

Conformations

Conformations are 3-dimensional shapes that can be taken by a molecule by rotating about single bonds.

• In the planar conformation, everything is eclipsed. In an eclipsed conformation, the bonds have dihedral angles of zero degrees. This maximizes the energy and leads to instability. Steric hindrance of eclipsing interactions also lead to torsional strain or the resistance to rotation about a single bond.
• In the chair conformation, everything is staggered. In a staggered conformation, the bonds have dihedral angles of 60 degrees. This minimizes the energy and thus leads to more stability.
• All the conformations in between are partially eclipsed.
• The Boat conformation has Flagpole interactions because axial groups attached to the head and tail of the boat clash.
• The Twist-boat conformation lessens these Flagpole interactions in addition to reducing the number of eclipsed interactions.

Organic Nomenclature

The IUPAC (International Union of Pure and Applied Chemistry) system of naming is a set of logical rules used to eliminate problems caused by arbitrary naming. It's most important features include:

1. The root or base which indicates the major chain or ring of carbon atoms found in the structure
2. A suffix or other elements which designates the functional groups present in the compound
3. Names of substituent groups that complete the molecular structure

On determining the major chain, one should first know the different terms used for differently numbered carbon chains.

code no. of carbon

meth 1

eth 2

prop 3

but 4

pent 5

hex 6

One should also familiarize himself/herself with the codes used when there is the presence of double bonds or single bonds.

code means

an contains only carbon-carbon single bonds

en contains a carbon-carbon double bond

Alkyl Groups

Members of alkyl groups are produced when you remove a hydrogen atom from members of a family of compounds called alkanes. For example, CH4 is called methane but upon removing one of its H atom, CH3 or methyl is produced.

Here's a table of functional group priorities for nomenclature.

Aromaticity

Six carbons once formed in a ring,

with sp2 hybridization.

The strain was relieved,

and all six achieved

electron delocalization.

‘The stability, itself is dramatic,’

said a puzzled o-chemist fanatic.

‘All these factors at work

just add a new perk.’

And thus was proclaimed aromatic.

D:

The first Ph Ch exam was hard. That was expected of course. What pains me though is that I hadn't been able to finish it. Anyway here's the reviewer I made for the said exam.

Sorry for the size. Just click on it to view it better. :)

Keep Calm and Carry On

Chem 18 exam on Wednesday and Chem18. 1 & Ph Ch 125 exam on Saturday. The dates are looming and I am not yet prepared. T___T

Resonance Structures

Lewis structures that are equivalent except for the placement of electrons are called resonance structures or resonance forms and the hypothetical switching from one resonance structure to another through electron delocalization is called resonance. By convention, resonance structures are separated by double headed arrows.

Seen above are the resonance structures of the ozone molecule. Notice that the only difference between the two structures is in the placement of the double bond and the placement of the lone pair.

Resonance structures are possible whenever there is a multiple bond and an adjacent atom with at least one lone pair. For example, the two resonance structures for the formate ion, HCO₂^- are

As represented by the arrows, in order to generate the second resonance structure from the first, one lone pair is turned into another bond, thus forming a double bond and consequently, this causes one bond to turn into a lone pair.

The general way of deriving resonance structures from one another is through shifting one of the lone pairs to and adjacent atom to form another bond and through shifting one of the bonds in a double or triple bond up to form a lone pair. This should not be applied to all cases though as the atoms' electronegativities should also be considered. For example, in fluoroethene, CH2CHF,

the resonance structure on the right is not reasonable as fluorine is the most electronegative element and in order to for it to form two bonds and two lone pairs, it would first have to lose an electron.

It is also possible to form resonance structures without the participation of lone pairs. An example is the benzene ring which involves a cycle of double bonds.

It should be taken into consideration that in drawing resonance structures, only the electrons may be moved. The nuclei of the atoms are fixed. The total charge and the total number of electrons are fixed as well.

With all the rules and all the other things to be considered, I find this lesson complicated. :c

3: Isomerism

Isomers are compounds with the same molecular formula but with different structural formulas. As part of the lesson, the professor drew structures in front and our task was to determine whether the said structures were isomers or just the same compound.

It is easy to determine that the compounds above are isomers based on which carbon the amino group (NH2) is attached. On the structure at the left, NH2 is attached to the 2nd carbon. For the one in the middle, NH2 is attached on the 3rd carbon and for the last one, NH2 is seen on the 4th carbon thus proving the difference on their structural formulas.

On this example, the compounds are also isomers as N is placed differently on each compound. To make sure that the compounds are really isomers and not just the same structure, one may try naming each one. Variations in the name generated such as with that seen above already indicate that their structural formulas differ from each other.

The concept of isomerism is basically simple to understand given that one already understands fully how to name structural formulas. In my perspective, the confusing part that may lead to errors in distinguishing identical structures from isomers is in the numbering of the longest carbon chain but once the skills in naming is mastered, I suppose that there wouldn't be further problems regarding the topic.

2: Atomic and Molecular Orbitals

Atomic orbitals are the regions in space where it is more probable to find an electron. This is somehow synonymous to the definition of molecular orbitals though for the latter, the electrons belong to the entire molecule and not to its individual atoms. Another way to put it is that an electron in an atomic orbital is under the influence of only one nucleus of the atom while an electron in a molecular orbital is under the influence of two or more nuclei, depending upon the number of atoms present in the molecule.

The 1s atomic orbital has no node (region where there is zero probability of finding an electron) and has the lowest energy. The 2s atomic orbital is bigger than 1s and is with one node, thus it has higher energy compared to 1s (as more nodes mean higher energy for the orbital). On the three 2p orbitals, the x, y, or z label indicates along which axis the two lobes are directed. It is also understood that in orbital labels, the number tells the principal energy level while the letter tells the shape. The letter s means a spherical orbital; the letter p means a two-lobed orbital.

All the topics above have already been discussed during our Chem14 days thus it wasn't that hard to understand that part of the lecture. The more complicated orbitals though need a bit more refreshing as they are much harder to visualize. If you want to get a better glimpse of them, click here. :)

1: The Basics

The class started with a brief introduction of our professor, Sir West. That was then followed by our introduction of our chosen partners. As today was our first meeting for Ph Ch 125 lec, the main goal was just to acquaint ourselves with the syllabus and the subject itself. Based on the list of topics covered and on the number of those who have to repeat the subject as well, I can already foresee the looming days of stress and hardship. My lack of background on topics 7 onward may also account for such negativity. I am quite positive on one thing though. Sir West said that organic chemistry allows him to think visually and that is possibly a good thing for visual learners like me.

Organic chemistry is a branch of chemistry that focuses on carbon-containing compounds. Life itself will not be possible without the unique ability of carbon to form multiple chains and rings at low energies. This property of carbon may be attributed to its four valence electrons that readily allow bonding to as many as four other atoms. Though silicon is tetravalent as well, it doesn't tend to form double and triple bonds and its high affinity for oxygen is quite disadvantageous (an example is in the formation of silicon dioxide).

It must be taken into consideration though that not all carbon-containing compounds are organic, with carbon dioxide and carbon monoxide as some examples. As I do not know the reason for this, I have tried to look for answers and according to what I have read, a fine line between organic chemistry and inorganic chemistry doesn't exist though some consider the presence of both carbon and hydrogen as the main determining factor as to whether a compound is organic or not.