Amino Acid

Glutamic acid is one of the twenty proteinogenic amino acids. It can be abbreviated either Glu or E. This amino acid is a non-essential amino acid. Glutamic acid is a key molecule in cellular metabolism, and is abundant in both animal and plant protein. However, in humans it is a non-essential amino acid because the body is able to produce it's own glutamic acid. In addition to this, the dietary proteins are broken down by digestion into amino acids which play as a metabolic fuel for other functional roles in the body.  A picture of glutamic acid is shown below:

The pKa value of carboxyl group for glutamic acid in a polypeptide is about 4.3. This may be a little high for a pKa value due to the inductive effect of the additional methylene group. The isoelectric point is around 5.65. Pka values are shown below in the diagram:

 

Glutamic acid can be easily converted to proline; due to the carboxyl group is reduced to the aldehyde. From here the aldehyde can react with the alpha-amino group which eliminates water. A diagram of this is shown below:

Electrophilic Substitution

This weeks goal was to find a peer review journal which shows a picture of an electrophilic substitution and why it is important in Organic Chemistry. After doing research on electrophilic substitution it can be defined as: a form of substitution reaction in which the leaving group (normally hydrogen) is replaced with an electrophile. It is important because it a way of introducing functional groups onto a benzene ring. There are two types of substitution one known as electrophilic aromatic substitution and electrophilic aliphatic substitution. Common aromatic substitution include: aromatic nitration, aromatic halogenation, aromatic sulfonation, and Friedel-Crafts, and common ones for aliphatic substitution include: nitrosation, ketone halogenation, and ketol-enol tautomerism,   A picture is shown below which shows electrophilic substitution:

This digram shows electrophilic aromatic substitution in which the final step is a decarboxylation rather than a deprotonation. This is due to the ketone carbonyl. 

References:

1. UC Davis ChemWiki. Section 15.5 Electrophilic aromatic substitution. 4 Feb. 2011. 6 March 2011.

<http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_15:_pi_electrons_as_nucleophiles/Section_15.5:_Electrophilic_aromatic_substitution>. 

Aromaticity

 Hi Grandma,

In class we have been talking about benzene rings, the functions of these compounds, as well as aromaticity. However, for you to even understand what this means I need to explain some of the terms. For compounds to be aromatic they must meet four conditions which include: it must be a ring, it must be flat(planar), it must have in each atom of the ring a p orbital that’s orthogonal to the plane of the ring. In other words, the atoms in ring are sp² hybridized, and it must have a Huckel number of pi electrons, which must follow the 4n+2 rule.

                With knowing these rules let’s look further in dept of ways to classify all other compounds which include: if the molecule meets the first three conditions, but only contains 4nπ electrons the molecule is considered to be anti-aromatic. However, if the molecule fails any or the first three conditions then the molecule is considered to be non-aromatic. Now with a little bit of background let’s now explore the conditions a little bit more in depth. Condition one it must be a ring means that only rings can be aromatic; acyclic (having an open chain structure) systems cannot be aromatic. The second condition it must be flat deals with the shape of the ring. Ring systems can be planar (flat) or three-dimensional. Most conjugated ring systems tend to be flat so that it maximizes the overlap between the p orbital’s. An example would be naphthalene which is planar, and cyclodecapentaene is nonplanar due to two of the hydrogen’s. Both examples are shown below.

                 

           (naphthalene)                                                                                                        (cyclodecapentaene)

           (planar showing aromactity)                                                                          (nonplanar due to two H’s).

The third condition deals with the p orbital’s. An aromatic system must have an unbroken ring of p orbitals, so that any ring that contains a sp³ hybridized carbon will not be aromatic. For example cycloheptatriene is non-aromatic due to the fact that one of the ring carbons is sp³ hybridized. However, carbocations’ (which have a positively charged carbon) are sp² hybridized (and contain an empty p orbital); with this cycloheptatriene cation has an unbroken ring of p orbitals and is an aromatic compound. An example of this is shown below.

                                          

The fourth condition deals with Huckels rule. A tricky aspect that comes into play with Huckels rule is that you must remember of counting the number of pi electrons in the pi system when the ring contains heteroatoms like O, S, N. So how do you know which lone pairs to count as part of the pi system and which to ignore. The general rule of counting substituent’s to determine the hybridization holds true, it does fail when the atom contains a lone pair which is adjacent to a double bond; which means when it is conjugated. A diagram of pi electrons is shown below:

Pi electron Counts

Integer(n)	Aromatic Numbers (4n+2)	Anti-aromatic numbers (4n)
0	2	--
1	6	4
2	10	8
3	14	12
4	18	16

After reading this letter grandma I hope that it gives you a little insight on what aromaticity means and how it relates to benzene rings. 

Muddiest Point

When looking over Chapter 13 one of the muddiest points for me is looking at infrared spectroscopy data and determining what the compound may be. Infrared spectroscopy can be defined as measuring the absorption of the infrared radiation of organic compounds. However, for the absorption to occur the energy of the photon must match the difference of the energy between two states. When a molecule absorbs radiation from the IR it can cause the bonds to bend, stretch which can cause deforming bond lengths and angles. So since different kinds of bonds vibrate at different frequencies they can absorb different frequencies of IR radiation, which then the functional group can be determined. To determine a particular bond on the IR spectroscopy one must look at   the bond strength and atom mass due to the fact that bonds form into four predictable regions of an IR spectrum.

References:

1. Characterization techniques for Organic Compounds. 25 January 2011. <http://www.chem.uky.edu/courses/che232/FTL/C1309.pdf>.

2.Infrared Spectroscopy. 25 January 2011. <http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/InfraRed/infrared.htm>.

3. Infrared Spectroscopy. 25 January 2011. <http://www.prenhall.com/settle/chapters/ch15.pdf>.