Organic Chemistry II Subscribe with Bloglines class wiki class vodcast

Saturday, August 20, 2005

Last Blog Assignment Deadline Over

All grades for the last blog assignment have been posted. It is now too late to add or change your posts.

I have been impressed with many of the posts. Most of you found relevant articles and extracted the information you needed. Several of the posts were about very practical things like environmentally friendly synthetic approaches, alternative fuels, breathalizer chemistry and the use of enzymes and biological agents to clean up pollutants.

One of the reasons I started this blog assignment is to help you understand how the reactions you are learning are used by chemists in the real world of research and industry. A side benefit is that I have learned some chemistry on each and every post. As a chemist you will never stop learning. What I am hoping is that in this class you have learned the skills to find the information you need to use chemistry productively in your career.

Another bonus is that other people from around the world are benefiting from your posts. Click on the SiteMeter button at the bottom of the blog then click on referrals to see how people are finding your posts.

I will be cleaning up the blog at the end of the term, removing unreadable or substantially incorrect posts. If you wish to keep your posts make sure to copy them before then. In Blogger you can copy a post from one blog to another easily. Just make sure you copy and paste in the "Edit HTML" view, not "Compose". Note that you can also convert the posts into Word. You may wish to do this also if you want to build an e-portfolio.

Friday, August 19, 2005

Bimolecular Dehydration of 1-Pentanol to Di-n Pentyl Ether (DNPE)

Regulations controlling diesel exhaust become more exacting with each passing year. Accordingly, diesel fuel properties are constantly being analyzed in an attempt to further reduce fuel emissions. There are many options, most often refinement processes or improving the cetane number. Essentially, short and branched ethers (used in gasoline) have a good octane number but poor cetane number, while those ethers used in diesel are linear and have a comparatively long chain (ideally 9 or more carbons). Di-n pentyl ether (DNPE) has shown most effective in reducing emissions, and is also relatively simple to synthesize via the bimolecular dehydration of 1-pentanol on acid catalysts, as seen below.

However, the dehydration reaction results in quite a lot of byproducts, including other ethers. As such, a selective catalyst is required to favor production of DNPE by reducing the amount of alkenes. Increased selectivity can be accomplished via gel-type acidic resins at a reaction temperature of 150°C. The article I looked at analyzed the selectivity and reaction rate of the dehydration of 1-pentanol to DNPE using a gel-type resin at various temperatures and alcohol flow rates. Article Link.

Recent advances in solventless organic reactions: towards benign synthesis with remarkable versatility

Recently there has been a paradigm shift away from using solvents in organic synthesis as solventless reactions can lead to improved outcomes, and more benign synthetic procedures, in for example an aldol condensation reaction as shown above. Sustainability is increasingly an important issue in broader context when you are talking about health, energy, and the sciences. Removing organic solvents in chemical synthesis is important in the drive towards benign chemical technologies. Organic solvents are high on the list of toxic compounds due to the problems in containing volatile compounds and the sheer large volume of them used in industry.
Some advantages of utilizing solventless reactions are that the compounds are often sufficiently pure to avoid extensive purification using chromatography, the reactions can be rapid, often reaching substantial completion in several minutes compared to hours in organic solvents, and the energy usage can be much lower.

For the full text click here.

Monday, August 15, 2005

Free-Radical Polymerization: Alkoxyamine Initiators

Polymers have important uses in both research and industry. Alkoxyamines are used in ATRP (atom transfer radical polymerization)-based polymerizations and can serve as efficient regulators in the preparation of polymers. In the past, the alkoxyamines were produced by the creation of radicals that are carbon-centered and were then trapped by nitroxide. This method, however, gave low yields and undesired byproducts. The reaction shown here takes place at low temperatures and in the presence of a nitroxide, utilizing an ATRP-based initiator that is treated with copper bromide. The ATRP is involved in the living radical polymerization system. Me6-tren ligand forms a catalyst complex for the reaction of the initiator with nitroxide. Equilibrium between the transfer to and from radicals and dormant species in the reaction is controlled by the Me6-tren ligand forming a complex with the Cu(II), which the free radicals can then interact with. The catalyst name Me6-tren stands for the chemical tris(2-(dimethylamino)ethyl)-amine. This is a more effective procedure for preparation that results in high yields. Discoveries such as this are important in areas such as nanotechnology.

Here is the CiteULike article.

Here are articles about the Me6-tren ligand and its naming.

This source discusses the use of alkoxyamines in free-radical polymerization.

Sunday, August 14, 2005

Diels-Alder reaction of Quinol Lactone

This is a Diels-Alder reaction, which does not follow the regiospecificity rules. What makes this reaction unusual is that normally quinol-lactone does not react with dienes. Also if we follow the regiospecificity rules we would logically expect to get the structure in Figure 2. However by using stannic chloride (SnCl4) in methylene chloride, the product shown was obtained. It was determined through NMR spectroscopy that this particular product was present, and not its isomer in Figure 2. TBSO stands for the tert-butyldimethylsilyl group.

The reaction is described in this article.

I found an article which looks more closely at the process of migration and elimination of TBS when the final product is synthesized, which produces TBSOTf. It states that stannic chloride causes the migration of the tosyl group (1st paragraph of "Results and Discussion" section). I believe this plays a role in the final "inversion" of the product in the posted reaction. Also this Diels-Alder reaction is performed in Lewis acid which gives the regioselectivity opposite to what we would expect in an uncatalyzed reaction.

The product in Figure 2 should be expected, because if we examine the ortho-para rules for regioselectivity through the formation of radicals without a catalysit (Lewis acid), we can see that the major product should resemble the one in Figure 2. There is an example on this page under the "Regioselectivity" section, which has the major product boxed in.

Thursday, August 11, 2005

Zinc reduction of alkynes

A traditional method for the reduction of alkynes to trans-alkenes is to dissolve metal reduction using sodium or lithium in ammonia. However, we can also use Zinc as a metal to reduce alkynes.

In this specific case, by changing the proton source in the reaction, the dissolving Zinc metal reduction of ethyl phenylpropiolate to the corresponding cinnamate ester can be stereochemically controlled.

The product of the reaction will be a mixture of cis and trans ester. By this reaction, we can see the efficiency of Zinc in the reduction of alkynes.

For more reference, please click on:

Monday, August 08, 2005

Benzoylation of a Polyol

Amino polyols are an important part of synthetically created amino acids. They are highly antibacterial and immunosuppressive and so are used in various antibiotics and antifungal products. This reaction shows one of the step necessary in creating the amino polyol.

Benzoyl chloride is added to the polyol to form a tribenzoate compound. In this reaction, the polyol has several R-O-H groups that act as weak nucleophiles. When the benzoyl-Cl bond breaks upon addition to the pyridine solvent, the benzoyl group acts as an electrophile. With the help of the DMAP (dimethylaminopyridine) catalyst in the reaction, the R-O-H group is deprotonated and the benzoyl group is added to the remaining R-O form the final tribenzoylated product. As seen above, the reaction has a yield of about 90%. The OTBS (t-buytldimethylsiloxy) groups do not participate in this reaction.

There is one hydroxyl group left on the molecule produced. All of the hydroxyl groups would be replaced by benzoyl groups if the reaction was not stopped after three groups had been added. To stop the reaction at this point, three equivalents of benzoyl chloride were used for every polyol.

For the full text of the article describing this process, see this report.

Friday, August 05, 2005

Asymmetric synthesis of monohydroxy tetradecanoic acids

Methyl 3-, 6- and 13-oxo tetradecanoates went through reduction with NaBH4 in the presence of 1,2:5,6-di-O-isopropylidene-Dglucofuranose (DIPGH) and menthol together with isovaleric and pivalic acids in THF solution. This work signifies the importance of positional
effect. The position of lower steric hinderance and higher enantiomeric excess and asymmetric reduction yield were noted down, namely the prochiral 13-keto isomer structures.
With this asymmetric reduction at normal atmospheric pressure together with inexpensive auxiliaries make it competitive with other reduction methods and is needed to assess the need in the market. Here's a link for this article

Chemistry of a Breathalyzer

A Breathalyzer makes use of the fact that alcohols (in this case ethanol) oxidize into carboxylic acids. It uses the strong oxidizing agent Potassium dichromate in a yellow solution of sulfuric acid, under the presence of a Silver Nitrate catalyst, to complete the reaction quickly. As ethanol oxidizes and the Potassium dichromate reacts, the chromate ion changes from Cr (VI) to Cr (III). This causes the color intensity of the yellow solution to decrease, and a spectrophotometer in the breathalyzer compares the absorbance of this solution with that of an unreacted solution

Using Beer's law, the spectrophotometer can relate concentration to absorbance levels of the chromium ion. The amount of alcohol present is proportional to the stoichiometric coefficients. An actual breathalyzer only needs to detect 25 micrograms of ethanol to give a reading 0.10 Blood Alcohol Level.

Journal of Chemical Education

Thursday, August 04, 2005

Synthesis of S-Adenosylmethionine Synthetase

The sulfonium salt S-adenosylmethionine is one of the most widely used biological methylating agents. It is formed by the ATP activation of methionine. One of the most benifical uses of this salt is to convert norepinephrine to epinephrine (adrenaline). Many times this conversion happens in flight or fight organs, which leads to vasodilatation. This vasodilatation in turn leads to an increased blood flow to the organ/tissue or interest.

The reaction shown is the formation of S-Adenosylmethionine. This process occurs in two steps as can be seen. The first step cleaves the whole phosphate of the ATP. However before the sulfur of methionine attacks the C5` atom of ATP (via SN2) there is further hydrolysis of the cleaved tri-phosphate into two inorganic phosphates (di and mono).

Here's a link

Synthesis of Phosphate Monoesters

The following paper presents an efficient and environmentally friendly method for producing phosphate monoesters, in which the only byproduct is water, as opposed to a different reaction, which also gives off pyridine hydrochloride as a byproduct.
The paper describes that it was experimentally determined that the best solvent, tertiary amine, and catalyst (or nucleophilic base) for the reaction are DMF-nitroethane, tributylamine, and N-butylimidazole, respectively, each giving the highest yield. This is a summary of the main reaction discussed in the paper.
* The article states that water was constantly removed by azeotropic reflux, so that the reverse reaction was prevented.

Article Link

I have also included an interesting extensive study on phosphate monoesters.

Wednesday, August 03, 2005

Reduction of Aldehyde to an Alcohol -- Synthesis of D,L-1,2,4-butanetriol

D,L-1,2,4-butanetriol can be made in two different ways; the first way is commercial synthesis through reduction of esterified D,L-malic acid with sodium borohydride, NaBH4, while the second way involves microbes. The latter method was the focus of the journal article. Nitration of racemic D,L-1,2,4-butanetriol results in D,L-1,2,4-butanetriol trinitrate, a compound that is the energetic equivalent of nitroglycerin, but is less shock sensitive, more thermally stable, and less volatile. One of the final steps in the synthesis of D, L-1,2,4-butanetriol via microbes is the reduction of a racemic mixture of D,L-3,4-dihydroxybutanal (aldehyde), to the final alcohol product, as seen in the reaction below. The catalyst for the reaction is dehydrogenase from E. coli.

For the full text of this article, click on the following link (and then the second listed link in citeulike):
Article Link.

Tuesday, August 02, 2005

Anaerobic Toluene Oxidation in the Metabolism of the Fe(III)-Reducing Microorganism GS-15

This is a potential pathway for the oxidation of toluene in Fe(III)-reducing microorganisms, which play important roles in sediments naturally composed of hydrocarbons. The oxidation of toluene, an aromatic hydrocarbon, in these microorganisms is coupled to Fe(III) reduction. GS-15 is the first microorganism discovered to link aromatic compound oxidation to the reduction of Fe(III). The oxidation of p-cresol and phenol in these organisms is also coupled to Fe(III) reduction. Under strict anaerobic conditions in these organisms, GS-15 can completely oxidize toluene to carbon dioxide by utilizing Fe(III) as the only electron acceptor in the reaction.
This mechanism can be used to clean up toxic oil spills or other toluene contaminations by introducing the microorganisms to the site.

Here is the link to the CiteULike article discussing these anaerobic metabolic processes.

Play for points

The final deadline for the 4th blog assignment is August 19th. Since you have had the benefit of my feedback for the first 3 assignments you should now be able to do this one without feedback or problems. It is worth 2% of your grade.

As an alternative to this final blog assignment you may volunteer to evaluate the Unreal Tournament maps we have available on the class material. The deadline for this is also August 19th. Don't wait too long to sign up for this because it will require scheduling. If you don't have UT I'll give you access to a computer.

Contact me if you are interested.

Monday, August 01, 2005

Cesium fluoride-Celite: a solid base for efficient syntheses of aromatic esters and ethers

In the syntheses of aromatic esters and ethers, CsF-Celite has been found to be a very efficient, convenient and practical reagent. In fact, it is used for the coupling reactions of a number of aromatic and heteroaromatic phenols with alkyl, acyl or benzoyl halides.

Many other organic reactions have recently been catalyzed by CsF-Celite, such as the reactions to synthesize carboxylic esters, γ-lactones, N-alkylation of anilines, or carboxamides.

For more reference, please click on