Preparation Of Biologically Active Privileged Structures Biology Essay


Cancer is possibly the most formidable word within the common human languages. Knowledge of cancers dates back to when human civilisations first began making records of their activities (Knowles M, 2005). Cancer is not just a single disease but rather a group of over 100 diseases and is defined as the abnormal growth of cells which tend to proliferate in an uncontrolled manner. Often people assume it to be a slow painful form of death, however in some cases people who suffer from cancers live longer lives than those who have never suffered from it. The main reason for this is that sufferers generally become more observant towards their health and therefore take better care of themselves. If the cancer is identified early on in its progression, it can be treated and the patient can lead a more normal life (Pilgrim A, 1998).

The majority of deaths in the UK are caused by cardiac diseases, however the prevalence of cancer is steadily increasing with more than 250 000 newly diagnosed patients annually (Cancer Research UK). Overall it is estimated that one in three individuals will suffer some form of cancer in their life time. Cancers are not just restricted to humans; they occur in most multi-cellular life forms since it involves disturbances in cell proliferation, development and differentiation (Khan M, 2006).

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Precise mechanisms are in place to control the proliferation, differentiation and death of any one cell. Stimulatory and inhibitory agents control this transition through the different stages. In cancer, tumour cells differ from normal cells as they are non compliant to these control mechanisms. There are three distinct types of tumours (Lewin B, 1998):

Benign- these are characterised by local uncontrolled growth, however they do not spread to other sites.

In situ- these tend to develop within the epithelium and generally remain small. They do not invade the basement membrane although they have the morphological appearance of cancer cells.

Malignant- these have the ability to destroy and invade surrounding tissues. The cells involved replicate at a high rate need a steady supply of nutrients and proteins; this is attained by the growth of blood vessels into the tumour. The newly formed blood vessels can be used as a medium to transport the cancerous cells throughout the body to form secondary tumours.

The development of cancer can be explained as a 3 stage process:

Initiation whereby mutations in DNA provoke the development of cancer cells.

Promotion of initiated cells through clonal expansion.

Progression of the cells into invasive and metastatic tumours.

There are three distinct groups of genes responsible for the development of cancerous tissue. These are oncogenes, tumour suppressor genes and mutator genes.

Oncogenes are derived from proto oncogenes which are responsible for the control of normal cell division, apoptosis and differentiation. The proto oncogenes are converted to oncogenes via viral or carcinogenic action. Tumour suppressor genes are responsible for the negative regulatory signals in normal cells, they code for proteins whose absence, expression, repression, inactivation or mutation promotes oncogenesis. Normal cells within the body have efficient repair mechanisms, however any alteration in the genes can increase the capacity to cause mutations and therefore provoke the formation of cancerous tissue, and such genes are referred to as mutator genes.

Risk Factors

Risk factors relate to the likelihood of developing a cancer, however not all people who have risk factors will develop a form of cancer. With this said, some people who have no apparent risk factors may still develop a cancer. Each type of cancer has its own set of risk factors and some of the key risk factors include the following:

The use of tobacco including smoking cigarettes or cigars, chewing tobacco, and using snuff all contribute towards developing cancers. It contributes to over 30% of all cancers and cancers associated with tobacco can occur at the mouth, larynx, bladder, kidney, cervix, oesophagus and pancreas (Kamangar F 2009).

Ultraviolet light exposure such as by strong sunlight or excessive use of sun beds increases the likelihood of suffering skin and eye cancers.

The risk factors for developing breast cancer include, age, hormonal changes, number of pregnancies, onset of menopause, obesity and physical activity. Studies have linked the consumption of alcohol to breast cancer and genetic links between family members have also indicated an increased risk (Hiatt RA 2009).

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Prostate cancer can affect all men however variations in diet, age, genetics and race can affect the risk of suffering from it. An increase in age is related to prostate cancer, Afro-American men have an higher incidence risk, a high fat diet is indicated, and if there is a history of prostate cancer within the family there is also an increased risk (Harvey B 2009).

Current Treatments

Cancer can be treated through a variety of methods ranging from drug interventions to surgery. The choice of treatment is dependent on several factors, the key ones being, the location of the cancer, the stage of the disease, the patients' general health and wellbeing aside from the cancer, and the resources available. The overall aim of treatment is to eradicate the cancer cells without causing damage to surrounding healthy tissues. This can be attained through surgery however due to the complexity and nature of cancers to invade, its effects may be limited. As mentioned earlier, cancer cells can enter lymphatic or blood vessels and circulate to normal tissue elsewhere in the body; this process is defined as metastasis and is the reason why surgery may be rendered ineffective (Pilgrim A, 1998).

The key treatment types are surgery, chemotherapy, radiation therapy, immunotherapy, hormonal therapy and the control of symptoms. Surgical treatment is often sought in patients suffering from breast cancer, mastectomy, or prostate cancer, prostatectomy. If a single cancerous cell is left within the normal tissue following surgery, it may infect local tissue to once again form a tumour, this process is referred to as recurrence. Considering this, once surgery has been conducted the specimen is analysed to determine if a border of healthy tissue is present, this indicates whether or not all the cancerous cells have been removed. Surgery can be used not just for removal of the tumours but also for identifying the progression of the disease and hence the prognosis. It is occasionally used to control symptoms such as in spinal cord compression, this is referred to as palliative treatment (Sah BK, 2010).

Radiation therapy uses high energy particles to shrink tumours by killing cancerous cells. It works by damaging the genetic makeup of cells limiting their ability to divide and grow. The process is specific to the point where you can target different tissue however it does not differentiate between healthy and cancerous cells. The aim of radiation therapy is to inflict as much damage to cancerous cells whilst restricting the harm done to healthy cells, and this is usually achieved as the high energy particles are emitted in a beam to the desired tissue. Also cancerous cells do not have the ability to repair DNA damage whereas normal cells do (Srokowski TP, 2008).

The process of using drugs to treat cancers is called chemotherapy; such drugs have the ability to kill cancer cells. Typically most of these drugs are cytotoxics and they affect the cell cycle through several pathways, for example they may limit the ability of new chromosome formation and therefore impede cell division. Generally most forms of chemotherapy target rapidly dividing cells as this is one of the traits of cancerous tissue. The treatment is however not specific to cancer cells only so some rapidly dividing cells within the body, such as cells of intestinal lining, are also affected but these normal cells retain the ability to regenerate whereas cancer cells do not (Hong YS, 2009). There are several different categories of chemotherapeutic drugs, and these are defined by their mechanism of action. Examples include (Tonini G, 2005):

Alkylating agents, e.g Cisplatin and oxaliplatin- These function by the addition of an alkyl group to electronegative species within a cell and also form covalent bonds with many biological groups to interfere with cell function.

Antimetabolites, e.g. azathioprine and mercaptopurine- These drugs mimic purines which form key components of DNA, this stops normal cell division as the normal purines are not taken into the cell cycle

Plant alkeloids and terpenoids, e.g. vincristine, podophyllotoxin and Taxol- These drugs originate from plants and function by restricting microtubule function during cell division. Microtubules are a key part of the cell cycle as they are responsible for the separation of the replicated chromosomes to opposite poles of the dividing cell. Vincristine specifically binds to tubulin inhibiting its potential to form microtubules. Podophyllotoxin works by preventing the cell entering the initial phase of cell replication, G1 phase. Taxol works by increasing the rigidity and stability of the microtubules and this prevents the separation of the chromosomes.

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Targeted therapy is a group of medications that aims to restrict the growth of cancer cells by disrupting specific processes responsible for cancer development. It is a relatively new field of treatment and has attracted much research as it is less harmful towards normal cells. There are two main types of targeted therapy, these are small molecules and monoclonal antibodies. The small molecule therapy entails the inhibition of enzymatic domains on proteins which are mutated, over expressed or necessary for the development of the cancer cell. Examples of small molecules include; imatininb which can be used for leukaemia and gastrointestinal stroma tumours, and also gefitinib which is used for some lung cancer cells. Monoclonal antibody therapy uses antibodies that bind to specific target proteins on the cancer surface and here they can disrupt the mechanisms of cell development or cause cell death. An example of such a drug is Avastin which contains the antibody bevacizumab; it targets vascular endothelial growth factor and is approved for the use against colorectal cancer (Qian H, 1993).

Cancer immunotherapy aims to use the body's immune system to reject and therefore fight off the cancerous cells. This can be achieved by administering a cancer vaccine which would help immunize the patient against the cancer, and therefore enable the patient to be equipped with the relevant immune cells to combat any cancerous cells (Cheever MA, 2008). The body's immune system functions by recognising foreign entities within the body, since tumour cells are derived from the body's own cells, they can go unnoticed by the immune system. However there are specific antigens which cancerous tissue secrete which are classed foreign to the body, glycosphingolipid GD2 is such an example and is therefore targeted when considering immunotherapy.

When treating a patient with cancer, several of the techniques mentioned can be used alongside each other to attain the most beneficial result. Due to pharmacogenomics, individuals may have different effects to the same treatment hence treatment should always be tailored to the patient specifically and all effects strictly monitored. Extensive research is being conducted to improve current treatment methods and to discover new techniques to treat cancer. The overall aims of the research are to produce anti cancer agents which are cheap to produce, limit damage to normal cells, and are effective at killing the cancers. One such effort is focused on a versatile entity termed an indole; derivatives of this molecule have shown great promise in anticancer treatment.


What are indoles?

Indoles are biologically active compounds which form the components of many naturally occurring compounds. They are aromatic heterocyclic organic compounds which have a bicyclic structure composed of a benzene ring attached to a pyrole ring which contains nitrogen. Indole chemistry is an interesting yet complicated area of study, more importantly indoles can be the precursors or intermediates of many pharmaceutical products. However they can also be the essential component of compound. Tryptophan is one particular example of a prominent indole, which is the precursor of the neurotransmitter serotonin. In recent times, much research has been carried out focussing on indoles as priveledged structures, which can then be further developed to produce ligands that act at a range of receptors(Fernando R, 2009). Indoles have been the focus of much studies, in particular the anti-cancer properties of indoles such as indole-3-carbinol (Meng Q, 2000).

Indoles are solid at room temperature. They can be synthesised by a number of chemical pathways and mechanisms, including the Leimgruber-Batcho indole synthesis, which is popular in the pharmaceutical industry to produce drugs from substituted indoles, this reaction is favoured for its high-yield. The Fischer indole synthesis is also used more commonly to produce indoles which have substitutions at 2-and/or 3- position. The Reissert indole synthesis and Bischler-Möhlau indole synthesis which is used to produce 2-aryl indoles are other pathways of synthesis. Indoles can also be produced by bacteria up on breakdown of the amino acid tryptophan (Douglas AH, 2003).

Substituted indoles, produced by electrophilic substitution of indoles often at position two or three are common precursors and active structural components of tryptamine alkaloids such as the hormone melatonin shown in figure1, and the neurotransmitter serotonin shown in figure2. In the central nerveous system Serotonin is a major neurotransmitter, it also controls smooth muscle activity within both the gastrointestinal and cardiovascular systems, and platelet function. The non-selective serotonin receptor agonist lysergic acid diethylamide also known as LSD, is a hallucinogenic drug which contains the indole ring (Douglas AH, 2003).

Figure1, shows the hormone melatonin with the highlighted indole ring.

Figure2, shows the neurotransmitter serotonin with the highlighted indole ring.

Some non-steroidal anti-inflammatory drugs such as indomethacin, used to treat and etodolac, and betblocker drugs such as pindolol are other examples of indolic compounds. Many indoles are found in nature, and when these are combined with other sources there are several hundred alkaloid derivatives (Douglas AH, 2003).

Figure3, shows the non-steroidal anti inflammatory drug indomethacin with the highlighted indole ring.

Figure4, shows the non-steroidal anti inflammatory drug etodolac with the highlighted indole ring.

Indoles and anti-cancer

An increase in dietary vegetable intake has been reported to reduce the risk of developing numerous different types of cancers (Temple NJ, 2003, Steinmetz KA, 1996). In particular vegetables such as broccoli, cauliflower, cabbage and Brussels sprouts, collectively known as cruciferous vegetables have been signified to reduce cancers of the breast, cervix, lung, prostrate and colon (Lewis S, 2002, Witte JS,1996) however these reports have proved to be controversial (Kristal A. R, 2004). The findings from studies have been inconsistent and the reason for these remains unknown, however it is believed that the content of the active components of these vegetables varies, and the genetic makeup of the individual consuming the vegetable is also an essential factor (Fowke JH, 2003).

The bioactive food component of the vegetables believed to show anti-cancer property is believed to be indole containing, this is indole-3-carbinol (I3C). Studies have suggested that differences in concentrations of the detoxifying enzymes M1, S-transferase (GST) and GSTT1 may have an impact on the anti cancer effect which the consumption of vegetables has. The anti-cancer attributes of the vegetables between individuals may also vary due to genetic polymorphisms in transcription factors and receptors which are associated with the bioactive components of the vegetables, and therefore the effect will vary between individuals after consumption (Beier RC, 1990).

I3C is a bioactive food component found within the vegetables. Once ingested it can be converted to 3,3'-diindolylmethane (DIM), in the gastrointestinal tract, which is a biologically active dimer. This biologically active compound accumulates within the nucleus of cells and is the likely location of where it basis its action. Changes in cell cycle, progression, apoptosis, carcinogen activation and DNA repair may be responsible for the anticancer actions of I3C (Young SK 2004).

The activity of I3C has been shown to be beneficial against cancers of the breast, colon, cervix, and prostate. A link between the concentration of the 2:16 hydroxyestradiol ratio and breast cancer has been established whereby breast cancer patients have elevated serum 16 hydroxyestradiol and similar 2 hydroxyestradiol concentrations as non sufferers. Urinary oestrogen metabolites can be used as a measure to estimate the likelihood of developing cervical cancer (Newfield L et al 1993). Women who have abnormal cervical epithelia have been shown to have reduced 2:16 hydroxyestrone ratios in comparison to women with normal epithelia. To counteract this there would need to be an up regulation of 2-hydroxylation to cause the metabolism of estradiol to a benign compound. I3C has been found to be one of the most potent compounds being effective of the up regulation of 2-hydroxylation (Newa T et al 1994).

Studies have shown that I3C has the ability to restrict the growth of oestrogen receptor positive breast cancer cells, and in vitro it limits the ability of breast cancer cells to invade any local tissues. This is understood to be caused by its ability to up-regulate certain tumour suppressor genes and adhesion molecules (Meng Q et al 2000). DIM may act as an oestrogen antagonist as it has been shown to selectively bind to oestrogen receptors (Riby JE et al 2000).

Research has shown that I3C can interfere with the development of prostate cancer. One such study highlighted how this indole can cause cell cycle arrest of prostate cancer cell lines at the G1 checkpoint. At concentrations of 25-100µM, I3C induces the expression of specific tumour suppressor genes and also down regulates protein complexes responsible for the transcription of DNA (Chinni SR et al 2001).


The discovery and development of new leads within the pharmaceutical industry has advanced with the use of combinatorial synthesis (Szostak JW 1997). Over recent years combinatorial synthesis has progressed from the identification of collective mixtures to preparation and development of single purified compounds. The techniques involved in purification and synthesis have advanced greatly. Hence combinatorial synthesis is now essential in the detection of new lead compounds which will act at different sites. This mixture synthesis allows the production of many analogues of a compound in one process. Minor modification in the molecular structure of a compound can have a great effect on the activity, and this leads to the study of structural activity relationships. The aim of this investigation was to determine various synthetic methods of preparing indoles, which have anti-cancer properties, in a simple and reproducible manner. Indoles are believed to be the single most important structural class in drug discovery. There number of compounds which contain the indole ring is very high and to produce a library of all their complete biological activities would be impossible. As a result this study focussed mainly on 2-aryl indoles, which are the building blocks of many biologically active compounds (Douglas AH, 2003).

Microtubules made up of heterodimeric α and ß-tubulin polymers are essential components of the cell structure. Microtubules are associated with maintaining cell shape, division, motility and also intracellular transport. (Downing KH, 1998). Drugs which have the ability to modify microtubule compilation by either inhibiting the polymerization of tubulin, or by deterring microtubule disassembly have been reported to be beneficial in the development of anti-cancer therapy. (Li Q, 2002, Prinz H, 2002). Many tubulin polymerisation inhibitors have been produced by semi-synthesis and also been identified from natural resources, the common trait between these compounds is the presence of an indole nucleus. 2-Aryl indoles such as 2-(3-methoxybenzoyl)indoles show cytotoxic activity. The indole containing drugs; Vincristine and Vinblastine, are two of the earliest anti-tumor drugs which inhibit tubulin polymerisation. Vincristine is commonly used in the therapy of acute lymphoblastic leukemia and Hodgkin's and non-Hodgkin's lymphoma. Vinblastine is used in the treatment of advanced hodgkin's disease against germ cell cancer of the testes (Duflos A 2002).

Structure activity relationship studies were carried out with different substitutions at differing positions, however some of the products made were inactive, while others showed differing cytotxicities. Strong cytotoxic activity was due to substitutions of a methoxy group at position 5- of the indole ring. However certain substitutions of a methyl group at this same position resulted in an inactive compound (Brancale A 2006). More research is being done to discover small indole containing molecules which act on tubulin, which have a greater activity and lower cytotoxicity. These are easy to synthesise at a relatively low cost. 2-Arylindoles have been identified as tubulin polymerisation inhibitors; this was discovered during research into new anti-mitotic drugs. These are drugs which have an effect on microtubules and tubulin (Mahboobi S 2001, Beckers T 2002). 2-Arylindoles were found to be microtubule destabilisers and ß-tubulin binders, and some of these compounds were reported to have action which was on a par with Paclitaxel used in cancer chemotherapy as a mitotic inhibitor (Mahboobi S 2001). Substitution at position 3 of phenylbenzoyl produced active complounds, in particular the 3-fluoro and the 3-methoxyphenyl derivatives showed increased cytotoxicity, and an effect which was very similar to that of paclitaxel (Brancale A 2006). 2-Arylindoles can be synthesised easily and with a high yield, and show intense cytotoxic activity against human ovarian adenocarcinoma and human cervical epitheloid carcinoma. However other studies of 2-arylindoles suggest that the mechanism of action of these may not only be exclusive to tubulin, and that they may interact with a different biological target (Beckers T 2002).

Methods of indole synthesis MORE DETAIL

There are several methods used to produce indoles, the main ones are the Fischer, Leimgruber-Batcho, Bischler-Möhlau, and Reissert methods. The Fischer indole synthesis method produces an indole from the reaction of phenylhydrasine with an aldehyde or a ketone using acidic conditions. For this reaction, either a Bronsted acid or a Lowry acid can be used, both have successfully produced indoles.

The Leimgruber-Batcho method uses o-nitrotoluenes as a starting material for indole synthesis. N,N-dimethylformanide dimethyl acetal and pyrrolidine are used in the first stage to produce an enamine, and this undergoes reductive cyclisation in the second stage to form the desired indole.

The Bischler-Möhlau method for indole synthesis uses α-bromo-acetophenone and excess aniline to form a 2-aryl indole. It involves the reaction of α-bromo-acetophenone with the aniline molecules to form a charged aniline, this forms a leaving group for an electrophilic cyclization to occur forming an intermediate; This quickly aromatises and tautomerises to give the desired indole.


Indoles are privileged structures which possess biological activity in a number of therapeutic areas. The aim of this project is to investigate and develop synthetic methods of preparation of indoles. The desired reaction scheme is required to be quick and efficient, and the product made should be available for further biological testing.

The selected reaction scheme will be the initial step of an investigation which will be further studied by biologists, with the hope of using the indole structures as lead compounds in the discovery and development of anti-cancer drugs.






Overall Reaction Scheme


Solvent/base screen for Ketone synthesis

2-NO2 Toluene (100 µl; 1eq) was dispensed into a vial with magnetic stirring. A combination of reagents and bases were introduced in 12 small scale reactions as below. Benzoyl Chloride (98 µl; 1eq) was added using a Gilson pipette. All reactions were followed by TLC.

Analysis of TLC








Benzoyl Chloride







































60% in oil

















Reactions were carried out on small scale as follows:













Scale up reaction of Tetrahydrofuran and Sodium Hydride (2, 5)

2-NO2 Toluene (100 µl; 1eq) was dispensed using a Gilson pipette into a 250ml conical flask along with Tetrahydrofuran (85ml) with magnetic stirring at room temperature. Sodium Hydride (340mg) was then added portion wise to the solution which was then left to stir for 15 minutes. At which point Benzoyl Chloride (980 µl; 1eq) was then added using a Gilson pipette and the reaction was left to stir overnight.

Sodium Hydride is a flammable solid so H2O (1ml) was added to quench it to form sodium hydroxide thus allowing the Tetrahydrofuran to be safely evaporated. A separation reaction could then be carried out by adding Ethyl acetate (20ml) to dissolve any starting material that had been produced. Water (20ml) was then added to wash away all the Sodium Hydroxide in the water layer leaving the starting material in the organic layer.

Also by adding a large amount of Sodium Hydroxide it would react with any unreacted Benzoyl Chloride converting it to Benzoic acid. Any Benzoic acid produced in the presence of Sodium Hydroxide would form the salt Sodium Benzoate. In other words it deprotonates the acid hence removing Sodium Hydroxide and Benzoyl Chloride leaving us with just the 2-NO2 Toluene and our product.

A TLC of the reaction was carried out in 1% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.

Points for Discussion

Solvent/base screen for Ketone synthesis - explain how anion attacks the electrophile.

Analysis of TLC


The TLC showed a spot on the product but because the reaction was carried out at room temperature we were uncertain if the reaction had gone to completion. For this reason it was important to isolate any product and run an NMR. By comparing our product against the NMR spectra and Rf values of our starting materials in the literature we would hopefully be able to rule out any starting material present and equivocally confirm the presence of a product.

Following on from looking at the NMR of SM-P1

Points for Discussion

Things to try:

Try heating? Boiling under reflux

Changing base?

Try different electrophile?

Try different nucleophile? Try the ethyl one

Try different solvent? DMF? DMSO?

Concluded we would do two reactions:

Repeat SM-1 in DMF at room temperature

Repeat SM-1 using methyl iodine instead of Benzoyl chloride


TJS carried out a similar reaction in DMF and his experience was that it didn't react. So he wanted us to repeat our reaction using the same solvent and characterise it by NMR to prove or disprove his theory.

The inky blue/purple colour he was getting suggested that deprotonation was taking place and after adding the Benzoyl Chloride to quench the reaction he observed a decolouration which further suggested that they had reacted together. However after isolation there was no product present meaning the reaction had not taken place?

Water could be present from glassware or due to the fact we were not using anhydrous DMF and the reaction was not carried out under a Nitrogen atmosphere. Another possible explanation could be that Benzoyl chloride was not a strong enough electrophile so by repeating the same reaction using Methyl Iodide and observing whether we are getting deprotonation or not we could rule out this possibility. If neither reaction worked it would prove that the electrophile was not reacting at room temperature so we may want to heat the reaction up to reflux.

Reaction 1

2-Nitrotoluene and Benzoyl chloride in DMF

2-NO2 Toluene (100µl; 1eq) was dispensed using a Gilson pipette into a 100ml round bottomed flask along with DMF (7.3ml) with magnetic stirring at room temperature. Sodium Hydride (29mg) was then added portion wise to the solution which was then left to stir for 15 minutes. At which point Benzoyl Chloride (85µl; 1eq) was then added using a Gilson pipette and the reaction was left to stir overnight.

The following morning a mini work up was carried out in a small vial using a small amount of 1M HCl and a small amount of ethyl acetate.

A TLC of each reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.

Reaction 2

2-Nitrotoluene and Methyl Iodide in DMF

2-NO2 Toluene (100µl; 1eq) was dispensed using a Gilson pipette into a 100ml round bottomed flask along with DMF (7.1ml) with magnetic stirring at room temperature. Sodium Hydride (29mg) was then added portion wise to the solution which was then left to stir for 15 minutes. At which point Methyl Iodide (46µl; 1eq) was then added using a Gilson pipette, the appropriate safety procedures were taken when adding this as it is very toxic compound and the reaction was left to stir overnight. A colour change was observed.

The following morning a mini work up was carried out in a small vial using a small amount of 1M HCl and a small amount of ethyl acetate.

A TLC of each reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.

Analysis of TLC

2-Nitrotoluene and Benzoyl chloride in DMF


Looking at mix- 2 products?

2-Nitrotoluene and Methyl Iodide in DMF


2-NO2 Toluene was still present however there was a possible spot for product. An NMR needed to be carried out to confirm whether we were getting deprotonation, and if the reaction was working.



Starting materials L-R Ethyl nitrobenzene, Methyl benzoate, mix of both+ product, product. On analysis under UV showed that there is something new in the mix which is also showing in product but very faint.

Evaporate and do NMR

Things to do

Repeat this reaction at reflux.

Points for Discussion

Comment on MeI and Benzoyl chloride from literature to see which is more reactive than the other.


Nitrotoluene and methyl benzoate run at same Rf value. It does not look like the reaction has worked as there is no product spot.

Things to try:

Possibly heat up?

Leave longer?

Use different solvents, like DMF?

Evaporate and NMR

New method using TJS1-65-1

TJS1-65-1(195mg) was added to a 250ml round bottomed flask along with THF (10ml) and K+OBr (112mg) with magnetic stirring for 10 minutes. An inky blue colour was observed. After 10 minutes Methyl Benzoate (125µl) was added. It was left to stir for 2 hours at which point a small scale acid workup was carried out using 1M HCl and ethyl acetate.

The reaction was left overnight at 40°C. The colour change suggests deprotonation but no product in TJS1-65-1m blue. After 24 hours TJS1 a further colour change was observed as the solution turned purple. The samples were left in fume hood for 1 hour.

A TLC of each reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.

Things to try:

Possibly try using a stronger electrophile such as MeI?

Possibly carry out reaction neat?

Heat to 80 °C using aldehyde?

Reaction of 2-Nitrotoluene and Benzaldehyde

To a round bottomed flask 2-Nitrotoluene, DMSO and NaOMe was added and left to stir for ten minutes. At which point benzaldehyde was then added producing a blood red solution and left to stir overnight.

A small scale acid work up was carried out using H2O and ethyl acetate.

A TLC of the reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.

Reaction of 2-Nitrotoluene and Benzaldehyde (New Method)

Reaction scheme


Benzaldehyde (3.68ml) was added to a 250ml round bottomed flask along with 2-Nitrotouene (4.29ml) and DMSO (50ml) with magnetic stirring. To that a solution of Sodium methoxide (2.32g) in MeOH (100ml) was added. At which point a light orange colour was observed and left to stir for 1.5 hours at which point the solution had formed a dark brown colour.

A TLC of the reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.


Interpretation of SMJH-2

The NMR of SMJH-2 proves that deprotonation has occurred using the aldehyde. We now know that in terms of the electrophile if:

X = OMe deprotonation does not occur

X = Cl deprotonation does not occur

X = H deprotonation occurs

Unfortunately SMJH-2 is an alcohol and not the ketone product we need. So the next step is to oxidise it up to the ketone.

Work up of SMJH-2

1M HCl (50ml) was added along with ethyl acetate (50ml) into a 200ml separating funnel. Shake the flask and take off the bottom layer (acid and DMSO). Run off the top layer (ethyl acetate) and put the HCl layer back in. Add another 50ml of ethyl acetate, shake and run off the bottom layer. Combine the two ethyl acetate layers. Add 50ml of H20 which washes out the DMSO. Add one 50ml wash of brine and drain off NaCl which washes off any water left. Add MgSO4; evaporate to give product SM-3-1

Oxidation of SM-3-1

SM-3-1(8.81g; 1eq) was added with 4A molecular sieves (8g) in DCM (250ml) and left to stir for 10 minutes before adding PCC (15.6g; 2eq) to give the product SM4-1

Reduction of SM4-1

A TLC of the reaction was carried out in 2% ethyl acetate in petroleum ether and the product was isolated and characterised by NMR.


Indole present - fluorescent blue colour

SM4-1 = 8.71 g.

Adding the gram you removed for the next reaction you therefore made 9.71 g of SM-4-1.


I purified SM-5-1 for you as well and got 94 mg of the desired product -

Future work

Future work


Work on different aldehydes to compare reactivity