Synthetics Assignment #5 – Choose your own molecule report!
Spring 2020 Chem 213W
Due: Thursday April 30th, 2020 by 11:59PM
NOTE: For this assignment, you must submit your report to TurnItIn and submit a PDF to Canvas. All
late penalties still apply to this assignment.
Name: Zhaolun Liang
Synthetic Molecule: Melatonin
Sections to be included in your Formal Report
(details/format in Chapter 3 and Chapter 11)
Possible
Points
Purpose of the overall experiment
The purpose of your report is very similar to an abstract and to the purpose
statements you’ve written in the past for your technique reports.
5
Introduction
This should include: A paragraph on the importance of the reaction
class/category, a paragraph on the importance of the chosen molecule, and a
paragraph on the chemistry being proposed including a full electronpushing mechanism in words and two schemes (reaction and mechanism).
30
Proposal, Discussion, and Conclusions
Please refer to the report outline for what to include in this section. It will
be extremely similar to the Results/Discussion/Conclusions sections you’ve
written for your Technique Reports so nothing extremely new here.
35
Experimental
Using your chosen synthesis pathway and the corresponding literature,
please write an experimental if we were to do this experiment in Chem
213W in the future. Please refer to the Chapter 3 of the lab guide to write
your experimental.
10
References
ACS Format - use reference formatting examples in Chapter 3 and
Workshop #6. MUST have AT LEAST FOUR peer-reviewed journal
articles in ADDITION TO the articles you were provided. If you use a
website, you will receive ZERO points.
Spectral Data
Obtained from the literature, annotated properly and labeled as Figures.
Neatness, grammar, overall organization
TOTAL
5
10
5
100
Earned Points
Zhaolun Liang
Synthetics Assignment #5
Melatonin
Purpose
The purpose of the experiment is to synthesis the Melatonin via 5-Methoxytryptamine and
anhydride. The main reaction within the synthesis was acylation of the nitrogen nucleophiles by
anhydrides. The products were liquid-liquid extracted by brine and purified by column chromatography.
Then Melatonin was characterized by 1HNMR,
13
CNMR and IR. The product was wildly used as the
medicine to synchronize the circadian rhythm and the reaction can help organic chemists to understand
the Friedel–Crafts reaction which was usually related to acylation in organic chemistry.
Introduction
Acylation is the reaction that adds an acyl group to a compound, forming a new molecule. The
compound which provides the acyl group is called acylating agent. Acyl halides were used most
common as acyl agent due to the being a strong electrophile. One of the importance of acylation is to
prevent the rearrangement reactions that would normally occur in alkylation. When the acylation was
performed, the carbonyl group would be removed by Clemmensen reduction or a similar process.1
One of the major substitutions in this reaction is Friedel–Crafts reaction, which can be classified
in aromatic electrophilic substitution. Friedel–Crafts reactions are usually the reaction between arenes
and acyl chlorides or anhydride. The final product via the reaction is usually deactivated hence can no
longer have another substitution. Friedel–Crafts reaction is a valuable alternative due to its ability to
produce polyalkylated products. However, Friedel–Crafts’ product can be easily produced via other
methods such as Clemmensen Reduction or Wolff-Kishner Reduction. The formation of the reaction is
usually not reversible under reaction conditions.
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In this specific reaction, the reaction was coupled with acylation and anhydrides being acylating
agent instead of using Acyl halides. Nitrogen nucleophiles were acylated and turned to Melatonin.
Melatonin, usually known as a hormone that regulates the sleep-wake cycle, is widely used as a
medicine to regulate people’s sleeping schedule. Melatonin is widely used as a supplemented method to
fix to trouble sleeping due to jet lag. Melatonin is usually taken by mouth hence might cause many side
effects including sleepiness, nauseous, headaches and diarrhea.2 However, a recent study suggested that
the function of Melatonin regulating circadian rhythm may lead to disrupt of immune system and cause
the failure of repairing damaged cells. Overly use of Melatonin may be one of the causes of cancer.3
Recently updated, Melatonin can also be used as an effective to slow down the progression of breast
cancer since Melatonin can involve in long non-coding RNAs. Melatonin can regulate the process of
breast cancer by lnc010561/miR-30/FKBP3 axis. Hence Melatonin can be a method to be an anticancer
strategy for breast cancer. A recent study indicated that Melatonin was discovered in fermented
beverages and foods. Although the concentration of Melatonin varies with the types of raw materials,
raw materials, culture environments, the facts of fermented environments can produce Melatonin lead to
new evidence of future direction of studying of Melatonin.5
For this specific reaction, the molecules used to acylate the nitro nucleophilic is not halides
group but anhydrides since anhydrides is another acylating agent to add acylate the starting material.
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Scheme 2: Mechanism of synthesis of Melatonin via acylation by anhydrides.
When the anhydrides was introduced to the starting material 1, the lone pair on nitrogen atom
attacks the alpha position of anhydrides and pushed the double bonds on one of the carbonyl group to
move upward, forming a negative charge on the oxygen. After anhydrides connected to the nitrogen
nucleophiles, the oxygen pushed back to the alpha carbon, pushing out the R group connected to the
carbonyl atom and formed the carboxylic acid. Finally, one of the hydrogen connected to nitrogen atom
pushed back to nitrogen atom to form the final product of this reaction. Except for using anhydrides and
acylation to form Melatonin, Melatonin can also be synthesis via thiocarboxylic acids and amines by
spontaneous reaction and electrosynthesis. Thiobenzoic acids could be automatically oxidized to
disulfides in air, thioaliph. Acids could be electro-oxidized to disulfides, and the resulting disulfides
reacted with amines to give the corresponding amides.6 Moreover, Melatonin can be synthesized via 1,3Diacetyl-1,3-dihydro-2H-benzimidazol-2-one since it just been proved to be a good acetylating agent for
amines. The acetylation of amines hence produced Melatonin.7
Proposal, Discussion, and Conclusions
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To synthesis the Melatonin for this experiment, the starting material 1, was mixed with acetic
anhydrides and pyridine, in dry dichloromethane as the solvents for 24hours under room temperature.
This is the process where the main reaction, acylation happens. Acetic anhydrides as the acylating agent,
was attached by the nitrogen nucleophiles. The R group on the acylating agent was kicked out and
formed carboxylic acid with the hydrogen on nitro group. The saturated hydrochloric acid was added to
the reaction mixture then the reaction mixture was extracted with dichloromethane. The reaction mixture
was then washed by brine and was purified via column chromatography. In this reaction, aromatic
electrophilic substitution is the main method to synthesis the Melatonin and it produces high yield
compared to other methods such as Wolff-Kishner Reduction. The product is more polar compared to
the starting material since a carbonyl group was connected to the nitrogen group. If the reaction was
monitored by TLC plate, Melatonin may have a smaller Rf value compared to that of the starting
material. No data relevant to the color of starting material but the Melatonin was reported having a white
or off-white color. No specific Rf values reported from literature in this case.
The reaction mixture was washed and extracted by using dichloromethane and brine. First of all,
dichloromethane was used to extract the organic layer in the reaction mixture due to its ability to
dissolve a wide range of organic compounds. The organic compound, which mainly contains the final
product 2 Melatonin, was extracted by dichloromethane under the room temperature. Other protonated
compounds left in the aqueous layer. Then, brine was added into the mixture to wash over the solution in
order to remove the leftover water in the solution. Since brine is highly concentrated, so it was used to
wash H2O existed in the organic layer extracted before. The organic layer needs to be washed over by
brine before exposed to solid drying agents such as sodium sulfate.
For this experiment, distillation is not appropriate since it's only applicable for liquid-liquid.
Since the starting material and the product are both solids and have similar polarities, column
chromatography is an appropriate method to separate and purify the starting material and final product.
The column will be packed as 50% dichloromethane/ 50% hexanes at first to be the mobile phase for the
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first 5 fractions. Then mobile phase show be adjusted to 75% dichloromethane/ 25% hexanes for the
next five fractions. Finally, the mobile phase will be adjusted to 100% dichloromethane for the next
following 10 fractions. If the separations were conducted successfully, the starting material 1, should
elute first and were observed at fraction 4 to fraction 8. Since the final product 2 was more polar than the
starting material due to the carbonyl group. Melatonin would be observed at fraction 11 to fraction 15.
To justify the polarities differences, Melatonin is more polar than 1 since the oxygen on carbonyl group
is more electronegative than carbon so it may form a partially charged dipole compared to starting
material. Hence, the reaction was separated by column chromatography and 5-Methoxytryptamine was
eluted before Melatonin.
100% yield was reported in this experiment since the starting material fully transformed to the
products based on the results reported in the literature.8 Low yield might be caused by the mistakes
during work-up. If the work-up is not conducted properly, starting material might be left in the organic
layer and was measured as part of the products. Also, incomplete reactions or loss of sample during
recovery may also be causes of low yield. For this experiment, appropriate temperature is the key factor
to produce higher yield. If the temperature was too high instead of room temperature, reaction mixture
could be evaporated can cause the low yield. No additional improvements are applicable to improve the
yield for this experiment.
Based on the data of 1H-NMR, the singlet peak at 8.35ppm represented the hydrogen connected
to secondary amine. The peaks located from 6.83-7.23 marked the hydrogen appeared on aromatic rings.
The small, singlet peak located at 5.71 represented the proton on nitro group connected to methylene
group outside the ring. The highest singlet peak located at 3.84 tells the appearance of protons on methyl
group connected to the oxygen atom. 2 mutiplet located at 2.92 and 3.56ppm showed the protons on
methylene. Finally, the tall peak at 1.91ppm represented the methyl group connected to the carbonyl
group of the Melatonin. To understand the transformation from starting material to final product, it is
obvious to observe that these two compounds have very similar structures except for the appearance of a
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carbonyl group. The singlet peak at 1.91ppm proves the transition between starting to Melatonin since
there’s not a carbonyl group appeared in starting material.
Based on the data from
13
C-NMR, it can be observed on the data that the peak appeared at
170.16ppm represented the carbon on carbonyl group. The peak at 154.13ppm, 100.64ppm, 112.66112.05ppm all represented the carbon atoms on the aromatic rings; the peak at 56ppm represented the
carbon on methyl group connected to the oxygen outside the ring. The peak located at 39.85ppm
represented the methylene group connected to nitro group outside the secondary amine. Finally, the peak
located at 23.35ppm marked the appearance of methyl group connected to carbonyl group. The most
downfield peak and upfield peak represented the transition between the stating material and products.
The most downfield peak at 170.16 represented the carbon on carbonyl group and peak at 25.33ppm
marked the methyl connected to carbonyl group. The observations based on these peaks marked the
transition from the starting material to Melatonin.
From the IR graph, the peaks from 2987-3336 marked the protons on the aromatic ring in all IR
spectra. The peaks observed at 1436-1476 represented the C-H umbrella bend. The peak at 1580
represented the C=C on the aromatic ring. The peak located at 1149 marked the ethers connected to the
aromatic ring. The strong peak at 1306 represented the nitro group connected to secondary amine. Based
on the data from IR spectra, the appearance at 1436-1476 represented the umbrella bend and it marked
the appearance of a methyl group compared only one methyl group within the starting material. The
peak at 1629 represented the C=O which is a critical factor to determine the transition from 1 to 2, since
carbonyl group is absent in the starting material. Hence, the peaks observed at 1629 and 1436-1476
represented the transition between the starting material to the final product Melatonin. The final product
Melatonin, has a way higher burning point compared to the starting material which also represented the
transition between these two compounds.
In conclusion, the synthesis of Melatonin in this experiment was achieved by acylation of
nitrogen nucleophiles via anhydrides. This experiment is doable and viable for Chem213W students
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since everything covered in this experiment has been introduced to students in Chem213W. No new
material or special conditions are needed for this experiment but students may experience a lower yield
compared to 100% in this experiment. When conducting this experiment involving acylation, proper
reagent and temperature are strongly needed. Also, proper use of brine and dichloromethane are also
needed in order to get higher yield.
Experimental
Melatonin. 5-methoxytryptamine (3.0 g), acetic anhydride (2.6 ml, 28 mmol) and pyridine (4.7 ml, 56
mmol) in dry dichloromethane (90 ml) were stirred for 23 hours at room temperature. Saturated
hydrochloric acid was added to the reaction mixture. The mixture was extracted with dichloromethane
(90ml). The organic solution was washed with brine. Finally, the solution was purified by column
chromatography (silica gel, 75%AcOEt) to produce an odorless, brown crytals (650mg, 100%). mp:
117 °C 1HNMR (400MHZ CDCL_3): σ 8.35 (s, 1H), 7.234 (1H, d), 7.03-6.86 (3H, m), 5.71 (1H, s),
3.842 (3H, s), 3.56 (2H, m), 2.93 (2H, m), 1.91 (3H, s); 13C NMR (100 MHz, CDCl3) δ (ppm): 170.16,
154.13, 131.70, 127.82, 122.85, 112.66, 112.41, 112.05, 100.64, 56.00, 39.85, 25.33, 23.35; IR Vmax
(cm-1) 3303, 3282, 3081, 2990, 1555, 1371, 1623, 1295, 1177, 927, 825.
References
1. Vollhardt, P.; Schore, N. Organic Chemistry: Structure and Function 2014, 714–715. ISBN 978-14641-2027-5.
2. "Melatonin- Oral". Government of Canada. Health Canada. 2018. Retrieved 9 January 2019.
3. Moradkhani, F.; Moloudizargari, M.; Fallah, M.; Asghari, N.; Khoei, H. H.; Asghari, M. H.
Immunoregulatory Role of Melatonin in Cancer. Journal of Cellular Physiology 2019, 235 (2), 745–
757.
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4. Liu, P.; Xie, X.; Yang, A.; Kong, Y.; Allen-Gipson, D.; Tian, Z.; Zhou, L.; Tang, H.; Xie, X.
Melatonin Regulates Breast Cancer Progression by the lnc010561/MiR-30/FKBP3 Axis. Molecular
Therapy - Nucleic Acids 2020, 19, 765–774.
5. Que, Z.; Ma, T.; Shang, Y.; Ge, Q.; Zhang, Q.; Xu, P.;Zhang, J.; Francoise, U.; Liu, X.; Sun, X.
Microorganisms: Producers of Melatonin in Fermented Foods and Beverages. Journal of
Agricultural and Food Chemistry 2020, 68 (17), 4799-4811
6. Tang, L.; Matuska, J. H.; Huang, Y. H.; He, Y. H.; Guan, Z. Amide Synthesis from Thiocarboxylic
Acids and Amines by Spontaneous Reaction and Electrosynthesis. ChemSusChem 2019, 12 (12),
2570–2575.
7. Kim, C. S.; Chung, I. H.; Cha, K. S.; Seo, J. H.; Kim, J. H.; Chung, B. Y. 1,3-Dihydro-1,3-Diacetyl2H-Benzimidazol-2-One: A New Versatile and Selective Acetylating Agent. Heterocycles 2000, 53
(3), 529.
8. Yokoo, H.; Ohsaki, A.; Kagechika, H.; Hirano, T. Structural Development of Canthin-5,6-Dione
Moiety as a Fluorescent Dye and Its Application to Novel Fluorescent Sensors. Tetrahedron 2016,
72 (39), 5872–5879.
9. Melatonin;
CAS
No.
73-31-4;
Spectral
Database
for
Organic
Compounds
(SDBS).
https://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi / (accessed April 29, 2020).
10. 5-Methoxytryptamine; CAS No. 608-07-1; Spectral Database for Organic Compounds (SDBS).
https://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi / (accessed April 29, 2020)
Spectral Data
13
CNMR:
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1
HNMR:
IR data for starting material:
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IR data for Melatonin:
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