Organic Chemistry: New methods for synthesizing peptides

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  • This TEMPLATE includes Essential sections that need to be completed and submitted as part of your work. You are free to add Extra sections to it in order to enhance your work.


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Please insert your own project title (title should be informative, focused and specific to your project)


1.0 Abstract 5

2.0 Index. 5

2.1 List of Contents. 5

2.2 List of Tables. 5

2.3 List of Figures. 5

2.4 Abbreviations. 5

2.4 Acknowledgments. 6

3.0 Introduction. 6

4.0 Aim.. 6

5.0 Methods. 6

6.0 Results. 7

7.0 Discussion. 7

8.0 Conclusion and Future Work. 7

9.0 References list 8

10.0 Appendix. 8

11.0 Laboratory Clearance Form (LCF) 8


1.0 Abstract


This should be no more than 300 words.

Should be formatted as a paragraph with no sub-headings

It should be self contained and it does not include references or referred to scientific figures

It should provide a synopsis of the dissertation stating the nature and scope of the work undertaken and the subject covered

The importance of the abstract must not be underestimated. It guides reader through the body of the text

The abstract should therefore be a brief summary of the aim, methodology, results obtained and interpretation (discussion) of the key findings.

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The abstract should be written last of all.



2.0 Index

By index we mean the list at the beginning of your dissertation. Like the index of a book it is there to help the reader find things. Make it easy to use.

2.1 List of Contents

The contents can be considered to be an outline of your dissertation (project report) divided into chapters, sections and subsections

Chapter titles serve to identify the organisational building blocks of your dissertation whilst divisions and sub-divisions reveal more of the contents.

Do not have 2 or 3 levels of subdivision in a chapter.



2.2 List of Tables

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2.3 List of Figures


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2.4 Abbreviations

Include everything, assume nothing, if in doubt include it in your list (list even common terms). In the text put it in full first time and put abbreviation in brackets.

Use accepted abbreviations if they are available no need to create your own abbreviation if there is already one in use by other scientists

List them correctly in an alphabetical order



2.4 Acknowledgments

It is all yours BUT it is time to be nice to the people who supported you during your project


Other academics

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Technical staff

ICT, Librarian

Anyone else you feel well disposed towards (family, friends and colleagues)



3.0 Introduction


In this section you are writing about the background to the project so you should include a literature review on the overall topic and a brief explanation of techniques in context.

Describe and discuss the implications of the key references to your subject. Put them in a broad context.

Write about subjects that are directly relevant to your project work do not stray into unnecessary peripherals.

You already had an introduction in your literature review and project proposal coursework. You can use some of the information from it but this is your final report you should not be just including your old introduction from previous coursework your report should be much improved.  At least you should implement the feedback you have received on your coursework.  You should have new literature support to your work showing how much more you have read during your project.


Any figures, tables, diagrams taken from literature sources MUST be referenced properly.

It should be in normal scientific style (third person, past tense).

Text should be closely referenced.



4.0 Aim

One or two sentences write your aim doing this project

Either hypothesis being tested or overall direction of work

5.0 Methods

Materials for your methods section should be in a named appendix

Your chosen method(s) can be outlined under this section. You need to give full description of the method(s) here.


In this section you are writing in paragraph format the experiments to begin to establish your hypothesis. Your methodology section should be in past tense as you have done all the work you are reporting


You should also include a description as to how you analysed your results (chromatography, spectroscopy, toxicology, statistics, etc), i.e. the data collation, interpretation and analysis.


6.0 Results


It includes properly labelled tables and figures with headings and legends; adequate data interpretation and statistics.

Numerical data should be quoted to an acceptable number of significant figures and have appropriate units.


Narrative to results that provides a coherent flowing connection between the results.

Only key information need be included – additional data can be given in an appendix.



7.0 Discussion

In this section should be used to analyse and compare the results with those of relevance obtained by other scientists (literature review). The results and discussion sections form the heart of the thesis. To a considerable degree the success of the dissertation as a whole will depend on how well this material is organised and presented.

The secret is to find the best order in which to present the experiments performed. The order should be a logical one bearing in mind the original aims. While recording the experiments in a time-dependent and orderly fashion you do not necessarily have to follow the order in which experiments were actually undertaken in the laboratory. You may have followed a different order in the laboratory (for example: your standard did not arrive on time so you have done another experiment on that day while you were waiting for your standard).


Interpretation of results found; relationship to aims and hypothesis; limitations of findings; extent of findings; internal contradictions; how results agree with other published work; how results depart from other published findings and possible reasons for this.

Text should be closely referenced.


Describe briefly what you have found

Outline the strengths and shortcomings of your work

How do your results move the subject on from the state of knowledge described in your introduction?

What is the new present state of knowledge? Did you prove or disprove your hypothesis?




8.0 Conclusion and Future Work

Brief statement in respect of the topic at the start of the work

Description of new findings taking care again to distinguish your own findings from those other scientists

A summing up of how your original aims are compare to your final achievements/outcomes


How further work might confirm or extend findings.

Expend on future work clearly and in such a way that the reader will be able to follow your reasoning include also literature support.


9.0 References list


Refence style; should be EITHER: Surname, Initial (Year) i.e. Harvard alphabetical style OR: Number, with an end reference list numbered in the order in which the references first appear i.e. Vancouver numbering style.



10.0 Appendix


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Appendices are given titles A, B, C and page numbers I, II, III

There are different appendices as they cover different topics


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Detailed calculations

Flow charts

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11.0 Laboratory Clearance Form (LCF)


You need to complete this form as proof of you cleaning your project area in the laboratory. It should accompany your project final report for examination. Your oral examination will NOT be scheduled without you submitting your LCF

Project Proposal Check list

  • Read the whole document
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  • Whole document spell checked
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  • All references included in text given in reference list
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  • References given in a consistent format (Harvard Style)
  • All figures/tables numbered in a consistent way
  • All figures/tables referred to in the text
  • All generic and species names, company names etc Italicised
  • Acronyms are given in full on first occurrence
  • Index is fully formatted and has correct page numbers
  • Appendices are attached


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Project Title:  New Methods for synthesizing peptides.


Aim: to find new ways of synthesising peptides, and to try and reproduce conditions in which peptides might have formed in the ‘early’ earth. This will involve treating amine and acid mixtures with a coupling agent, to see if they form peptides. The common coupling agents used in the lab for this type of reaction are di-imide derivatives such as DCCI (see the reaction scheme below), but these are decomposed by water. So the reactions have to be carried out under anhydrous (water-free) conditions. In the early earth peptides first formed in the oceans – possibly by use of a coupling agent such as carbon disulfide (isoelectronic with di-imides).


One of the earliest attempts to show how the organic precursors to complex biomolecules might have originated was carried out by Miller and Urey in 1953. They subjected a mixture of methane, ammonia, hydrogen and water to electrical discharge (to simulate atmospheric lightening) and obtained a variety of simple organics as a result. More complex molecules can only have been formed (possibly from these) in solution – i.e. in the oceans. There will have been books published on developments since then – provide a summary as the introduction to your proposal.


Of course, there will be many factors that might influence a successful reaction – pH, the mineral content of the oceans at the time, the atmospheric compostion at the time (since this would be reflected in the ocean by dissolved gasses), temperature, pressure, and more. Try and find out what is known about the conditions at the time for inclusion in your report. We will be able to investigate a few, but by no means all. One theory is that life developed near alluvial (hydrothermal) volcanic vents – a ready source of gases, minerals and high temperatures.


In order to make it easier to detect peptide products from coupling reactions you will spend the first few weeks of the project making a ‘model’ peptide to compare the product of your reactions with. This is benzoyl valine anilide (3), the coupling product of benzoyl valine (1) and aniline (2). We will subsequently use compounds (1) and (2) as precursors in ‘early earth’ coupling attempts and use compound (3) as a reference to determine the success (if any) of the reactions using nmr, hplc and other chromatographic methods.



This is not an amino acid coupling since aniline (2) is an amine, rather than an amino acid. But it should serve as a model and the structural features of (3) make it easy to detect (which ones?).


The anilide (3) will be prepared by an enzyme-catalysed coupling reagent – the enzyme (papain) acts to make an ‘activated ester’ analogous tom that in the coupling reaction with dicyclohexylcarbodiimide (DCI) in the reaction illustrated below. This will be characterised and we will look at ways of improving the yield of (3) from this reaction – procedure in separate file – by changing factors such as concentration, pH, reaction time and so on. We will then look at other methods for converting R.S-benzoylvaline to the anilide – starting with use of DCI as the coupling reagent (which works), then moving to iso-electronic reagents such as CO2, CS2 or SO2 which might mimic chemicals available to promote peptide coupling under ‘early earth’ conditions.




Background notes:


Coupling methods for –NH2 + HO2C-  à  -NHCO-


Most coupling reactions involve making a ‘mixed anhydride’ of the acid or an ‘activated ester’ – both of which activate the carbonyl carbon of –CO2H towards nucleophilic addition.


Solution-phase peptide synthesis

Two possible ‘mixed’ peptide products – and also Ala-Ala and Phe-Phe. The groups which are supposed not to react must be ‘protected’.


-CO2H – protected as ester

-NH2 – protected as Boc derivative or Fmoc derivative. In the project we will use N-benzoyl-protected derivatives.


The scheme below shows the mechanism of a DCI coupling reaction:



The byproduct from the reaction is DCU (dicyclohexylurea), which is soluble in water. The protected dipeptide can now be purified, and the protecting groups removed to give Ala-Phe.







  1. Jones J (1992) Amino Acid and Peptide Synthesis  Oxford Scientific Publications
  2. Miller S A Production of Amino Acids Under possible primitive Earth conditions (1953) Science New Series, 117 (3046), p528-529.


Project Title:  New Methods for synthesizing peptides.


Please note: The discussion part of my project is probably the most important part so please make sure you discuss everything in detail.

Please find the PDF documents for the following methods(1-6) (The PDF documents contain all the information from my logbook and NMR results for each product).

I Synthesised Benzoylvaline Anilide as a ‘model’ peptide to compare the product of my reactions with (reactions 2-6 bellow).

Use Benzoylvaline Anilide as a reference to determine the success (if any) of the reactions (reactions 2-6 bellow), using nmr and TLC analysis results… but first check if my Benzoylvaline Anilide is correct.

Use benzoylvaline and aniline as precursors in ‘early earth’ coupling attempts.


  1. Synthesising Benzoylvaline and Benzoylvaline Anilide.

This was the first procedure. I produced Benzoylvaline and used it for making Benzoylvaline Anilide and also to make the following products. (I produced some extra benzolyvaline a few weeks later as I needed more).

Benzoylvaline Anilide is the coupling product of benzoylvaline and aniline.

  1. Coupling Reaction between Leucine and Benzoylvaline
  2. Phenylalanine Methyl Ester synthesis
  3. Glycine Methyl Ester synthesis
  4. Phenylalanine Methyl Ester Hydrochloride synthesis
  5. Benzoylvaline reaction with Phenylalanine Methyl Ester Hydrochloride (Coupling Reaction)

This was a coupling reaction between Benzoylvaline and Phenylalanine Methyl Ester Hydrochloride (which I produced in step 5).

Word count: 4500 words (this does not include the references)