UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 1 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ Guidelines for writing a thesis
1 Introduction
These guidelines apply to the Bachelor of Science project report and theses written for
the degrees of Bachelor of Science, Master of Science and Licentiate of Philosophy at
the University of Jyväskylä’s Department of Chemistry. The guidelines can also be used
when reporting on laboratory assignments. There are separate guidelines for the general
layout and practices related to doctoral dissertations.
The purpose of these guidelines is to clarify issues related to the format of your thesis.
The specifications must not be interpreted literally – you should rather use your
common sense in order to create a thesis that is as clear and readable as possible. In
addition to the content, a well-organised structure and consistency (of abbreviations,
references, the layout of tables and figures, etc.) are of major importance and should
receive special attention. Finnish students may write their theses in English with their
thesis supervisor’s consent.
There is no absolute standard length for the thesis, because it depends on the topic. As a
general rule, the bachelor’s thesis should contain approximately 15–20 references and
15–25 pages, the literary part of the master’s thesis should have around 50 references
and 50–90 pages, and a licentiate thesis should include about 100–200 references and
consist of 80–100 pages.
The experimental part (of the laboratory report and master’s thesis) must specify the
background, methods, test arrangements, and instrument parameters related to
experimental work so comprehensively that anyone with a corresponding chemistry
education is able to repeat the conducted measurements based on the instructions.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 2 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ 2 Parts of the thesis
The thesis consists of the following parts, in the following order:
A. Title page
B. Abstract
C. Preface
D. Contents
E. Abbreviations
F. Text pages
G. Produced chemical compounds (organic chemistry)
H. Bibliography (titled References)
I. Appendices
A. Please see Appendix 1 for an example of the title page.
B. The purpose of the Abstract is to present the study results briefly (max. one page) in
a way that allows the readers to get a clear idea of the contents and to decide whether to
read the entire thesis. Nothing else is written on the Abstract page.
C. In the Preface (of one page) you clarify when and where the thesis has been created,
whether it has been undertaken in cooperation with a particular industry or enterprise,
etc. Furthermore, you clarify how the literature has been examined and where the cited
publications have been found. The names of the supervisors are also mentioned here.
The Preface ends with acknowledgements.
D. In the Contents, the thesis is divided clearly into numbered sections (see Appendix
2).
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 3 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ E. Less common abbreviations (or symbols, code names) must be listed if they occur
more than once in the thesis. Nothing else is written on the Abbreviations page. When
an abbreviation occurs in the text for the first time, it is given in brackets after the
complete term, for example: “Capillary electrophoresis (CE), also known as…”
F. The main text consists of a literary part and an experimental part (see Appendix 2).
The literary part begins with an Introduction, in which the topic and test arrangements
are presented at a general level. It is followed by the actual thesis text, which is
structured by presenting first the reviewed literature and background theories, after
which comes the experimental part. The experimental part clarifies the applied methods,
instruments, reagents and achieved results / produced molecules, etc. While presenting
your results, pay particular attention to error analyses. The text should be well
structured and flow logically. The thesis ends with the Conclusions, in which you
summarise the most important issues and results, as well as discuss the contribution
(significance) of the results. The Conclusions section resembles the Abstract, but it is
broader and more detailed. In addition, the Conclusions should include discussion on
whether the objective was achieved and whether it would be possible to continue the
study based on the results. After the Conclusions, there is a detailed description of how
the tests were carried out (e.g. synthesis instructions).
G. The structural formulas of the produced chemical compounds (organic chemistry)
are presented in numerical order in this section.
H. The bibliographic references are listed in the References section, after the main text
and before the Appendices.
I. Selected appendices necessary for understanding the content, but not reasonably
presented in the main text, are appended at the end of the thesis (e.g. measurement
results, spectra, large tables).
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 4 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ 3 Layout and typography
3.1 General layout
The thesis is written on an A4 sheet, leaving a margin of 4 cm at the left of the page for
binding, 2.5 cm at the top, 1.5 cm at the bottom, and 2 cm at the right of the page. Page
numbers are placed 1 cm from the top edge of the page and centred. The text font is
Times New Roman (or corresponding), font size 12 and line spacing 1.5. However,
section headings may be written using font size14.
If you use the LaTeX typesetting programme for layout, please see instructions for its
use in Appendix 3.
3.2 Sections and paragraphs
Paragraphs are not indented; they are justified to the left margin. One blank line is left
between paragraphs. Two blank lines are left after each section, before the heading of
the following section. Section headings or potential molecule numbers are
emboldened. If you wish to emphasise something in the text, you can either write it
in bold, in italics, or underline it. However, do not use these means of emphasis too
often.
3.3 Figures and tables
Only the most relevant figures and tables are included in the main text, and all others
can be presented as appendices. Be careful not to create tables that are too large and
compact, because they become difficult to read.
Separate consecutive numbering is used for figures, tables, reaction equations,
compounds and graphs. Figures and their captions are centred. A blank line is left under
the caption not to make the layout look too heavy. Tables and table captions are leftjustified (aligned along the left margin), and the captions are separated from the body
text by a blank line. Table captions are written above tables. Italicisation is not used in
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 5 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ figures or tables (except for e.g. Latin plant names, which should always be italicised).
The text should always include a reference to each figure and table. The reference is
added, for example, to the end of the relevant sentence in brackets ( ... (see Figure 1) or
(....see Table 1)). If the figure or table has been taken directly from a reference, the
figure caption or table heading must include the number of the reference (Figure 1,
Table 1).
1
2
Figure 1. Two crown ethers: 16-crown-5 (1)2 and 21-crown-7 (2).3
Every row in a table must have a label (i.e. an explanation). The values presented in the
table columns must be, as a rule, given without units and with reasonable precision.
The units of the columns are provided in the column heading. Error analysis must be
performed on the presented numerical values whenever possible. For rounding
numerical values and error analyses, the 15-unit rule is applied. A large table can be
placed crosswise, but tables can be divided on different pages only in exceptional cases.
A decimal point (.) is used in English (even though decimals are separated by a comma
in Finnish). There is no full stop at the end of a table title, but there is one at the end of a
figure caption.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Date: 13-Sep-13
Version: 1.2
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Author: Juhani Huuskonen
Guidelines for writing a thesis
_____________________________________________________________________________ Table 1 Standard molar entropy S
O
(298 K) for some compounds and chemical
elements4
Element (standard state in 298 K)
SO(298 K) / J mol-1K-1
Ag (crystalline)
42.6
C (graphite)
5.7
C (diamond)
2.4
Fe (crystalline)
27.3
I2 (crystalline)
116.1
HBr (gas)
198.7
PCl3 (liquid)
217.1
3.4 Page numbering
♦ The title page is not numbered.
♦ The Abstract, Preface, Contents and Abbreviations are numbered with lower case
Roman numerals: i, ii, iii, iv, v, etc.
♦ The main text is numbered with Arabic numerals 1, 2, 3, etc.
♦ Appendices are numbered separately as APPENDIX 1, APPENDIX 2, etc.
♦ The heading APPENDIX + its number should appear at the top right corner of each
appendix.
3.5 Using tenses
The passive voice and the same tense are used consistently and logically throughout the
thesis. In the experimental part, while presenting one’s own activities, the past tense
passive voice is used: ‘...the reaction mixture was stirred with a magnetic stirrer for six
hours ...’ When presenting other people’s results, one should primarily use the present
perfect, for example: ‘...has studied...’ or ‘...have undertaken research...’ In order to
express a general conclusion or ‘literal truth’, the present tense is used, for example:
‘The results show that concentration increases...’
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 7 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ 3.6 Referencing
The general principle in referencing is that everything cited in the text (if it cannot be
regarded as common knowledge) must have a reference to the original source in which
the topic was handled for the first time (and potentially quite in detail). The reference
specifies an easily accessible source (a book, academic article, electronic file or
presentation, etc.) that provides the reader with the necessary background and additional
information. Even though the basic principle is to use the source that has first addressed
the issue (primary reference), in some cases it is justifiable to refer to a source or
handbook that has been published later and is more easily accessible. Research
publication series each have their own referencing styles, which must be considered
when writing manuscripts for articles based on theses.
Source references are given in the text in the order of appearance with a superscript
number.7,11-15,23 Note: a sentence-ending full stop comes before the superscript number
(e.g. ...text.15). If a paragraph deals with a specific theme found in specific sources, the
reference numbers are placed immediately after the first sentence, not after the whole
paragraph. The reference number can also be placed within a sentence, for example:
‘Earlier studies6 show...’
Sometimes you can also give the authors’ names in the text, next to the reference. In
such cases you should remember that
i) for one author, the reference is marked like this:
... Shimada2 has discovered...
ii) for two authors, the reference is marked like this:
... Armarego and Reece1 have discovered...
iii) for three or more authors, the reference is marked like this:
...Knabe et al.8 have discovered...
Note: et al. is italicised.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 8 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ If you are mentioning a relatively general issue that is accessible in various sources, you
can refer to one of the sources in question:
... as noted before (cf. Reference 7)
The list of references (the alphabetical list of works cited, which appears at the end of
the paper, titled “References”) must be consistent and as detailed as possible, so that the
reader can find the literature if needed. Special attention must be paid to author names
and article headings. In the References, the expression et al. is not used at all, as all
author names must be listed. There are no exceptions to this rule.
3.6.1 Journals
1. Consecutive numbers and a full stop.
2. The first letters of authors’ forenames (no space), no comma, a space, family
names in full, potential Jr. or Sr. after the family names, (e.g. M. Kilmberg Jr.
and M.A. Klimberg Sr.)
3. Article titles are written entirely and in the way they have been printed, even
though there were clear errors. However, individual words in the titles of articles
and presentations are generally not capitalised (except for the first letter of the
first word). German is an exception to this rule.
4. Journal titles are italicised. Names are usually abbreviated according to CAS
Source Index (CASSI).
5. The journal’ s year in bold, a space, volume number in italics, journal number
in brackets, a space, the first and the last page of the article separated by a
hyphen, and always a full stop at the end, e.g. 1994, 27(3), 4-11.
6. If you have not had access to the original journal, the actual source used is
specified in the reference, e.g. Chemical Abstracts (Chem. Abstr.).
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 9 (19)
Author: Juhani Huuskonen
_____________________________________________________________________________ Examples
1. W.L.F. Armarego and M. Reece, Quinazolines XXV. The synthesis of 8-chloro-2-[4(2-furoyl)-piperazin-1-yl]-6,7-dimethoxyquinazolin-4-amine
hydrochloride
(8-
chloroprazosin hydrochloride), Aust. J. Chem., 1981, 34, 1561-1566.
2. K. Shimada, Organic compounds in kraft bleaching spent liquors. V.
Photodegradation of red-pine chlorinated oxylignin, Mokuzai Gakkaishi, 1982, 28, 376382. Chem. Abstr., 1983, 97, 129328v.
3. G. von Weizmann, H. Kubel, and W. Lange, Untersuchungen zur Cancerogenität von
Holzstaub. Die Extraktstoffe von Eichenholz (Quecus robur L.), Holzforsch., 1989,
43(2), 75-82.
3.6.2 Books
1. Consecutive numbers and a full stop.
2. The names of authors in the same way as for journals (3.6.1).
3. Book titles are italicised. The first letter of all main words in the title of books or
dissertations are capitalised in English (but not the linking words such as ‘of’,
‘the’). However, the titles of books in Finnish or Swedish are not capitalised in
the same way (except for the first letter of the first word).
4. Edition (if the book is not the first edition), publisher and year of publication.
5. The first and the last page number, for example, pp. 19-31. It is common to refer
generally to the whole book, and then it is not obligatory to give the page
numbers. On the other hand, sometimes you may want to indicate the total
number of pages in the book, e.g. 670 p.
6. It is common to refer to books consisting of chapters written by various authors,
which may have one or more editors.
7. You can also refer to master’s theses, special practical reports or doctoral
dissertations, which are treated in the same way as books.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Date: 13-Sep-13
Version: 1.2
Page: 10(19)
Author: Juhani Huuskonen
Guidelines for writing a thesis
_____________________________________________________________________________ 8. If you refer to the same book more than once, give the book’s reference number
(the one given when referring to it for the first time) in the text, as well as the
pages referred to in the book. For example: ..text, Reference 13 p. 88. / ...text,
Reference 13 pp. 88-90.
Examples
4. A. Kivinen and O. Mäkitie, Kemia, 3rd ed., Otava, Keuruu, 1981, pp. 23-35.
5. L. Eberson, Organisk kemi, Almqvist & Wiksel Förlag AB, Stockholm, Sweden,
1969.
6. E. Sjöström, Wood Chemistry Fundamentals and Applications, 2nd ed., Academic
Press, San Diego, USA, 1993, 293 p.
7. G.A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, 2nd ed.,
Springer-Verlag, Berlin, Germany, 1994.
8. C.W. Dence, The determination of lignin. In: S.Y. Lin and C.W. Dence (eds.),
Methods in Lignin Chemistry, Springer-Verlag, Berlin, Germany, 1992, pp. 32-61.
9. J. Kotoneva, Steroidit supramolekylaarisessa kemiassa, Master’s Thesis, University
of Jyväskylä, Department of Chemistry, Organic Chemistry, Jyväskylä, 1995.
10. J. Leppänen, Design and Synthesis of Entacapone Prodrugs and L-Dopa Entacapone Codrugs, Kuopio University Publications A. Pharmaceutical Sciences 59,
Dissertation,
University
of
Kuopio,
Faculty
of
Pharmacy,
Department
of
Pharmaceutical Chemistry, Kuopio, 2002.
3.6.3 Presentations and posters
The presentations given at scientific conferences are often published as compilations
(Conference Proceedings or Proceedings, abbreviated as Conf. Proc. or Proc.). When
you refer to such presentations, it is also important to clearly indicate the date and
organiser of the conference. The following abbreviations are also common in this
context: Int. (or Intl., International) and Symp. (symposium); for example, Int. Symp.
Pulping Chemistry.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
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Author: Juhani Huuskonen
_____________________________________________________________________________ 11. J. Hyötyläinen, Characterization of lignin and humic compounds in receiving water
system of pulp industry. Use of model compounds and CuO-oxidation-HPLC-method,
Conf. Proc. TOCEON 93, Toxic Compounds in Environment, Znojmo, The Czech
Republic, 1-3 June 1993, pp. 78-84.
12. M. Ristolainen and R. Alén, Characterization of effluents from TFC bleaching of
hardwood kraft pulp, Proc. 1996 Int. Pulp Bleaching Conf., Book 2, Washington, D.C.,
USA, 14-18 April 1996, TAPPI Press, Atlanta, USA, 1996, pp. 523-525.
3.6.4 Other references
You can indicate the origin of an essential “unofficial” source, such as an expert’s
interview statement as follows:
13. J. Paasivirta, personal communication on 24 July1996.
If you have used software in the work, the name must be listed in the references in
capital letters, for example:
14. G.M. Sheldrik, SHELXL-97- A program for crystal structure refinement, University
of Göttingen, Germany, 1997.
References to patents:
15. S. Kanbe, Y. Shinazaki and K. Takei, Substituted phenyl benzoates and their use in
liquid crystal composition, Ger. Offen, 3,001,423, Jan26., 1979.
16. J. Pystynen, A. Luiro, T. Lotta, M. Ovaska, J. Vidgren, Cathecol derivatives, US
Pat., 6,150,412, 2000.
The reference can also be a work in the official publication series of a large research
institution or university:
17. I. Tuominen, MILOX-prosessin kemikaalitaseen tarkastelu tuotantomittakaavassa,
PSC Communications 80, 28 August 1995, Oy Keskuslaboratorio- Centrallaboratorium
Ab, 1995, 123 p.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Date: 13-Sep-13
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Author: Juhani Huuskonen
Guidelines for writing a thesis
_____________________________________________________________________________ References to websites can be made directly to the internet address if it is informative
and fully traceable. The date on which you read the reference is written in brackets at
the end of the reference. In addition, the internet page is printed, but not attached to the
thesis.
18.
High
Performance
Liquid
Chromatography
(HPLC):
A
Users
Guide,
http://www.pharm.uky.edu/ASRG/HPLC/hplcmytry.html, University of Kentucky, The
Advanced Science and Technology Commercialization Centre, Analytical Spectroscopy
Research Group (accessed 15 April 2002).
3.7 Naming compounds
Chemical compounds are named and formulas written according to the IUPAC rules.
You should give the chemical formula after the name of a chemical compound and the
structural formula after the name of an organic compound when you mention them for
the first time (except for commonly known compounds such as water). The trivial
names of compounds can be used particularly when the compound is commonly known
by that name (e.g. acetone). For clarity, you can also add the systematic name of the
compound together with the trivial one.
3.8 Quantities and units
Quantities and units are given in SI units. In addition, you can use the following units:
degree Celsius °C, litre (l), Ångström (Å), minute (min), hour (h), day (d), year (a),
wave number (cm-1) and electron volt (eV).
3.9 Unit-specific instructions
The unit of Applied Chemistry has instructions of its own.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 13(19)
Author: Juhani Huuskonen
_____________________________________________________________________________ 4 Further guidelines for the thesis process
First you make a written supervision agreement with your thesis supervisor, specifying
the schedule and other relevant matters.
Your thesis process begins by collecting the literary material, reading it and organising
it into groups. Next you create a table of contents based on the grouping and discuss it
with your thesis supervisor. The table of contents will later form a skeleton for your
work, which you can potentially change or complement as your work progresses. You
should agree on a regular meeting schedule with your supervisor, taking into account
that she/he may be busy.
Enough time should be reserved for theses, particularly the master’s theses. In practice,
you should have very few or no other studies (lecture courses, etc.) at the same time.
This allows you to concentrate on the thesis and complete it in a reasonable time frame.
The experimental part of the master’s thesis consists of approximately 16 weeks of
research work at a laboratory (Mon-Fri from 8 a.m. to 4 p.m.).
You should pay special attention to the language of your thesis, as readability and
clarity are very important for the usability and value of your work.
The units provide separate safety instructions for laboratory work. They are discussed,
explained and signed with the supervisor.
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Date: 13-Sep-13
Version: 1.2
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Author: Juhani Huuskonen
Guidelines for writing a thesis
_____________________________________________________________________________ APPENDIX 1
Title of the thesis
Master’s thesis
University of Jyväskylä
Department of Chemistry
Laboratory of Xxxxx Chemistry
xx Month xxxx
Your Name
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
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Author: Juhani Huuskonen
_____________________________________________________________________________ UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 16(19)
Author: Juhani Huuskonen
_____________________________________________________________________________ APPENDIX 2
CONTENTS
ABSTRACT…. .......................................................................................... i
PREFACE .................................................................................................. ii
CONTENTS …………............................................................................... iii
ABBREVIATIONS ……………………………....................................... iv
LITERARY PART
1 INTRODUCTION.................................................................................. 1
2 FRIEDEL-CRAFTS ALKYLATION REACTIONS OF THE
BENZENE RING ...................................................................................... 3
2.1
2.2
2.3
2.3.1
2.3.1.1
Note: Max. four heading levels
...
EXPERIMENTAL PART
9 REACTANTS USED ………….............................................................. 52
10 PROTECTION OF ALDEHYDES ..................................................... 55
10.1
.....
13 CONCLUSIONS .................................................................................... 75
14 SYNTHESIS INSTRUCTIONS........................................................... 77
15 SYNTHESISED MOLECULES ......................................................... 84
16 REFERENCES ………………............................................................. 90
APPENDICES
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Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
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Author: Juhani Huuskonen
_____________________________________________________________________________ APPENDIX 3
LaTeX typesetting programme for layout
If you use the LaTeX typesetting programme, you can apply your discretion to the
layout of the thesis. The main thing is to follow the general instructions related to the
order of chapters/sections. The layout should be clear and neat.
The page settings of LaTeX need not be changed, as the default settings allow binding
in book form. If you wish to change the page settings closer to the requirements of the
Department of Chemistry, the text may not be typeset as nicely as it would be with the
LaTeX default settings. Common sense should be applied here as well.
Examples of setting to start with:
\documentclass[a4paper , 12pt , finnish]{report} %or article
\usepackage[T1]{fontenc}
\usepackage[latin1]{inputenc}
\usepackage[english]{babel}
\usepackage{overcite}
\usepackage[dvips]{graphicx}
\linespread{1.5}
\begin {document}
\parindent0pt
\parskip3mm
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 18(19)
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_____________________________________________________________________________ \pagestyle{headings}
\newcommand{\frontmatter}{\pagenumbering{roman}}
\newcommand{\mainmatter}{\newpage%
\pagenumbering{arabic}%
\setcounter{page}{1}}
\newcommand{\backmatter}{}
\setcounter{page}{1}
\begin{titlepage}
\vspace*{6cm}
\begin{center}
\Huge{Title page heading}
\end{center}
\vfill
\begin{flushright}
Master’s thesis \\
University of Jyväskylä \\
Department of Chemistry \\
31 December 2050 \\
Your Name
\end{flushright}
\end{titlepage}
UNIVERSITY OF JYVÄSKYLÄ
Department of Chemistry
Guidelines for writing a thesis
Date: 13-Sep-13
Version: 1.2
Page: 19(19)
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_____________________________________________________________________________ \frontmatter
%begins page numbering with Roman numbers
\include{abstract}
\include{preface}
\include{abbreviations}
\pagebreak
\tableofcontents
\pagebreak
\mainmatter
% begins page numbering with Arabic numbers
\include{introduction}
\include{main text}
\include{main text}
\include{main text}
\include{main text}
\include{conclusion}
\addcontentsline{toc}{chapter}{Literature}
\bibliographystyle{unsrt}
\bibliography{ref}
\end {document}