(In effect from February 2021. Last Update 27th August 2021.)

The main idea behind this handbook is to provide you with a clear picture of all the steps towards the completion of your PhD studies, in a chronological order. Please, remember that you should never hesitate to ask your supervisor, Director of the PhD program, or assistant supervisor at the department for additional information and advice.

On our department website (www.organ.su.se), you can find more information about the PhD program, documents and forms related to your PhD studies as well as information about other activities at the department, such as seminars, meetings and half-time or thesis presentations.

The Head of the Department, the Deputy Head of the Department, and the Director of the PhD Program have the responsibility for you as a PhD student in the department. These are also the ones you should turn to if you have problems with respect to your relation to your supervisor, your co-supervisor or other colleagues at the department. You can also turn to a person in the TA-staff who could guide you further.

The PhD studies consists of four years of full-time studies, equivalent to 240 ECTS credits (60 course credits and 180 thesis credits). In addition to the thesis work, you will most likely also be engaged in teaching. Information about teaching can be found in the “Teaching” section below. The pathway towards the completion of your PhD degree will be a very exciting period. We hope you can find this handbook helpful on your journey towards becoming an experienced researcher. We wish you good luck and success in your research and studies.

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First days – Getting to know the department

The Department of Organic Chemistry is located in the 6th and 5th floor of Arrhenius Laboratory in the Frescati campus at Stockholm University. Our postal address is:

Stockholm University
Department of Organic Chemistry
Arrhenius Laboratory
Svante Arrhenius väg 16C
SE-106 91 Stockholm

Who’s who?

During the first days at the department you will get familiar your research group and supervisor, you will need to interact with other faculty members, administration staff and technical personnel.

Your supervisor is mainly responsible for the scientific part of your PhD training, such as project discussions and planning, training of scientific writing and presentations. Together with your supervisor and your co-supervisor, you will prepare an Individual Study Plan (ISP) that will help you to successfully meet the requirements for the PhD degree.

A co-supervisor is suggested by the Director of the PhD program, and assigned by the Prefekt. She/he will take part in your studies by proof-reading your half-time and thesis reports, as well as in the elaboration of your ISP. She/he will also give you feedback after your oral presentations (SDMs, preparations for your half-time or your thesis). Do not forget to
keep her/him informed.

You can always turn to your supervisor or your co-supervisors for scientific as well as nonscientific discussions, and for any advice you may require. During the first weeks, you will need to take different safety and instrument trainings that will allow you to work in the research laboratories. Here you will find name and contact details of people holding relevant roles at the department:

Head of the Department

Kálmán Szabó, room A633, 08-674 74 85.
Main responsible for you as a PhD student at the department.

Deputy Head of the Department

Fahmi Himo, room A 521, 08-16 10 94.
Takes the responsibilities of the Head of Department, and of the director of the PhD program when absent or when there exists a conflict of interest.

Director of the PhD program and Ämnesansvarig

Belén Martín-Matute, room A607, 08-16 24 38.
Responsible for the PhD Program, PhD positions announcements, graduate teaching, accreditations of courses and ISP. Checks half-time reports and theses.

Director of Undergraduate Studies

Joseph Samec, room A615, 070-559 2511.
Responsible for undergraduate teaching and staffing plan.

HR/Finance

Mathias Ulander, room A663, 08-16 4329.
Salary and scholarship, personnel administration, employment, healthcare, reimbursement for health maintenance activities, questions regarding vacation, expenses and expense claims (for employees), LADOK, Archiving, publications in DiVA, help with announcing of seminars, dissertations, licentiate/halftime, access-card, information for new employees.

Finance manager

Gabriella Ågren, room A611, 08-16 1191.
Finance, budget, Invoices, project administration and accounting, reporting etc, authorize invoices and order supplies.

IT Manager

Ola Andersson, room A617 08-16 3743
Computers/IT, phones, invoices, procurement, travel bookings for guests, webpages.

Technician

Martin Roxengren, room A525, 08-16 4330.
KLARA, SUKAT accounts, LC/GC-MS training, LC/GC-MS responsible, Technical and practical issues, vacuum pumps, hoods etc., disposal of solvent waste and hazardous waste.

Research Engineer/Safety Officer

Kristina Romare, room A631, 08-16 2030.
NMR training, safety training, NMR responsible, Safety.

 

The Department of Organic Chemistry has an extensive research program. This research program covers many areas of experimental and theoretical chemistry including metal catalysis, organocatalysis, and photocatalysis, asymmetric synthesis, several areas of bioorganic chemistry such as carbohydrate chemistry, and enzyme chemistry.

Here you can find the current research groups at the department:

Pher Andersson Research Group: Asymmetric catalysis.
Margareta Blomberg Research Group: Theoretical biochemistry.
Jan-Erling Bäckvall Research Group: Metal catalysis and directed evolution.
Fahmi Himo Research Group: Quantum Chemistry.
Belén Martín-Matute Research Group: Organic synthesis and catalysis.
Berit Olofsson Research Group: Hypervalent iodine chemistry.
Joseph Samec Research Group: Green chemistry and biomass valorization.
Per Siegbahn Research Group: Theoretical biochemistry.
Kálmán Szabó Research Group: Organometallic chemistry and catalysis.
Göran Widmalm Research Group: Bioorganic chemistry.
Björn Åkermark Research Group: Supramolecular Photochemistry and Artificial Photosynthesis.

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Planning your doctoral studies – The beginning of your PhD

The main rules and regulations of the PhD program in Organic Chemistry are described in the “General Study Plan” (ASP, Allmän studieplan) that you will find on our website. The ASP may be updated, but you should follow the one that was on place at your starting date. Alternative, you can communicate to the Director of the PhD program that you want to follow
the newest version.

The objectives and aims of the doctoral degree in Organic Chemistry are in accordance to the Higher Education Ordinance described in the Swedish Law. This handbook will cover more practical and logistic aspects that you will find useful on your way to your PhD degree.

Your first day

Your very first day you will be welcomed by your supervisor, who will introduce you to the premises and the staff.

During the first week as a PhD student at the Department, the Director of the PhD program will arrange a meeting with you and your supervisor. During this meeting the Director will give you information about the PhD program, your co-supervisor, the Department, and the PhD council at the Department. The meeting is documented in the Form PhD1 New PhD student. After this meeting, you should send the Form PhD1 to your co-supervisor, and discuss with her/him about your PhD plans.

Your first day you will also be given important information by the administration regarding safety rules, as well as an introduction handout for new people at the Department. You will also be informed of our Code of Conduct.

You must also read the Ethical Guidelines given by Stockholm University and The Chemistry Section. These are for “both students and teachers to behave in a professional way and abide to the rules and guidelines that have been put forward by Stockholm University. This information can be found here:

su.se/medarbetare/råd-stöd/forskning/etik-i-forskningen
su.se/staff/researchers/research-ethics
su.se/staff/organisation-governance/governing-documents-rules-andregulations/research/stockholm-university-s research-integrity-and-ethics-policy-1.540778

Check point 1 Individual Study Plan (ISP)

Within two months after your first day, you together with your supervisor and cosupervisor will prepare your ISP. You then meet with the Director of the PhD program, who will make sure that the ISP is understood and agreed upon by you. The Director of the PhD program will then accept the ISP. You can find the ISP forms on our website.

The ISP is a formal document, and includes the following:

• Information about your supervisor and your cosupervisor.
• A research plan including a time plan.
• Information about management and supervision.
• The compulsory PhD courses, which you must take within the first three semesters from the starting date.
• Other PhD courses you intend to take (can be updated in the following ISP revision).
• A plan for your participation in seminars and other academic activities. This section should be completed continuously during your PhD.
• A plan for your responsibilities and tasks during your training.
• A financial plan covering the entire period of study (to be filled by your supervisor).
• Together with your supervisor fill the PhD Goals document (Attachment 5). This is not needed for your first ISP (latest two months after your start), only upon the yearly update.

The ISP is a living document and it must be updated continuously. Do not forget to fill in your research progress, as well as seminars, SDM presentations, group meeting presentations, attendance to lectures by invited speakers, attendance to half-time presentations and theses, specialized training, etc. The ISP is fully revised by you, your supervisor, your cosupervisor and the Director of the PhD program at least once per year. Instructions of this process are given by the Director of the PhD program well in advance.

 

Teaching

During your time as a PhD student, you will most likely act as a teaching assistant. The time you spent teaching is regulated by your contract. Normally, students teach 10% or 20%. If you teach 10%, your contract as PhD student is prolonged by 4.8 months. If you teach 20%, your time is then prolonged by 9.6 months. The main responsible for the teaching staffing plan is the Director of Undergraduate Studies. Undertaking teaching in the department is a great
opportunity to develop your teaching skills, which could be of tremendous importance for your future career. Important: check that your teaching duties do not overlap with compulsory PhD courses that must be taken during the first three semesters of your PhD studies. If this is the case, discuss with the directors of Undergraduate Studies and of the PhD program. Likewise, before planning attending conferences or taking vacations, double check the staffing plan to make sure that you have no teaching obligations.

The staffing plan is finalized in May each year, in effect for the following academic year. The amount of teaching is depending on your contract; up to 20 % but typically, 10% of your time will be devoted to teaching, distributed over your PhD. This corresponds to participation in 1 - 2 undergraduate courses per year, in the form of a lab teaching assistant or exercise teaching assistant. Ask the Director of Studies for a work description, how the hours are
calculated, and information on how to obtain a teaching certificate.

Before undertaking any teaching activity, you must take the course “Teaching Chemistry” which is mandatory in your PhD program. Apart from this, the University organizes introductory courses on pedagogics and teaching along with many interesting workshops that could help you improve your pedagogic and teaching skills (more information in su.se/ceul/english). To be able to fulfil the role of teaching assistant, you will need preparation; it is strongly recommended that you have a thorough read about all necessary information involved in the course. In most cases, you will be acting as lab assistant, and safety has to be handled before the start of the course together with the course organizer. Teaching is a very important task, because you will be representing the department in front of students. By being an efficient and inspiring instructor, you are influencing the education of our undergraduate students!

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Half-time Control – Halfway through your PhD

Check point 2

The purpose of the half-time report is to follow your progress, and to help you to continue towards completing your PhD studies. The half-time control should take place 22-26 months after your acceptance. Specific instructions are given in the document “PhD program at the Department of Organic Chemistry” (point 5), which you can find in our webpage. There you can also find the timeline, and you should plan this ahead! The half-time control will be documented in Form PhD 3 Half-time and registered in LADOK by the Director. In the case the PhD student wants, the half time control can be in the format and with the formalities of an examination for a Licenciate degree.

The half-time control consists of a written report and a seminar:

• Written report. A 25-35 page summary of the conducted research. It follows the format of a PhD thesis with the published articles (if any) and manuscripts attached as appendices. Supporting information that is not published should also be attached. The report will be archived at our department. The report should be written in your own words and any quotations clearly marked and cited. See antiplagiarism guides (in Swedish) here: su.se/ceul/resurser/examinera-dina-studenter/motverka-plagiering1.3049, under “Andra Resurser”. Do not miss “Refero – an anti-plagiarism Tutorial”, which you can read in English or in Swedish. Refero is a web-based tutorial which shows you how to implement other people’s texts in your writing and how to avoid plagiarism. Do not forget to give a printed as well as an electronic copy to our administrators (room A609).
• Seminar. It is open to the public, you first present your work during 25 minutes. After this, the opponent leads a discussion with you, and asks critical questions for approximately 30 minutes. Apart from a scientific discussion, the opposition includes formative feedback on the written report as well as the oral presentation. The opponent must have a PhD degree. The opponent should not have any research projects in common with you or with your supervisors, and should not have any other conflict of interests.

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Licentiate Degree

Alternative to the half-time control, a licentiate degree can be obtained when you are halfway through your PhD degree. The same Form PhD 3 Half-time is to be filled Similarly, to obtain your licentiate degree you will need to produce a written report and deliver a seminar with the same features as the half-time control. A total of 120 ECTS credits are needed to obtain the Licentiate degree. Of these, 30 must be course credits. More information can be found in the General Study plan (ASP). The main difference between half-time seminar and Licentiate thesis regards the fact that the Licentiate constitutes a formal academic degree, and is published as an open document in DiVA. DiVA at Stockholm University contains publications produced by the university´s researchers and students.

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Dissertation and Defense – Almost there!

Dissertation: One of the final parts of your doctoral studies is to write an academic thesis. The thesis should reflect your ability to complete the selected research task in a scholarly and independent manner, with or without collaboration. The doctoral thesis is normally written as a compilation thesis. Your published articles and manuscripts are attached to the thesis, and your contribution to each of them must be clearly stated. The thesis is normally written in English. Although not a formal requirement, the thesis is normally based on ca 3-4 published, peer-reviewed articles and/or manuscripts, to meet the quality and quantity standards at the Department.

For more information about rules and regulations, consult the department website and the Faculty of Science website.

Public Defense: The public defense of the PhD thesis or disputation is the very last part of your doctoral studies. During your defense there will be a thesis committee (normally 3, alternatively 5) that evaluates your work, as well as an opponent. During the defense, either you or the opponent will present the most important research findings of your PhD thesis. Discuss with your supervisor how you want this to be carried out, and revise again our PhD Program, available
at our webpage! The guidelines concerning defending your thesis can be found at the Faculty of Science webpage.

Timeline for completing your PhD

The list below is aimed at helping you, however, read again our Phd Program and follow carefully the instructions given by SUB, Stockholm University Library

1. At least 6 months before the defense, You and your supervisor should decide on a date and time for the defense. Make a plan for how long time you will need to write your thesis, and whether you will divide the time between research or write fulltime. In your planning, make sure you will plan time for your supervisor and the proof readers to give you feedback. Also keep in mind that this process may be repeated. Important: proper references to data and information must be given. Your thesis must be written in your own words, and you cannot copy text or pictures from published articles, not even your own articles. In most cases a permission to include already published papers must be obtained from the publisher, as indicated on the journal ́s website. Do not use non-peer- reviewed web sources. Check also the document “Guidelines regarding the design of doctoral dissertations” available at our webpage.
2. Six months before the planned date for the PhD dissertation, you should contact the Director of the PhD program, and submit a list of publications/manuscripts that he/she will base the thesis on, using the Form PhD 4 Publications for thesis. At this point you should have all credits required, or at least within two months.
3. Your supervisor should at the same time inform the Director of the PhD program about suggested opponent, who should have been contacted, and suggested examination committee.
4. If Form PhD 4 Publications for thesis is approved by the Director of the PhD program, the supervisor should confirm the date with the opponent, and should also contact the proposed examination committee members. If they all accept the supervisor should fill in the Disputationsblankett and mail it to the Director, who after checking it, will forward it to the Head of Department, who in turn will send it to the Faculty of Science.
5. Book a time for your dissertation by sending an email to disputationer@su.se. IMPORTANT: if you change your dissertation date or cancel it, you must inform “disputationer” again as soon as possible! When communicating with “disputationer”, make sure you cc the Director of the PhD Program as well as our administrators (mathias.ulander@su.se). As soon as your date of dissertation has been registered in the Disputationskalender, you must contact SUB, The University Library. Arrange a meeting with the librarians, as they will explain you in more detail the schedule for your thesis submission, including the nailing of it. SUB will also give you information about how and when to register your articles and your thesis in DiVA. They will also give you information
   about the cover, page type, and help you to get an ISBN for your thesis.
6. Before writing your thesis, check our webpage, where you will find guidelines from the faculty to write your thesis (Guidelines regarding the design of doctoral dissertations).
7. No later than nine weeks before the dissertation, you should give a copy of the thesis to the Director/ Ämnesansvarig. Your supervisor and the co-supervisor are expected to have read and commented the thesis prior to this. The Ämnesansvarig will within one week read and comment the thesis preferably in a meeting with you. The Ämnesansvarig will also check the thesis for plagiarism. If there are serious problems Ämnesansvarig will inform the Head of the Department. Prefekt.
8. Two weeks before the final printing (ca 6.5 weeks before your defense), an electronic copy of your thesis is sent to the opponent and the committee members, including the reserve committee member and the chairman. Contact Mathias Ulander for this.
9. If you are having your thesis printing done through the library, they will require you to submit a draft at least 6 weeks before the defence to be printed as a test copy. If you choose to use another print-service, for instance AJ E-Print, the time could be shorter, for print-service, see avropa.se/ramavtal/ramavtalsomraden/kontor-ochinredning/Tryckeritjanster/Tryckeritjanster/ (in Swedish)
10. The order for the final print has to be placed by You no later than 8 working days before the nailing (ca 5 weeks before the defense). The printing process may take one week (but depends on the print-service chosen).
11. The library will tell You when to upload the thesis in DiVA, ca 6 working days before the nailing.
12. Three weeks before your defense, your thesis is nailed electronically and it is made publicly available (as indicated by the library). This is a very important date and cannot be changed, except under very specific circumstances! Permission has to be given by the ViceChancellor!). If you want to organize a nailing (spika) ceremony, make an announcement to the whole department and prepare snacks and drinks.
13. Three weeks before your defense, you have to post hard copies to the opponent and committee members, including the reserve, the chairperson and the contact person (commonly, chair person and contact person are the same).
14. Three weeks before your defense, you must send hard copies of your thesis to departments around Sweden (ca 22 addresses and 1 for archiving at our department, admin). You can get the list from the administration at our department.
15. Now it is time for you to start preparing a presentation for the disputation. Rehearse and schedule a pre-defense with your group, or with the whole department!
16. Prepare (you) an errata list to the thesis.
    17. At least a week before the defence, your supervisor should book a lunch venue for the day
    of the defence, and a room for the evaluation committee meeting after the defence is
    over.
    18. If at SU, you should test your presentation in the same room where the defense will take
    place.
    19. If the defence takes place on line, the Chairperson of your thesis should send the Zoom
    links to the opponent and the committee members, to yourself and to the whole
    department. It is recommended that you and the Chairperson test the Zoom setup with
    the opponent and with the members of the committee before the thesis. The Zoom link
    should be made public. Guidelines about online dissertation during the Covid outbrake
    can be found in our webpage.
    20. One day before the defense, with the help of your group member or friends, arrange (you)
    drinks and snacks for the day of the disputation.
    
    Finally, the day is here!! The day of the defense:
    
    21. You must bring enough copies of your errata list if any, and 5-10 copies of your thesis to
    the venue.
    22. With the help of your group, prepare the room and make sure that bottles of water are
    available.
    23. Enjoy your disputation (YOU!!).
    24. YOU got it, it is done. CONGRATULATIONS!
    25. Last, but no least, do not forget to apply for your degree!

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General information

The department’s website is www.organ.su.se. In “Internal pages” you will find more information about the main procedures and protocols involved in the department. The department is part of the Faculty of Science:

Faculty of Science

Scholarships

As a PhD student at Stockholm University, you can apply for scholarships from the university’s scholarship trusts:

Scholarships

Action plan Gender equality and equal condition 2020–2021

An action plan for equality at our department can be found at our webpage:

Internal

Employment terms

Salary: Your salary follows the regulations by Stockholm University (Doktorandstege). You can find additional information about the terms of employment at SU in ‘You and Your Workplace’.

Leave: As an employee at SU, you are entitled to some types of leave, including parental leave, and leave for care of loved ones and urgent family matters. Check: ‘You and Your Workplace’.

Parental leave and Pregnancy: If you are pregnant, immediately discuss with your supervisor/cosupervisor or with the Director of Doctoral Studies. Together with the administration, they will guide you. Parental leave is reported in Primula (the personnel administration system at SU). When possible, inform your supervisor and group that you will away well ahead of time. You must inform Försäkringskassan and then apply for the payment of compensation. You can get help from the HR /finance officer at our department.

Sick leave: Should be entered into Primula the same day you get sick. When you are back, you must open your case and make a fresh notification. More information about health care and occupational health care can be found at SU in ‘You and Your Workplace’. If further information is needed, you can contact the HR/finance officer at our department.

Vacation: Is requested in Primula (the personnel administration system at SU) under “My page”. If you for some reason want take back your requested and approved vacation, this is done through a form (ask the administration) and don’t forget to inform your supervisor and someone in your group that you are on leave. You must take out a minimum of 20 days/year in vacation. You can find additional information at the SU webpage.

Insurance: During your employment you are insured during work time with legal, financial and administrative services agency. More information can be found at SU webpage at “You and Your Workplace’. Ask the HR /finance officer at our department for more information on what is covered.

Insurance when travelling abroad: Employees are insured during travel abroad for work purposes; however, you need to bring the insurance card. You can obtain this from the HR/finance officer at our department. More information can be found at SU webpage at “You and Your Workplace’.

Safety: You can find the “General Safety Framework” of the department at our webpage:

Internal

Report on damage or incident: Report of injury or threat of injury takes place in Stockholm University reporting system SAMIR (if you do not know how to do, contact our Safety Officer).

Leaving the department: After completing your PhD studies at the department, organize and get support from the Head of Administration for your departure. Check with your supervisor and with Lab Contact in your lab what you need to do before leaving the lab and office.

Career information: Follow the LinkedIn group “Alumni – Organisk kemi, SU” to keep in touch with current and
previous colleagues of the department. Stockholm University also continuously offers talks and workshops:

su.se/english/education/calendar

Unemployment insurance for university graduates: can be obtained for a small monthly cost from Akademikernas a-kassa. It is recommended you look into this no later than your year 3 and decide if you want to become a member. Information about their conditions and benefits can be found in their webpage, in English and in Swedish.

Every single person who contributed to produce this Handbook is greatly acknowledged!

The PhD Handbook is also available as a pdf-document:

PhD_Handbook-v21_August_2021.pdf (626 Kb)