The School of Chemistry

School of Chemistry FACULTY OF MATHS AND PHYSICAL SCIENCES

Handbook for Postgraduate Research Students 2015/16

Welcome The School of Chemistry welcomes new postgraduate students to Leeds and welcomes back returning students. This handbook is intended to give you information that is relevant for your time spent in the School, including information about facilities to support your research, and administrative procedures that affect postgraduate research students. This booklet should be read in conjunction with the Research Student Handbook, Faculty Protocol for Research Degree Candidature and the School of Chemistry Safety Information. The University’s on-line system to support postgraduate personal development may be found at https://www.pdr.leeds.ac.uk/. The system will be used to support many aspects of your postgraduate studies, and you will need to become familiar with it. You will need to use the system to:  find details of your supervisory team and your assessor(s)  archive and receive feedback on your formal monthly meeting reports  archive the formal reports that you will produce throughout your PhD  upload your training plan on an annual basis  see the record of other formal meetings that you have attended You can find templates for many of the forms that you will need to complete during your PhD at http://www.chemistrystudents.leeds.ac.uk/research-postgraduates.html

Professor Michaele Hardie Director of Postgraduate Studies

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Contents Welcome ............................................................................................................................ 2 Equality and Diversity Statement..................................................................................... 5 Who’s Who in the School of Chemistry .......................................................................... 6 School of Chemistry PhD Student Report and Assessment Structure ........................ 7 1)

Formal Progress Reports

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2)

Annual Training Plans

8

3)

Formal Meetings

8

4)

Participation in the School of Chemistry PGR Conference

8

5)

Annual Progression Meetings with PGPT

8

6)

Formal Supervisory Meetings

8

7)

Taught Modules

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Year 1 Progression

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General Information ........................................................................................................ 12 Administrative Matters

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Change of Name or Address

12

Computing

12

Council Tax

12

Clarkson Travel Fund

12

Demonstrating

13

Fees

13

Fire Alarm

13

International Students

13

IT Support

14

Keys

14

Leaving the University

14

Libraries

14

Lost Property

14

Maintenance Payments

14

Mail

15

Maintenance Payments

15

Photocopying

15

Registration

15

Registration Statements and Letters to Open a Bank Account

15

Staff/Postgraduate Student Committee

16

Useful Numbers

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Emergencies (fire, police, ambulance)

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University main switchboard

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Accommodation Services

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Training ............................................................................................................................ 17 Skills Training and Development

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Foundation Training and Development Package

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Training and Development Opportunities

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Personal Development Plan (PDP)

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Information for students in the Inorganic and Materials Chemistry Section ............. 20 Information for students in the Organic Section .......................................................... 29 Information for students in the Physical Chemistry Section and Colour Science Section ............................................................................................................................. 44 Introduction to Intellectual Property Rights ................................................................. 53 Use of Computer Systems .............................................................................................. 55 Electronics Support in Chemistry.................................................................................. 56 Mass Spectrometry Services ......................................................................................... 57 Microanalysis .................................................................................................................. 58 NMR Spectroscopy ......................................................................................................... 60 The Analytical Laboratory and Services ....................................................................... 62 Chemistry Stores............................................................................................................. 63 Student Services: useful contact details ...................................................................... 66 help@leeds

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LUU Advice Centre

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Leeds Student Medical Practice

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Student Counselling Service

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Student mental health advisor

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Disabled Students’ Assessment and Support and Leeds Assessment Centre

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Nightline

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UNIPOL Student Homes

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Equality and Diversity Statement

The University of Leeds is proud to be a multi-cultural community. We value diversity, and are determined to ensure:  that we treat all individuals fairly, with dignity and respect;  that the opportunities we provide are open to all;  that we provide a safe, supportive and welcoming environment – for staff, for students and for visitors. We recognise that we still have work to do to secure a truly inclusive community, and we are committed to a wide-ranging plan of action to tackle discrimination and to promote diversity. The Equality and Diversity Statement forms part of the University’s Equality and Diversity Policy, which applies to staff and students alike and is available on the University’s website at: http://www.equality.leeds.ac.uk/university-policies-2/

The University has published the following policy and code of practice which are linked to the Equality and Diversity policy. They are also available on the University’s website:     

Dignity & Mutual Respect Equality & Diversity Policy 2010 Single Equality Scheme Policy on support for students who are parents or carers Student Mental Health Policy Further information and advice are available from The Equality Unit, Equality Service Ground Floor, Social Sciences Building University of Leeds, LS2 9JT Telephone: 0113 343 3927 Email: [email protected] Web: http://www.equality.leeds.ac.uk/

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Who’s Who in the School of Chemistry Contact details of all staff members may be found at http://www.chem.leeds.ac.uk/people.html Head of School:

Professor Steve Marsden

[email protected]

Director of Postgraduate Studies:

Professor Michaele Hardie

[email protected]

Postgraduate Progression Tutor:

Dr Terry Kee

[email protected]

Director of Research:

Professor John Plane

[email protected]

Heads of Section: Colour Science Inorganic Chemistry Organic Chemistry Physical Chemistry

Professor Long Lin Dr P McGowan Professor C Fishwick Professor B Whitaker

[email protected] [email protected] [email protected] [email protected]

Anna Luty

[email protected]

Gail Cole Michelle Parker

[email protected] [email protected]

Mandy Clarkson

[email protected]

Administrative Support: Postgraduate Research Support Officer Contact for Organic Section reports Contact for Colour Science Section reports/ reception Contact for Inorganic and Physical Section reports / keys

Technical Staff Technician (Safety Adviser) Laboratory Instructor Technicians (Teaching Laboratories) Technician (Spectroscopy) Technician (NMR) Technician (NMR/Microanalysis) Robotic Screening and Instrumentation Specialist Technician (Mass Spectrometry/HPLC) Technician (Mass Spectrometry) Technician (Electronic Workshop) Technician (Mech Workshop)

Mr Steven Richardson Dr Stephen Gorman Miss Jennie Dickinson Mr Dave Fogarty Mr Mohammed Asaf Mr Simon Barrett Mr Ian Blakeley Dr Christopher Empson

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

Mr Martin Huscroft

[email protected]

Mrs Tanya Marinko-Covell Mr John Spence Mr Matthew Broadbent

[email protected] [email protected] [email protected]

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School of Chemistry PhD Student Report and Assessment Structure As a research student in the School, you are likely to have contact with your supervisor(s) most days. You are, however, required to comply with the formal requirements of the University through a number of mechanisms. Set out below is the minimum requirement for the School. This structure of reports and assessment complies with the University’s guidelines. Failure to comply with these requirements may result in you being prevented from registering for the following academic year

1) Formal Progress Reports Supervisors may want more frequent reports for their own use. Please discuss the content and structure of your reports with your supervisor before you start writing. Please read your specific research section (Organic, Inorganic or Physical) later in this booklet for further details on specific content, formatting and contextual issues of your reports. Type 4 Month Report

Content Literature review to be completed by end month 4 for full time candidates. Transfer report (10 Substantive Report* (end month 10) and viva voce (ca. 1h, end months) month 11) with Head of Section; Independent Assessor; with Supervisor/s present Report and viva voce (ca. 30 mins) with Independent Assessor 21 month report and Supervisor/s present 30 month report A thesis chapter or similar substantive body of work Thesis submission between 36 – 48 months *Specific deadlines will be provided to you on registration. You may also receive reminders by email. You are expected to meet these deadlines (eg by planning in advance around holidays etc) You should take care to ensure that you comply with the following requirements in the preparation of formal progress reports: Electronic copies of all reports must be uploaded at https://www.pdr.leeds.ac.uk/. In addition, hard copies of your reports are required for your supervisor, any co-supervisors and your assessor (except the 1st year transfer report when an additional copy is required) are to be handed in to Gail Cole (Organic Section, G30), Mandy Clarkson (Inorganic and Physical Sections, G30) or Michelle Parker (Colour Science Section, G36) no later than 3.30pm on the deadline date.

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Relevant AISDE and Progress reports should also be submitted. See http://www.chemistrystudents.leeds.ac.uk/research-postgraduates/report-submission.html Reports will be read by your assessor and your supervisor(s). The feedback may be reviewed by your Head of Section, and will be provided to you.

2) Annual Training Plans Each year, within one month of registration, Lead Supervisors and their students are expected to discuss their training and development needs for the coming year. Use of the Training and Development Needs Analysis Tool, available on the PDR, can assist in this by identifying those areas which are most lacking. A Training Plan will need to be completed each year, signed by both student and Lead Supervisor, and then uploaded to the PDR. From this you can gain access to the VLE, the tool used for taught module attendance.

3) Formal Meetings Formal meetings will take place at 11 and 21 months. The transfer assessment meeting at 11 months is particularly important as it forms the basis of recommendation about transfer to full PhD status (see detailed guidelines of preparation for viva’s). You will be informed of the date and time of your transfer assessment meeting by Mandy Clarkson (Inorganic and Physical Sections), Gail Cole (Organic Section) or Michelle Parker (Colour Science Section). Your transfer assessment meeting is likely to take place in your 11th month and you must be available on the date which has been arranged. Therefore, you are strongly encouraged not to book and holidays during this time until you have been informed of your transfer viva date. Your 21 month formal meeting will be arranged by your supervisor and will involve a discussion of your progress since transfer along with a forward look at towards your third year.

4) Participation in the School of Chemistry PGR Conference The School of Chemistry Postgraduate Conference takes place in June each year. In Years 2 and 3 you will present your research at the conference in the form of a poster (Year 2) or an oral presentation (Year 3).

5) Annual Progression Meetings with PGPT The postgraduate progression tutor acts as advisor for most postgraduate research students, and meets with students 6, 18, 30 and 36 months. In advance of these meetings, a confidential assessment is completed by the student and their lead supervisor. The meeting will be arranged by the Postgraduate Office and you will be informed of the dates and times for all meetings with the PGRT at the beginning of each year.

6) Formal Supervisory Meetings You are required to have at least 10 formal, recorded meetings with your supervisor(s) each academic year. The formal record of each meeting must be uploaded at https://www.pdr.leeds.ac.uk/.

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7) Taught Modules You may be required to undertake some taught modules alongside your PhD study (this is a requirement for students in the Organic section and details will be provided separately). If your supervisor requires you to take a taught module, you should inform the Postgraduate Office ([email protected]) who will arrange for you to be added to the module on the VLE. Assessment is usually undertaken informally, after those students who are formally registered on the module have taken the examination.

Templates for monthly meeting reports, training plans, and coversheets for reports may be found at http://www.chemistrystudents.leeds.ac.uk/research-postgraduates.html

Year 1 Progression 4-Month Stage At the end of month 4 all students are expected to submit a written report, and receive feedback from their Lead Supervisor on their progression thus far. Both actions are required before a student can be deemed as having completed this stage of their progression: 1) Student 4-Month Report: The Lead Supervisor is expected to comment on content, style, clarity, thoroughness and execution. Details on the contents must be agreed between the student and Lead Supervisor, and should meet the requirements of the individual School or Section concerned (vide infra). To meet the University’s policy on ethics and academic property, any submitted written report should be accompanied by an Academic Integrity, Safeguarding Data and Ethical Requirements (AISDE) form. Once complete, both the report and the AISDE form must be submitted in two ways: a) Uploaded to the PDR as the ‘First Formal Student Report’ b) Two hardcopies handed to the relevant administration staff (see above) – these will be passed to the Assessment Panel for informal feedback, and returned via the Lead Supervisor. 2) First Formal Progress Report: The student is expected to complete the first section of this document, after which it is passed to their Lead Supervisor for their feedback on the student’s progress, and then on to the PGR Administrator. It is in the student’s best interest to ensure that this document is completed, and is handed in by the end of month 4.

Transfer Stage On arrival, a student’s initial registration is as a ‘provisional’ candidate, with their first year acting as a form of probation. The Transfer process exists to ensure that only those students capable of completing the final degree are accepted as full PhD students and therefore ‘transferring’ to full PhD status. This activity is completed at the end of the first year (or in the

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case of DTC, CDT and other 4-year programmes, at the end of year 2), and comprises of a series of reports and a viva voce assessment: 1) Student Transfer Report: This written report should be submitted before the end of Month 10. The main body of the report should be not less than 30 pages (20,000 words) of A4 including illustrative figures. Detailed guidelines for the preparation of the report (including guidance of the length of each section) is provided below for students in each of the Sections within the School. If you want to produce a much longer report, please discuss this with your supervisor. The report should have, in addition to the main text, a summary of not more than 2 pages stating the aims of your project and to what extent these have been achieved, exceeded or changed. The body of the report should be divided into Introduction, Results, Discussion, Conclusion and, if needed, Appendices. 1. Introduction: you should describe some of the literature relevant to your work and also how your work advances knowledge. 2. Results and Discussion: these are self explanatory, but if these are not conveniently separated then combine them as ‘Results and Discussion’. 3. Conclusion: this should present a concise and accurate account both of what has and has not been achieved, for whatever reasons, and also your aims for the forthcoming year. 4. At the end of the report there should be a list of the seminars and any other courses you were expected to attend during the year and you should indicate how many you have attended. If you have been to meetings in other Schools or universities, include these also. 5. Appendices: Extra information such as spectra, mass analyses, etc. of a routine nature could be added as an appendix with only a typical example shown in the report. 6. References: The report should contain references and a list of references is to be included at the end of the report in a style typical of a scientific journal, but titles of papers need not necessarily be included. The final report will be critically read by your supervisor and by at least two other faculty members who are familiar with the research topic.

Again, as a submitted written report, this document should be accompanied by an AISDE form. Once complete, both the report and the AISDE form must be submitted in two ways: c) Uploaded both document to the PDR as the ‘Transfer Report’ and ‘Academic Integrity Form’ 10

d) Hardcopies handed to the relevant administration staff (see above) – these will be passed to the Assessment Panel.

2) Transfer Progress Report Form As before, the student is expected to complete the first section of this document, after which it is passed to their Lead Supervisor for their feedback on the student’s progress. The completed form is then passed to the PGR Administrator, and will accompany the Transfer Report and AISDE to the Assessment Panel. 3) Transfer Viva Voce Assessment The date for this assessment will have been arranged at the beginning of the year by the PGR Administrator. It should be held before the end of month 11 of the Transfer year, and attended by the student and Assessment Panel. The Lead Supervisor is allowed to attend, but as an observer only, and will be asked to leave towards the end to allow the student to speak freely and in confidence regarding any issues why they may have. A formal report is then completed by the Chair of the Assessment Panel, which is passed to the PGRT via the PGR Administrator. 4) Transfer Outcome Notification Each student will receive a letter, signed by either the Chair of the Assessment Panel or the PGRT, informing them of the outcome of the Transfer Viva. If the student has not passed the Transfer, they will be given instruction on the next steps, i.e. resubmission, 2nd viva assessment, etc. All reports, both student and academic, will be available on the PDR following the various stages of the process. Only the student, members of the Supervisory Team, Assessment Panel, the PGRT and PGR Administration will have access to these records. Registration Following successful completion of the Transfer process, the student will be contacted by the PGR Administrator confirming a) the decision of the Assessment Panel, b) the recommendation by the PGRT for the student to be transferred to full PhD status, and c) the removal of any registration hold, thus allowing the student to register for the following year. Registration is sometimes authorised without progression, e.g. due to an unavoidable delay in holding the viva assessment. The PGRT will be asked to give their approval, and will usually give a deadline for completion of the progression exercise.

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General Information Administrative Matters The members of staff with specific responsibilities for research students are: Professor Michaele Hardie, Director of Postgraduate Studies, has overall responsibility for postgraduate research students. Contact: Room 1.26a, Ext 36458, email [email protected] Dr Terry Kee, Postgraduate Progression Tutor, has responsibility for the progression of postgraduate research students and acts as their advisor. Contact: Room 1.08, Ext 36421, email [email protected] Anna Luty, Postgraduate Research Administrator: administration of all postgraduate matters. Contact: Room G34d, Ext 36552, [email protected]

Change of Name or Address The name recorded on your student record should be the one by which you are legally known, and will be the name displayed on all documentation produced by Student Services, including your degree certificate and transcript. You must notify the University about any change to your name immediately. To do this, visit the Student Services Centre counter or email [email protected]. The University needs to hold your permanent home and term time addresses together with telephone numbers, your next of kin and emergency contact details. Please update your address and emergency contact details through the Portal.

Computing All new postgraduate students will see Dr David Waller (see Introductory Programme) to register for IT services. Please observe Conditions for Computer Use in the School of Chemistry, printed in this booklet.

Council Tax If you're a registered full-time research degree student, and you enter your term-time address when you register, your details will be sent to Leeds City Council four times a year at the end of October, January, April and July. You should complete a Council Tax Enquiry Form (PDF) available from Leeds City Council, which they will cross reference against our supplied data. More information can be found here http://students.leeds.ac.uk/info/10200/finance/598/council_tax_exemption

Clarkson Travel Fund The Clarkson fund was established in 1986 to provide funds for postgraduate students, postdoctoral research fellows and younger members of staff to attend a conference 12

overseas. The committee meets twice a year (in May and November) to consider applications for funding, though applications may be made at any time. More information and application forms can be found here: http://www.chemistrystudents.leeds.ac.uk/researchpostgraduates/clarkson-travel-fund.html

Demonstrating Full-time postgraduate research students are a valuable asset to the School of Chemistry in providing demonstrating duties within the School’s teaching laboratories. All PhD students within the School are encouraged to express an interest in carrying out demonstrating activities which are paid for on an hourly basis. This also applies to international students. Demonstrator training is available to all PhD students within the School and will take place as part of the School of Chemistry induction programme. You will also be invited to attend a training session delivered by SDDU. Demonstration and other teaching activities may only be carried out after the appropriate training has been provided. Please contact the Postgraduate Office ([email protected]) if you are interested in demonstrating and have not already signed up for demonstrating duties or completed training during induction.

Fees Self-funded students can pay in full before completing their registration or in two instalments. The first instalment of 50% must be paid before or at registration and the remaining 50% must be paid 5 months after their start date on the 1st of the month by Direct Debit from a UK bank account. This must be a current account and not a savings account. Alternative methods of payment are not acceptable. Students wishing to set up an instalment plan can do so during online registration. To complete this step you must be in a position to input your UK bank account details and the fees must have received the payment of the first 50%. Details of how to pay the tuition fee and information for externally sponsored students can be found here can be found here: http://students.leeds.ac.uk/researchstudentguidance

Fire Alarm This is a continuously sounding siren. If you hear this alarm you should exit the building as quickly as possible and assemble in the Green Car Park behind the Chemistry building. There will be a practice alarm during Semester 1.

International Students The International Student office, located within the Marjorie and Arnold Ziff Building, provides specialist advice and welcome and orientation support for international students. International students are strongly encouraged to attend an induction at the international office upon arrival at the University. http://www.internationalstudentsupport.leeds.ac.uk/

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If English is not your first language you should ensure you take the University English Language Test at the start of the academic year. If required you will have access to a number of resources (including extra English language sessions). Please make sure you take advantage of all of the university resources available.

IT Support IT staff are based in room G.52b. Please note that all IT jobs should be submitted via the form which can be found at www.maps.leeds.ac.uk/ITsupport. Staff are happy to discuss issues and provide advice however users will be asked to submit jobs for tasks arising from discussions. Please also see the School of Chemistry Use of Computer Systems Policy

Keys Keys are available from Mandy Clarkson in Room G30 and will be issued during the introductory programme for students commencing in October. Deposits for replacement costs are £50. The deposit is refundable on return of the keys.

Leaving the University If you find it necessary to leave the University either temporarily or permanently before completing your studies, please discuss this with your supervisor or with the Postgraduate Progression Tutor (Terry Kee). If it’s agreed that you should leave permanently then you will be given a leavers’ form (DOC) to fill out, available from your school and return it to your school with your student ID card. Leaving the University may affect your maintenance payments and/or your visa.

Libraries The University library consists of a number of separate libraries. The important one for chemists is the Edward Boyle Library with the Science and Engineering on Level 11. Your student card provides access to library facilities and loans. Please see the University Student Handbook for opening hours.

Lost Property Lost property within the School should be handed in to the School of Chemistry Reception, Room G36. Property lost or found outside of the School of Chemistry should be reported to the University Security Office near the main university entrance for vehicles.

Maintenance Payments You usually receive your scholarship maintenance payment monthly in advance. Student maintenance is only paid to centrally-funded scholarship award holders who have completed registration and provided UK bank account details. Please note that you will not be able to register for study until approximately four weeks before your start or renewal date at the earliest, to allow time for us to put your funding in place.

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Any queries relating to centrally-funded scholarship awards should be directed to the Postgraduate Scholarships Office. Queries relating to departmental scholarships should be directed to Anna Luty [email protected]

Mail Incoming mail is sorted each day by 11am and is put in the pigeon holes in the Chaston Chapman Lounge on the ground floor. Internal University mail and stamped external mail can be put in the trays in the mail room by the Chaston Chapman Lounge. School facilities can only be used for academic business. Mail from the Postgraduate Office will generally be communicated to you by email; please check your email daily.

Maintenance Payments Unless your study is self-funded or you have an external sponsor, you will receive your maintenance payments directly into your bank account. Student Maintenance is only paid to students who have completed stage three of the registration process and provided their bank details. Since the University of Leeds work to strict payment deadlines it is imperative that you register as early as possible and enter your bank details via the portal to ensure your ‘money’ is cleared by the due date. The due date for the majority of awards is the first of the month, however, due to the constraints of the system if the 1st of the month does not fall on a Tuesday your instalment will clear on the Tuesday immediately before the 1st. A schedule of payment dates can be found here: http://www.leeds.ac.uk/studentservicescentre/financial_admin/pg_maint.htm

Photocopying Photocopying machines are located in room beside the Chaston Chapman Lounge. These machines operate with paper photocopying cards available from the Chemistry Store, chargeable to your supervisor’s account.

Registration Registration is the formal process of becoming a student of the University. Every student is required to register at the start of their studies and then re-register each year before the anniversary of their start date. Registration enables students to receive supervision and access services including the University Library and computing facilities. Full details and the link to online registration can be found here www.students.leeds.ac.uk/registrationguide

Registration Statements and Letters to Open a Bank Account If you require a letter confirming your registration status or to open a bank account, you should visit the Student Services Centre counter which is located within the Marjorie and Arnold Ziff Building Opening times: 9am-5pm Monday, Tuesday, Thursday, Friday. 10am - 5pm Wednesday.

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Staff/Postgraduate Student Committee This Committee comprises around 8 postgraduate students, and 4 members of staff including the Director of Postgraduate Studies. The committee meets at least three times per year to discuss matters pertinent to postgraduate students. The committee also assists with the running of the Introductory Programme, Postgraduate Conference and a range of social activities within the School. Staff-Student Committee meeting minutes and a current membership list can be found here http://www1.chem.leeds.ac.uk/School/Information/PostgradCommittee/

Useful Numbers Emergencies (fire, police, ambulance) For emergencies on campus you should call University Security on 0113 343 2222 requesting the service you require. The Security Service will liaise with the emergency services immediately and help the vehicles reach the site of the incident as quickly as possible by the fastest access route. Security staff are specially trained to have knowledge of the access routes across campus. University main switchboard 0113 243 1751 Accommodation Services 0113 343 7777

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Training Skills Training and Development For more detailed information, see the Faculty Researcher Development website: http://www.maps.leeds.ac.uk/home/researcher-skills.html Developing personal and professional skills is an important part of the postgraduate research degree. A PhD is no longer purely about getting on with your research and publishing the findings - though these will remain the key focus. A PhD in the UK now also places importance on developing you and your skills - as a researcher and an individual – to become more effective in your research, and to enhance your future employability whether this is in or outside academia.

Foundation Training and Development Package To provide Postgraduate Researchers with a strong foundation of generic skills, all students are required to complete certain courses/workshops according to their current year: Year 1 School Induction (including Health & Safety) Faculty Induction Starting your Research Degree Project Managing your Research Degree LaTeX for Beginners/Improvers OR Word for Thesis & Long Documents Preparing for your Transfer Year 2 Health & Safety Renewal Writing for Research Students in the Sciences OR in-house training Effective Poster Presentation Effective Seminar/Conference Presentation Options Outside Academia OR Developing your Academic Career Year 3 Health & Safety Renewal Preparing for your Viva OR confirmation of practice viva Final Stages of your Research Degree Although some titles may change over the course of a year, the basic aims of each workshop, course or activity is designed to provide the basic framework of skills. Specific additional courses are highly recommended (see details in Appendix) Postgraduate Researchers, together with their Supervision Team, should use this framework to build a bespoke training and development plan, providing them with the skills and training required to support them through their studies. This can include generic and research-

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specific training, attendance at taught courses (either as full or non-assessed students), and local, central or external courses. Details of which courses to attend should be recorded on the Annual Training Plan, and attendance will need to be logged on the PDR’s ‘My Training Plan’.

Training and Development Opportunities This section covers the range of free transferable skills training opportunities that are available to PhD students in the Faculty of Maths and Physical Sciences. Research-specific skills development is the responsibility of the supervisor / research group. The Team also manages the Faculty Researcher Development website http://www.maps.leeds.ac.uk/home/researcher-skills.html providing up-to-date information about courses, online booking and links to useful resources for PhD students and their supervisors. You will also receive a regular electronic newsletter with news about training and development opportunities and resources in the Faculty and beyond. Centrally-provided training provision The Library, Information Systems Service (ISS), SDDU and Careers Centre contribute to the Faculty Skills Training Programme described above. However they also run their own University wide programmes which include free courses for PhD students – so it is worth checking their websites too. For a full overview of what is available across the University for PhD students, see the “Personal and Professional Development Opportunities” booklet provided by the SDDU Graduate Training and Support Centre, or go to: www.leeds.ac.uk/rtd. SDDU Graduate Training and Support Centre As well as contributing to the Faculty Programme, the GSTC offers a comprehensive range of free courses for students across the University see www.leeds.ac.uk/gts for a full list. Information Systems Services (ISS) ISS offers a popular range of free IT skills training courses for PhD students throughout the year (note some of these are also offered through the Faculty), see: https://uolr3.leeds.ac.uk/temcatsearch/courses.htm?gd_keywords=roberts Library As well as the specific sessions for PhDs by the subject librarians which are part of the Faculty programme, the Library also runs free training courses on using library facilities and information skills as well as providing online resources. See: http://library.leeds.ac.uk/skills Careers Centre The Careers Centre runs a regular series of workshops for PhD students, topics include Interview Techniques and CV Preparation. The Careers Centre can also provide individual support, see: http://careerweb.leeds.ac.uk/ Language Centre International students may find the courses in academic http://www.leeds.ac.uk/arts/homepage/249/language_centre

writing

useful.

See:

Residential summer workshops UK Research Council funded PhD students are eligible to attend a GRADschool workshop free of charge, see www.vitae.ac.uk/gradschool. Alternatively Leeds PhD students may 18

attend WRISS. Either workshop is strongly recommended for second and third years. They develop personal skills, are highly rated by attendees and are highly competitive! PDR ‘My Training Plan’ The PDR tool, ‘My Training Plan’, is used to log all training courses completed. Most centrally organised courses have their details automatically added following attendance, and some Faculty or School sessions may also be logged in this way. However, the student is expected to check that this has occurred, and to add details of any School, Faculty, or external training events missing The Online PDR system is also used for recording training plans. You should discuss your training needs (in both research-specific and transferable skills) with your supervisor and agree a training plan within your first month at the University. This should then be uploaded into the Online PDR system. You and your supervisor should monitor your progress against the training plan regularly; as a minimum, at the mid-point of your first year and at the transfer stage and annually thereafter. The online PDR system https://www.pdr.leeds.ac.uk contains an online Training Needs Analysis section that you might find useful. Personal Development Plan (PDP) You are also encouraged to reflect privately on your training and development activity throughout your PhD. There is a Reflection area in the Online PDR system: https://www.pdr.leeds.ac.uk Note that your PDP is private to you, it is not part of your official, documented Personal Development Record (and is only visible to you).

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Information for students in the Inorganic and Materials Chemistry Section

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INORGANIC AND MATERIALS CHEMISTRY Reports The minimum number of reports that you will be required to produce each year is determined by the University. The School of Chemistry adds to this and a table of what is required of you is given elsewhere in this booklet, but note that your supervisor may require you to produce more reports than this minimum. You must discuss the content of your report with your supervisor before you begin writing. You will also produce a poster in your second year and give a talk about your work in the Postgraduate Conference in year three.

Guidelines on the 1st year PhD Transfer Exam including preparation and presentation of the Transfer Report The purpose of the examination The purpose of the exam is twofold: First, to convince your examiners that you have the intellectual capability and skill to successfully produce work that will lead to a successful PhD. Second, to convince them that the topic you have chosen to study is sufficiently intellectually challenging, is novel and important, ie, not so esoteric that nobody cares about it, and can be completed within the allotted time period. The examination Your 1st year transfer report, literature review, and other interim reports produced during your first year, and the viva voce all form part your University Transfer Examination which, if successful, will allow you to transfer from provisional to full PhD status. The examination will normally last for no more than 1 hour. The examiners are the Head of the Research Section and one other academic member of staff who will normally be your PhD Internal Examiner. Your supervisor will also attend but will only enter into the process if asked to do so by the examiners. You will be questioned in detail about your research and your report and on any background science on any topic (not only Chemistry) that is pertinent. You will be told the result of the exam immediately after it is completed and after the examiners have consulted privately. A report will be written by the examiners and you will have to make any changes to your report, notebooks or lab working methods that they recommend. Following the exam, the examiners may recommend: (a) Pass (b) Pass, but require that changes are made to the report and/or in your future lab books etc. You will be given a specific time period in which to do this. Your supervisor will review and approve changes. (c) Defer your transfer because the report needs to be re-written either in part or in its entirety and a further oral exam may need to be held. You will be given a specified time period in which to do this. This report will be re-read by the examiners. Transfer

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(d)

to full PhD status will be put on hold until your work is considered by them to be satisfactory. Fail. If you fail you will be entitled use the University’s postgraduate appeals procedure.

The content of your report Your supervisor will advise you on the style in which the report is to be produced as there is not a single set format. Your report must be substantive, its content must be of a high standard, and the overall quality must be must be similar to that of a PhD thesis or scientific paper. It should typically be between 50 and 100 A4 pages long, including diagrams and a full Experimental Section if appropriate. The report will contain: (a)

an Introduction, including: (i) a clear description of the Objectives of your research and how it will improve the state-of-the-art, and why the scientific community will be interested in your work. (ii) a discussion of what is already known about your research topic and other closely related areas. This will effectively be a review of the current state of knowledge. (iii) a description of how you are going about studying this problem, including a discussion of any experimental techniques to be used if these are out-of-the-ordinary.

(b)

Results and Discussion, describing the results you have achieved during your first year and what you have learnt from them. You should include unsuccessful experiments, describing how they led you to change your approach to your goal(s). Do not include trivial detail.

(c)

a Conclusion. Make a short conclusion drawing together what you have discovered.

(d)

information about Future Work. There may be several ways to extend your work, you may not wish to follow all of them; describe your plan for your next year’s work.

(e)

an Experimental Section. This will vary in format according to whether you are doing a project in synthetic chemistry, or in materials chemistry. For synthetic projects, describe the procedure followed and list the relevant characterisation data for each reaction you performed. This should be presented in sufficient detail to allow direct incorporation of your data into a paper. In particular, mass peaks should be assigned; and, 1H NMR coupling constants should be given, where possible, and all NMR spectra should be assigned. See the advice on formatting an Experimental Section in the Information for Organic Chemistry PhD students for more detail. For materials chemistry projects, the Experimental Section should contain a description of the equipment you have employed. Any relevant characterisation data, that has not been given in the Results and Discussion, should also be included here. A description of the procedure for each experiment should only be included, though, if that information has not already been given in the Results and Discussion.

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If in doubt, please consult with your supervisor for more advice on the format of the Experimental Section of your report. (f)

a list of Acknowledgements. Restrict this to colleagues who have really helped you during the year, readers of drafts of your report and your supervisor. Don’t forget to acknowledge who funded you.

(g)

References. The report must be well referenced, showing that you have read the international literature not just that from your supervisor’s group. If your references indicate that the latter is the case the examiners will immediately be concerned that you do not know your subject. It is difficult to indicate how many references should be included, but successful reports contain at least 50.

(h)

your own work. Any text directly copied from another source must be put in parenthesis, because it is a direct quote, and any other material, diagrams, equations, text, ideas and so on, taken from another’s work must be properly referenced. Referencing others work does not diminish what you have done. Make sure that you have read and understood the University’s code on plagiarism.

There are some more notes below on preparing references, tables, graphs, equations and so forth.

Your role in the examination (a) You have to defend what you have written in your report. This means answering the examiners’ questions, but not necessarily agreeing with them about the interpretation of your data or veracity of your experimental method. ‘Defending’ means presenting logical arguments to back up statements and conclusions made in your written report. (b) You will almost certainly be asked why your project is important, how it relates to other work, what you have achieved during the last year and what is planned for the future. (c) You are expected to be the expert on the experiments you have performed and to be fully conversant with any background and basic science needed, even if it is not Chemistry. This is most important because many students are poor at answering questions on basic science, even Chemistry. If you mention a named reaction, a particular effect or an acronym, make sure you know what it is! Three types of typical question areas are outlined below. (i)

(ii)

(iii)

If you mention a named effect or equation such as the Boltzmann distribution make sure you can write down the equation and can describe what it means. In this example a really good answer would include a description of partition functions and perhaps who Boltzmann was and something about what he did. Similarly if, in the context of NMR, you use a particular pulse sequence make sure you can explain this fully and also describe related sequences. In this context ‘fully’ means not only in terms of pulse durations relative to delay times but also what happens to the magnetisation vector and so forth. In a statement such as “The Knoevenagel condensation is a modification of the Aldol condensation.” You will probably have described the Knoevenagel condensation in the text, and will most likely be asked to describe what the Aldol condensation is, and give to another example. The examiners may then ask

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general questions about other addition reactions depending on how well you answered the first question. (d) If you do not know the answer to a question, ask for it to be reworded; if you are still having difficulty go back to the basic science and try to work it through step-by-step. If you are still at a loss say so; do not try to ‘blag’. (e) You may be asked to draw reaction schemes on the board or describe effects or phenomena; practice doing this beforehand.

NOTES ON PREPARING YOUR REPORT Word Processing Use MS Word where possible. Customise this programme to make it quicker to use by adding icons onto the screen using the tools → customise commands and searching for what you want. Turn on the ‘spelling as you type’ and grammar checker. Make the default language UK English. Whilst the grammar checker is not perfect it does alert you to times when you miss verbs out of sentences or need to add commas. Set up a style for the main text and choose a suitable font and set paragraph spacing and tabs etc. To set up a style go to the menu bar then tools →customise → commands→ then locate styles in the format menu. Drag the style icon from the box and place into a menu bar. Close the customise dialog box. When you click on the style icon you can now modify whatever style you are using, say to ‘body text’ rather than ‘normal’. You can then define several different styles, one for figures, or for headings etc. To use numbering for figures, define a style with ‘numbering’ in the style dialog box its reference will appear in the cross-reference box under insert → reference → cross-reference. Next go to a place in the text where you want to insert a reference to a figure and click on the fig number in the cross-reference box and it will be inserted. The figure numbers will be undated automatically and kept in order. References The style of the reference should be that of one of the major journals such as JACS or Angewante Chemie. The references should be numbered in the text either as square brackets [2] or, preferably, as superscripts, Bloggs et al.2 The references should be numbered in order throughout the text and included at the end of the report. Use Endnote to keep consistent sequential numbering and accuracy of page numbers and so forth. Variables, Equations and Units (a) Variables are italicised in the text and in equations. Units are not italicised. “Assume the bond extends as a harmonic oscillator and use Hooke’s law; force  extension or f  k (r  re ) , where k is the bond force constant in Nm .” (b) Always use SI units. All measurable quantities have units so always include them. A unit is written with a space after the quantity 12.3 J or  1.0544  1034 Js . The unit is not italicised and spaces are not left between units. Reciprocal units are written as ms or K 24

not m/s or 1/K. Degrees have the superscript circle ‘degrees symbol’ immediately after the number, and are only used for centigrade: as you are using SI units you didn’t need to know this because degrees Kelvin do not have a superscript circle after the number. (c) To insert equations use MathType, or the MS equation editor provided with Word which is a cut down version of MathType. eg “ if k1 and k2 are rate coefficients at temperatures T1 and T2 respectively show that  k  E T T  (0.1) ln  2   a  2 1  .  k1  R  T2T1  Using equation (0.1) plot a graph …….”

Diagrams, Reaction Schemes, Graphs and Tables If you import diagrams from elsewhere do not to forget to reference where they came from. If they are not of a good enough quality redraw them using a drawing package. For simple line drawings the Word drawing package is suitable and easy to use.

Reaction schemes Reaction schemes or structures should be imported from IsisDraw, Chemdraw and so forth and scaled to fit the text. The method of labelling of molecules and reaction conditions should be discussed with your supervisor or taken from JACS or other high quality journals. The scheme should be labelled in a similar way to figures to allow easy reference from the text.

Graphs Label both axes so that the axis is dimensionless, this means that the label is written as shown below. The temperature is divided by the unit to make the axis dimensionless, similarly for the pressure. Adjust the number of tick marks on the scale to suite the purpose of the graph and label the graph as appropriate. Do not use different colours to differentiate lines as these are often indistinguishable when reproduced and also fade with time. Use different line styles, dots, dashes, and labels to distinguish where there is ambiguity. There are plenty of examples in the literature, choose a style that you find clear. liquid solid

vapour

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Tables The contents of tables are numbers and are dimensionless, as with graphs, so that the headings are divided by the units.

Grammar & Writing Get hold of a copy of Strunk and White “Elements of Style” (£5), an invaluable book which includes some gems on how to write. You can easily look up points of grammar, similarly Zinsser “On writing well: An informal guide to writing nonfiction”. “Eats, Shoots and Leaves” by Truss is a good rant about grammar and also an amusing book to read. Additionally, read the notes from your Scientific Writing course. The short article “Writing Readable Prose” (EMBO reports vol. 7, p846, 2006) discusses in a clear way how to write scientific papers. When you have finished a section of writing, read it through and remove unnecessary words. Leave it for a day and re-read; you will usually find many things to clarify that you did not originally see. Avoid the first person, “I did this” or “I did that”, for example “I did these experiments using a Nicolet FTIR spectrometer and then I did other experiments on the 400 MHz Bruker NMR instrument”, does not read well. “We did this and “we did that” sounds better but is odd as it is only you who has done the work. It is better to write using a passive voice, in this example something along the lines of “The experiments were performed using a Nicolet FTIR spectrometer and the 400 MHz Brucker NMR”.

Summary (a) ”system”: this word can always be changed to “reaction”, “instrument” or something more specific. (b) “In order to”: Avoid this and rewrite the sentence. (c) “so that”: Remove completely and rewrite. Change “So that the reaction could be completed acid was added” to “The reaction was completed by adding acid”. (d) “since” and “as”: Remove “since” and replace with “because” unless “since” refers to something happening in time. “As” is used colloquially but it is usually better to replace it with “because”. “It has been a long time since I saw you”. “Since the solution was acidic, base was added” or “As the solution was acidic, base was added”, should be changed to “Because the solution was acidic…”.

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(e) Semicolon “;” and colon “:” Use the semicolon to emphasise a phrase that is a consequence of the first part of the sentence. Use a colon in a similar way when the two statements do not need separating into two sentences with a full stop. “Critically evaluate you work; include weak points as well as successes”. “Tuberculosis is still a major killer in the world; between 1990 and 1999 approximately 30 million people have died from the disease” [1]. (f) That vs. which Use that' for restrictive clauses, e.g. "the grass that grows in your garden"; Use 'which' for descriptive clauses, e.g. "The grass, which is green, grows in your garden". (g) However. “however” is surrounded by commas when used for emphasis: but see the next section. “There have, however, been a few cases of instant death from diphtheria and tetanus vaccines and there is much controversy about the vaccine for Anthrax for the military” [1]. (h) Avoid repeating a word in a sentence; this usually reads awkwardly. “However, although vaccines are generally extremely safe, no medicine is totally riskfree, however small the risk may be” [1]. Notice also the different meanings of however. (i) Lists. These are usually separated by commas. “As people in the west forget the ravages of polio, measles, diphtheria, rubella and so on, many will become less keen to have their children vaccinated because of the risk even if it is very small” [1]. “The symptoms of the progression of the disease are, among others, high temperatures, body filling with fluid, particularly the lungs, the apparent wellbeing of a person in the morning and death the same day or within a day or two”. [1] Notice here the use of the phase “particularly the lungs”, see below. (j) Commas. These cause more annoyance to some readers than almost anything else. As a rule of thumb use a comma to break up a sentence so that when spoken out loud it sounds correct. o Place a comma before the conjunction in an independent clause. “Our fuel was running out, but there was still enough left to finish the race”. o Phrases. Separate a phrase within a sentence by placing it between two commas. The phrase can be omitted and the sentence should still make sense. “The appearance of new diseases, and the resurgence of old ones, makes the case for interdisciplinary involvement even more pressing”[1]. o Commas or not before “and”. As a rule of thumb add a comma if the “and” introduces a new topic. “I played football this afternoon and scored a goal” “I played football this afternoon, and had a lift home” o Too many commas tend to confuse. Consider this sentence which discusses the prevalence of Tuberculosis in New York; “Control of the W-strain of the disease, which first appeared in the city in 1992, is resistant to every available drug and kills over half of its victims, has already cost more than $1 billion.” [1] This is hard to follow on first reading and should probably be split into two. An alternative could be, 27

“Control of the W-strain of the disease has already cost more than $1 billion. It first appeared in the city in 1992, kills over half of its victims, and is resistant to every available drug”. (k) Set formats: Some words almost invariably come in pairs. either … or , neither … nor , not only… but also. (l) Plurals o The word “data” is plural, “datum” is singular. o Plural-singular subject – verb agreement. Sometimes the correct version seems to read awkwardly. “The number of possible mistakes is large” is correct, whereas writing “are large” is not because number is singular. o Apostrophe “s”. If the word does not end in “s”, not only is the apostrophe added but also the “s”. If the word already ends in ”s” only the apostrophe is added. “Peter’s hat is red”. “The government has wasted £150m of taxpayers’ money” (m) Split infinitives. The most famous is the Star Trek “to boldly go”; this expression seems more natural nowadays than not splitting the infinitive by writing either “to go boldly” or “boldly to go”. [1] Murray. Mathematical Biology. Publ. Springer Verlag 2002.

Laboratory Books. The way in which you report result in your lab books should first be discussed with your supervisor. Preferably one of the models outlined in detail by other research sections should be followed. These are described in other sections of this booklet. If you work is likely to lead to patents then it is important to date and sign each page and to cross out, with a line, any blank spaces on each page so that there can be no question of information being added at a later data.

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Information for students in the Organic Section

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Some of this material is specific for PhD students; however general guidelines, such as those on report writing apply to all students carrying out research in the organic chemistry laboratories. Keeping a laboratory notebook Laboratory notebooks are formal documents, and remain the property of the University after submission of your PhD. They will provide the basis of your experimental section of your thesis, and so are extremely important to your future as a chemist. It is expected that you adhere to the following guidelines on the maintenance of your notebooks: • They should be kept neat and tidy • They should contain all the necessary information to enable a competent synthetic chemist to be able to reproduce the experiment • Details should be written directly into your lab book, not on scraps of paper to be transferred at a later date. • The amounts of each reagent and solvent used should be clearly specified; if solutions are used, the volumes, solvent and molarity should be stated (e.g. 1M nBuLi in hexanes, 1M HCl (aq) etc.). The source of a starting material should be given (e.g. prepared in experiment number 23) in case of batch variation. The number of mmol, the molecular weight and the volume or mass of each reagent should be provided. For extraction procedures, you should specify the volume of solvent used. • You should not use pencil • You should not obliterate any details • You should reference each experiment to a COSHH assessment (and reference each COSHH assessment back to an experiment number). COSHH assessments should be completed and signed before attempting experiments. • Your should provide a clear sketch of tlc plates, specifying the R f of each component and the composition of the solvent system used. Retention times and methods (column type, solvents, temperature) for analytical HPLC and LC-MS should be provided. Postgraduate lectures Throughout the first year, you will be expected to attend a series of postgraduate lectures within the Department; the most appropriate lecture series should be chosen in conjunction with your supervisor during the first week of term or earlier. A separate handbook for these will be provided. It may be appropriate to substitute departmental postgraduate lecture series with other scientific courses; in this event, you should agree in advance with your supervisor and Prof. Rayner how many postgraduate lecture courses the external course is deemed to substitute. You are expected to make notes on the lectures attended in a hardback notebook. The hardback notebook, with notes on the postgraduate lectures, courses and seminars attended, should be submitted to Gail Cole with your PhD transfer report. In the event that the lecturer provides an extensive handout on a lecture series, you should submit your annotated version of the handout to Gail Cole. Your supervisor may elect to substitute up to three of the postgraduate lecture series with literature reviews which are not directly related to your research project. In this event, you should prepare a one-page summary of the topic(s) concerned. Departmental colloquia and seminars It is expected that you attend the colloquia and seminars which are organized within the department. The aim of these sessions is to broaden your scientific knowledge by exposing you to work outside your ‘comfort zone’. Your supervisor may require you to attend 30

additional seminars both within the department and more widely; for example, the monthly Astbury Centre seminar series will be relevant to many students, particularly those with interests in Chemical Biology, or seminars in Engineering for those with interests in Process Chemistry or Energy research. You should include a list of seminars attended with your first year transfer report.

Reports All reports will be read by your supervisor and your internal assessor. You will be required to submit a revised version if reports are judged to be below an acceptable standard. Details of the reports required are listed below, and guidelines for report preparation then follow. Reports for PhD students. 1. Four month report The report should include a literature review summarizing the background to your project (ca. 15-20 pages). You should consult your supervisor on the content of the literature review. In addition, you should provide a short commentary (1-2 pages) on the initial goals of your project. The report should include a summary of the progress made on the project (4-5 pages). You should provide a list of objectives to be met before your next report is prepared (as a list of bullet points). Reporting experimental data effectively is an essential skill. You should, therefore, provide full experimental procedures for experiments performed. At this stage of the project, it is likely that your supervisor will need to be intimately involved in proof-reading your experimental section. It is expected that the experimental that you submit in this (and every) report will be of an extremely high standard (suitable for publication). Some guidelines on reporting experimental procedures are provided below and additional information can be found in authors guidelines for publication in any of the major chemical journals. In the case of larger peptides and proteins, it may be impractical to fully assign all resonances in an NMR spectrum, and a greater reliance will thus be placed on mass spectrometry to confirm the identity of the compound; you should talk to your supervisor about the level of characterization which would be appropriate. In such cases, some indication of purity should also be provided, for example HPLC or polyacrylamide gel electrophoresis data. Note that a Scheme usually consists of a reaction scheme (e.g. A to B with reagents etc.), whereas a Figure is usually a single structure or diagram. 2. PhD Transfer report and viva At the end of your first year, you will be assessed to determine whether you have made enough progress and have the potential to complete a PhD. This will be on the basis the reports submitted, results obtained, and your chemical knowledge in your specialist area and more general chemistry (e.g. that gleaned through postgraduate lectures, colloquia and seminars). You will need to collate the following documents in advance of the transfer viva:  First year transfer report following the guidelines below (submitted in advance to Gail)  A sheet summarizing the postgraduate lectures and all seminars and colloquia that you have attended (submitted in advance to Gail)  Your 4 month report with comments from your Supervisor/Assessor (submitted in advance to Gail)  Laboratory notebooks 31

 COSHH assessments  Experimental data, including spectra  A hardback notebook with notes from postgraduate lectures, colloquia and seminars. In addition, any annotated notes taken in postgraduate lectures that you have attended. This first year viva is very important - your PhD transfer could be deferred, or in extreme cases, your studentship terminated if progress in any of these areas is unsatisfactory. Your supervisor(s), internal assessor and Head of Research Section will be present at your transfer viva. You will be asked to provide a 5-10 minute summary of your progress. Your reports will provide details of relevant background to your project, and the problems to be addressed in your PhD. Your three first year reports and the summaries of the postgraduate lectures and seminars attended (notes written in hard backed book), will form part of the assessment. You may be asked questions on your general chemistry background, the chemistry underpinning your project, and the postgraduate lectures and research colloquia that have attended. It is expected that the transfer report will:  include an introduction which has been updated and corrected from your first report (15-20 pages)  summarise the goals for your PhD project (2-4 pages)  contain a Results and Discussion section discussing all work undertaken in your first year (15-20 pages)  include a full Experimental section covering all of the experiments undertaken in your first year. It is expected that any deficiencies highlighted in previous reports by your supervisor and your internal assessor will have been addressed. The main body of the transfer report should be no longer than 30-40 pages plus a full experimental section. 3. 21 month report The format of the report is the same as the 6-month report. 4. 30 month report A full thesis Chapter, usually the Introduction. You are not required to prepare a progress report or an update on your experimental at this stage. You all have a good first degree and will have carried out final year projects which will have involved the preparation of a detailed report. What you learnt from that should be carried on in your PhD. Producing an accurate and detailed report is vital to your development as a PhD chemist – the quality of your reports is an indication of your level of professionalism as a chemist. Report content Read the guidelines of what is required before you start, and stick to them. Work should generally be written in the past tense, unless you are talking specifically about something you are going to do. Ensure that any statements you make are clear and justified, and can be proved to the level described either by your own work, or what is in the literature (give relevant reference).

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You should submit an advanced draft to your supervisor in good time to allow him/her to make comments, and you should then act upon them. However your supervisors should not be expected to correct or proof read basic English or any other obvious errors (e.g. subscript numbers in formulae, unclear/untidy diagrams, and schemes). If you know you have problems here then make sure you prepare everything well in advance. Note: Plagiarism is potentially very important in theses and reports. You should NOT copy any significant amounts of text in your reports, and ideally not diagrams either. Text in reports can easily become incorporated into other reports, papers, reviews, grants applications etc., and if it was copied it can lead to very serious problems for you AND your supervisor. Presentation. Use the same font and font size throughout the document unless there is a specific reason not to do this. Use bold and italic text sparingly for impact. Ensure spacing between words etc. is consistent (not too many or too few spaces). If necessary use the show formatting function (¶ symbol on toolbar) in Word to show how many spaces there are. Don’t waste paper. Don’t have large gaps in text – however double spacing is fine and recommended. Whilst spell check and grammar functions in scientific documents can lead to many ‘false positives’ you should still use them to ensure there are no trivial errors present (e.g. simple spelling mistakes). Use references extensively, particularly when you are discussing or relying on previous work in the literature. Schemes and Figures. Don’t confuse a Scheme with a Figure. A Scheme is usually a reaction scheme (starting materials, reagents over arrow, going to products), whereas a figure is usually a single diagram. The words Scheme and Figure begin with capital letters in the main body of the text even if they are not at the beginning of a sentence. If your diagram is just a single chemical structure on its own then it should just be referred to by a number (and is not a Scheme or a Figure). Don’t put schemes in boxes! You have never been told to do so before so don’t start now! Structures in Schemes should all be of consistent size (bond length/width) and arranged to minimise space. Ensure text is in the right direction (-OAc not -AcO). Reagents etc. above reaction arrows should be centred above the arrows and evenly distributed above and below. Give yields and/or selectivities when relevant to help the reader assess efficiency. Note when you have a specific complex, e.g. boron trifluoride etherate, you should use the specific symbol (bullet point from character code 2022, via Insert then Symbol command in Word), so BF3•OEt2, not BF3.OEt2. Be consistent with use of stereochemical bonds (dashes and wedges); consult your supervisor if you are unsure. If you really have no choice other than to scan/copy schemes, make sure the quality is acceptable. You should make sure that you reference the document from which a scheme has been reproduced or adapted. A list of schemes/figures is not required in reports. Number compounds throughout and in the order they appear in schemes. Do not start again half way through or miss any numbers out! In a lengthy document such as a thesis, it is possible to number within a particular chapter by preceding the number with the chapter number, e.g. 3.12 is the twelfth new structure in chapter 3. Mechanistic arrows on reaction schemes can look messy if they are not drawn very carefully. Bezier curves (available on ChemDraw using the fountain pen tool) look much nicer than half circles, and you get much greater control of where arrows start and finish. However when 33

mechanisms are obvious or unremarkable, arrows should be omitted (although you may wish to consult your supervisor on this). Latin words/phrases are given in italics. When abbreviations are used, the abbreviated word ends in a full stop (so use e.g. not eg; et al. not et al; Fig. not Fig ). in situ in vitro in vivo in silico vide infra vide supra via in vacuo i.e. (id est) et al. (et alia) e.g.

in the place in glass in life in silicon (obtained computationally) see below see above by the road (by way of) in a vacuum that is (to say) and others exempli gratia, for (the sake of) example

Non-standard abbreviations should be listed at the beginning of the report or thesis. Note a chemical formula (e.g. CDCl3) is standard so does not require listing. There are other common words which are often confused. For example ‘literature precedent’ (an example in the literature which suggests your reaction should be successful), NOT ‘literature precedence’ (which refers to a priority position or rank). Experimental Write up experimental accurately and in a manner such that a competent chemist can reproduce your experiment. It is all too common for students to be unable to reproduce work of previous students – this is often because inadequate experimental details were recorded at the time of the original experiment. Include initial introductory section stating what types of machines (NMR, MS, IR etc.) are used. This section also contains information about characterisation of compounds, any general purification methods used (e.g. to purify solvents). For preparative work, each experiment is usually headed by the full name of the compound (and the number used to refer to it in the text). If you use autonom to name your compound, it quite often is incorrect (e.g. naming silyl protected alcohols as silane derivatives) and includes many unnecessary hyphens. You should be familiar with most of the rules of nomenclature and use them to ensure the name you give a compound is sensible. You should check to see if any compound you have prepared has been made before using Scifinder or Beilstein.  

If it is a new compound then full characterisation should be obtained. If it has been reported before then the relevant reference should be given at the end of the name. Sufficient data should be gathered to confirm that you have prepared the same compound (a simple 1H NMR spectrum is not enough for this).

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Experimental procedures should be written in the style found in typical journals (e.g. OBS or JACS – but not both). They should be grammatically correct; capital letters should not normally be used other than at the beginning of a sentence (including names of compounds). Use a consistent and sensible number of significant figures when quoting reagent quantities (mass, mmol and/or ml). Proton NMRs spectra should be assigned wherever possible (with the necessary additional NMR experiments carried out to enable this). Reports with extensive use of multiplets will be scrutinised particularly carefully – this is an important part of confirming structure, and it is not simply enough to write down the raw NMR data. Chemical shifts are always quoted to 2 decimal places, coupling constants to 1 decimal place. Take great care is reporting data, e.g. dt should have 2 different coupling constants, with the doublet value first then triplet. Make sure the coupling constants are consistent with what would be expected. When solids are isolated, they should not be described as ‘white crystals’. Wherever possible you should try to be more descriptive, e.g. needles, platelets, cudes. Note crystals which appear white are actually colourless if you look at them through a microscope, so terms such as ‘colourless needles’ are most appropriate. Such crystalline compounds should generally be recrystallised (state solvents), and melting points quoted as a range, e.g. 95.1-96.3 ºC. Note use of degree sign available through Insert then Symbol commands in Word. Also note there is always a space between the number and the degree sign. Guidelines on compound characterization It is a fundamental obligation of all scientists that they publish in the open literature experimental details and data, which can be subsequently reproduced and verified. Therefore, it is essential that all students and post-doctoral associates provide experimental descriptions and data, which are clear, accurate and informative. The following notes are intended for projects with a strong synthetic component; the notes are intended as a guide for writing the experimental section of theses, reports, and papers. Some PhD projects in the Chemical Biology Research Section will not be dominated by synthetic chemistry. The experiments performed will still, of course, need to be rigorously reported. However, your supervisor will be able to provide advice on the format which is most appropriate to the experiments performed. Furthermore, the methods used to characterise certain classes of compounds and materials (for example complexes, small molecule libraries and polymers) will differ significantly from those used to characterise small organic molecules; you should ask your supervisor for advice on the level of characterisation that is appropriate in these cases. You need to make sure that you name your compounds correctly. Autonom can be a useful starting point for naming compounds. However, Autonom does over-hyphenate names, and often devises daft names (eg compounds with silicon protecting groups which are named as silanes rather than silyloxy-substituted skeletons). In addition, you must use stereochemical descriptors properly: ‘R’ and ‘S’ are used to describe enantiomerically enriched compounds. However, for racemates, the descriptors ‘R*’ and ‘S*’ are used to describe relative configuration; the convention is to name the enantiomer whose first descriptor would be ‘R’ ie (1R*,2S*) rather than (1S*,2R*). There should be a space between the number and the unit (e.g. 5 kJ), and also between 35

different types of units (e.g. 5 kJ mol-1). The origin of all non-trivial compounds cited in a scientific paper or thesis must be stated. You must take the trouble to look up every compound you report in Chemical Abstracts– however simple it may seem–and determine whether or not it is known. Note that Beilstein covers only a small fraction of the literature. Consider the following cases: Known Compounds–Citation of Prior Art If a compound is known, a reference to the original literature must be cited and the basis for comparison of your synthetic product with the data reported in the literature (IR, NMR, optical rotation, boiling point, melting range, etc.) must be made explicit. You should consult your supervisor on the data for known compounds to provided in reports. Many supervisors may not require a detailed experimental procedure if one has already been described; in such cases an experimental might read as follows: Compound X was prepared in 82% yield on a 25 mmol scale by the method of Corey and coworkers* and gave mp 125-127 °C (EtOH) [lit.* mp. 126.5-128 °C (EtOH)]. The product was identical by IR and 1H NMR spectroscopy (270 MHz) with the data reported. [* = a numeral superscript referring to a paper cited in the reference section of the paper or thesis]. You should be in a position to be able to provide evidence of the purity and spectroscopic properties of known compounds even if they are not reported. An external examiner in a PhD viva can justifiably request such information. If a compound is known but was prepared before the advent of, for example, high field NMR spectroscopy, you should provide any new data and cite the original reference and the basis for comparison. Some supervisors may require further characterisation details of known compounds to be included in reports and/or theses. If you have prepared a known compound by a new route or by a significant modification of a published route, you should provide complete experimental details. Although different journals have adopted different conventions regarding the reporting of experimental details and spectroscopic data, a "standard" experimental description is given in the appendix, which includes some useful tips on common problems. Characterisation of Novel Compounds Publication of research in theses and journals demands that the structure of all novel compounds be beyond reasonable doubt; i.e., the compound must be adequately characterised. This means that data should be cited which attests to purity, functional groups present (IR spectroscopy), the structure of the carbon skeleton (NMR spectroscopy and mass spectrometry), and elemental constitution (accurate mass measurements, combustion analysis). It is not possible to define precisely what methods will constitute adequate characterisation since the combination of methods will very much depend on the nature of the problem and the compounds under scrutiny. Many supervisors and students find the use of compound data sheets very helpful in ensuring adequate characterisation is obtained for each compound. A suggested template is provided at the end of this document. You will find it useful to keep one copy of each type of characterisation data for each compound in a folder. 36

The following comments are intended as a rough guide to characterisation. If in doubt, you should consult your supervisor. For comparatively simple intermediates in a synthetic route leading to a known compound whose identity can be proven by comparison of detailed spectroscopic data or other physical measurements (e.g., mp) the minimum acceptable level of characterisation would be IR spectroscopy (and UV if the molecule contains a chromophore), high field 1H and 13C NMR spectroscopy, and low resolution mass spectrometry on compounds purified by crystallisation or distillation wherever possible. Key intermediates in a synthetic route should also be subjected to accurate mass measurements in order to verify constitution. Because of expense, accurate mass measurements should not be sought for every compound or for trivial compounds. The problem of characterisation becomes more complicated with compounds whose origin is uncertain. For example a product derived from an unusual pathway or rearrangement or a natural product isolated from natural sources will require a wider range of techniques to define structure. In such cases accurate mass measurements and/or combustion analysis will be required because NMR and IR spectroscopy may not detect the presence of halogen atoms, sulfur, or metals and so greater pains must be taken to ascertain elemental composition. If a compound is enantiomerically pure, its optical rotation should be recorded. Citation of References. Accuracy of references is very important – you will realise this as soon as you have to find something that has been inaccurately referenced! Use a consistent format for your references. Details are given in the following section. List all authors. Et al. is not appropriate unless very long list of authors. Use proper journal abbreviations, and if words are abbreviated, they should have a full stop, e.g. J. Am. Chem. Soc. not J Am Chem Soc. Note that issue numbers (often shown in brackets in databases such as SciFinder) should not be included. Do not give the same reference two different numbers. Books require specific range of information to be referenced properly, including publishers, city and year (see below). Avoid using internet sites as references, including Wiki, unless essential. If they cannot be avoided then the full link and date accessed should be listed. The following is taken from the Royal Society of Chemistry web site, and should be used as the standard format unless your supervisor has advised otherwise. You are encouraged to use Endnote to format references for reports and theses, however any resulting errors will not be accepted as an excuse for inaccurate or unformatted references which would easily be identified by careful proof reading. Journals The style of journal abbreviations to be used in the Society's publications is that defined in Chemical Abstracts Service Source Index (CASSI). The abbreviations listed in CASSI are based upon internationally recognised systems. A list of CASSI-style abbreviations covering the most commonly cited journals is available from http://www.rsc.org/Publishing/ReSourCe/AuthorGuidelines/AuthoringTools/JournalAbbreviati ons/index.asp. It is not, of course, a full list; CASSI plus its quarterly supplements run to more than 2000 pages. If you cannot locate an authoritative abbreviation for a journal, and if it is not obvious how the title should be abbreviated, please cite the full title.

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Bibliographic details should be cited in the order: authors (initials then surname, with and between last two authors), journal (in italics), year, volume (in bold), page. Where possible, page number ranges are preferred over single values, but either format is acceptable. Where page numbers are not yet known, articles may be cited by DOI (Digital Object Identifier). e.g. A. R. Jones, Dalton Trans., 2005, DOI: 10.1039/B503459J. Books For example: J. Barker, in Catalyst Deactivation, ed. B. Delmon and C. Froment, Elsevier, Amsterdam, 2nd edn., 1987, vol. 1, ch. 4, pp. 253–255. Patents Patents should be indicated in the following form: Br. Pat., 357 450, 1986. US Pat., 1 171 230, 1990. Reports and bulletins, etc. For example: R. A. Allen, D. B. Smith and J. E. Hiscott, Radioisotope Data, UKAEA Research Group Report AERE-R 2938, H.M.S.O., London, 1961. Material presented at meetings For example: H. C. Freeman, Proceedings of the 21st International Conference on Coordination Chemistry, Toulouse, 1980. Theses For example: A. D. Mount, Ph.D. Thesis, University of London, 1977. Reference to unpublished material For material presented at a meeting, congress or before a Society, etc., but not published, the following form is used: A. R. Jones, presented in part at the 28th Congress of the International Union of Pure and Applied Chemistry, Vancouver, August, 1981. For material accepted for publication, but not yet published, the following form A. R. Jones, Dalton Trans., 2003, DOI: 10.1039/paperno. is used for RSC journals, and A. R. Jones, Angew. Chem., in press. is used for non-RSC journals. If DOI numbers are known these should be cited in the form recommended by the publisher For material submitted for publication but not yet accepted the following form is used: A. R. Jones, Angew. Chem., submitted. For personal communications the following is used: G. B. Ball, personal communication. If material is to be published but has yet to be submitted the following form is used: G. B. Ball, unpublished work. Reference to unpublished work should not be made without the permission of those by whom the work was performed. Names The surnames and initials of all authors are always given in the reference; they must not be replaced by the phrase et al. This does not prevent some, or all, of the names being mentioned at their first citation in the cursive text: initials are not necessary in the text. Composite references

38

Whenever possible, composite references should be used rather than a series of individual references. The style for composite references is as follows: A. B. Jones, J. Am. Chem. Soc., 1956, 78, 1234–1246; A. B. Jones and C. D. Brown, J. Am. Chem. Soc., 1957, 79, 567–569; A. B. Jones and E. F. Green, J. Am. Chem. Soc., 1957, 79, 999–1048. Idem, loc. cit., and op. cit are not used in references. IV. Combustion Analysis, Accurate Mass Measurements and the Problem of Purity The role of combustion analysis in compound characterisation is a cause of considerable controversy. Many believe that combustion analysis should be secured for all new compounds and some journals are chary of publishing papers devoid of combustion analyses. The argument frequently put forward is that combustion analysis is a stringent test of purity, and therefore, experimental technique. This assertion is only partly true since high field NMR spectroscopy frequently reveals impurities in compounds, which give correct combustion data (i.e., C and H analyse to within 0.3% of theory). Moreover, high field NMR spectroscopy can distinguish isomeric impurities, which go undetected by combustion analysis. A good illustration of the limitations inherent in combustion analysis for the determination of elemental composition comes from the structure elucidation studies on mangostin-a pigment isolated from the mangosteen tree [see P. Yates, Structure Determination, W. A. Benjamin, New York, 1967, Chapter 2]. Several groups reported the molecular formulae for mangostin based on combustion analysis but as the calculated data in the table show, comparatively small changes in composition produce a wide range of potential molecular formulae-a problem, which magnifies with more complex structures. Formula

Mol. wt.

C16H16O4 C16H18O4 C20H22O5 C21H24O5 C23H24O6 C24H26O6

272 274 342 356 396 410

Calculated composition (%) C H 70.57 5.92 70.05 6.61 70.16 6.48 70.76 6.79 69.68 6.10 70.23 6.39

Another limitation frequently encountered with molecules containing a large number of heteroatoms (especially nitrogen) is incomplete combustion and special precautions must be taken in such cases. If NMR spectroscopy is to be used as the principal technique for assaying purity, the spectra must be devoid of contamination by solvent, stopcock grease, etc. Solvent contamination is a sure sign of sloppy experimental technique and therefore the results are suspect. External examiners are entitled to examine spectra during an oral examination in order to ascertain if data was acquired on compounds of adequate purity and they are entitled to reject a thesis on the basis of slovenly experimental work. Some journals now also demand the submission of copies of spectra for examination by referees. Most journals now accept high resolution mass spectra (HRMS) instead of combustion analysis data as an assay for elemental composition. HRMS is certainly more accurate but a compound may give a "correct" molecular ion even though it is a minor component in a 39

complex mixture. Therefore, HRMS must be used in conjunction with other techniques that provide an accurate gauge of purity. Furthermore, a pure compound may not give a molecular ion at all in which case HRMS measurements can only be made on fragments. In summary, combustion analysis remains a fairly blunt instrument and compared with the combination of NMR and HRMS, it conveys comparatively little useful information. Nevertheless, there are many advocates of the technique who may query the absence of combustion analyses in theses and papers. In certain cases it has a useful role to play in the characterisation of new compounds and it should be used when necessary. Your supervisor should be consulted about specific cases. In the absence of any other criteria, we suggest that combustion analyses be obtained for all crystalline compounds at least. The following statement taken from the Instructions for Authors (1990) of J. Chem. Soc., Perkin Trans. 1 is an example of 'official' policy: Referees will assess, as a whole, the evidence in support of the homogeneity and structure of all new compounds. No hard and fast rules can be laid down to cover all types of compounds, but evidence for the unequivocal identification of new compounds should wherever possible include good elemental analytical data; an accurate mass measurement of a molecular ion does not provide evidence of purity of a compound and must be accompanied by independent evidence of homogeneity. Low resolution mass spectrometry must be treated with even more reserve in the absence of firm evidence to distinguish between alternative molecular formulae. Where elemental analytical data are not available, appropriate evidence, which is convincing to an expert in the field may be acceptable, but authors should include, for the referees, a brief explanation of the special nature of their problem.

IT IS THE RESPONSIBILITY OF ALL RESEARCH STUDENTS TO ENSURE THAT THEIR COMPOUNDS ARE CHARACTERISED TO THE STANDARD NECESSARY FOR PUBLICATION IN PEER REVIEWED JOURNALS.

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An example experimental, using the Royal Society of Chemistry guidelines is shown below. You should consult your supervisor about which format should be followed. (2R*,2′S*,3S*,7S*)-2-(2′-Furan-2-yl(-2′-hydroxyethyl)-3methyl-7-pentyloxepan-3-ol Me OH OH pent

H

O

H

“R” and “S” are in italics, but numbers are not. Where compound is racemic, use the asterisk sign after each chiral centre. Names for relatively simple structures can be obtained using Autonom The numbering in your NMR assignment MUST match the numbering in the compound name Use the “prime” sign and not an apostrophe (“Insert, Symbol”)

O

XX

Cerium chloride (13.1 g, 35.1 mmol) was added to a solution of the ketone XX (7.20 g, 23.4 mmol) in MeOH (430 mL) at 78 °C. Sodium borohydride (1.06 g, 28.1 mmol) was added

Numbers within brackets are given to the same number of significant figures. Use a space between number and units except % Minus sign not dash, and degree superscript “o” (“Insert, Symbol”)

sign

not

portionwise and the reaction mixture was stirred at 78 °C for 1.5 h and poured into saturated aqueous ammonium chloride solution (250 mL). The layers were separated and the aqueous layer extracted with EtOAc (3 × 300 mL), dried (MgSO4) and concentrated

to

give

the

crude

product.

Column

chromatography, eluting with 1:1 EtOAc–Petrol, gave the diol XX (6.24 g, 20.1 mmol, 86%) as pale yellow needles, m.p. 6973 °C (from Et2O–Hexane); Rf 0.29 (1:1 EtOAc–Petrol); (Found: C, 69.9; H, 10.00; C18H30O4 requires C, 69.6; H, 9.74%); H (500 MHz, CDCl3); 7.38 (1H, d, J 1.7, furyl 5-H),

Multiplication sign not letter x (“Insert, Symbol”)

Long dash for solvent mixtures not hyphen (“Insert, Symbol,”) Use italics to describe a novel compound Describe form of the crystals (e.g. “needles”, “plates” etc and not “solid” unless it is amorphous). Specify as “colourless” not “white”. If it is a literature compound, quote and reference the literature value. Micro: Carbons, nitrogens etc. are given to 1 d.p. and hydrogen to 2 nearest 0.05%. The % sign is only used once. Must be correct to within 0.3%

6.33 (1H, dd, J 3.2 and 1.7, furyl 4-H), 6.27 (1H, d, J 3.2, furyl

NMR: Chemical shift values are given to 2 d.p. but coupling constants are only given to 1 d.p. The letter J should be in italics.

3-H), 4.94 (1H, dd, J 8.0 and 5.1, 2′-H), 3.56-3.51 (1H, m, 7-H),

Ensure that mutual coupling constants match

3.44 (1H, dd, J 10.2 and 3.0, 2-H), 2.21 (1-H, ddd, J 14.2, 5.1 and 3.0, 1′-HA), 2.17 (1H, s, OH), 2.01 (1H, ddd, J 14.2, 10.2 and 8.0, 1′-HB), 1.81-1.74 (2H, m, 4-HA and 6-HA), 1.69-1.62

Give a chemical shift range for a multiplet (from high to low ppm) If you observe a broad signal write e.g. “br s”

(2H, m, 4-HB and 6-HB), 1.59-1.51 (2H, m, 5-HA and pentyl 1HA), 1.45 (1H, app dtd, J 14.0, 10.0 and 5.1, 5-HB), 1.40-1.34 (1H, m, pentyl 1-HB), 1.35-1.19 (6H, m, pentyl (CH2)3), 1.21 (3H, s, Me), 0.89 (3H, t, J 6.8, pentyl CH3); C (75 MHz, CDCl3); 156.4 (furyl 2-C), 141.9 (furyl 5-C), 110.1 (furyl 4-C), 105.9 (furyl 3-C), 84.8 (2-C), 82.4 (7-C), 75.2 (3-C), 67.3 (2′-C), 44.0 (4-C), 37.1 (5-C), 36.4 (pentyl 1-C), 35.9 (1′-C), 31.9 (pentyl 3C), 25.6 (pentyl 2-C), 23.4 (CH3COH), 22.5 (pentyl 4-C), 19.5 41

Note that the field strength for a carbon is different to that for a proton. 125 MHz for the 500 spectrometer and 75 MHz for the 300 spectrometer Carbon shifts are quoted to 1 d.p. Full assignment may not be possible but if possible DEPT data should be given for each signal. If necessary, use italics to clarify which carbon the signal is for. IR: Give method used and quote all sig. bands >1200.

(6-C), 14.1 (pentyl CH3); max/cm–1 (film); 3398, 2930 and 2859; m/z (ES) 333.2 (100%, MNa+); (Found MNa+, 333.2039. C18H30O4 requires MNa, 333.2036). Mass Spec: Give method used here, and details of equipment in the general experimental section. Include nominal masses (and %) of significant fragments in the mass spectrum. Accurate mass for one mass only.

This compound is racemic. However if an alpha-D was required, it would be quoted just before the NMR data, and would take the form: “[α] D20 +17 (c = 1, chloroform);”. The units are 10-1 degcm2g-1 and should be specified only in the general experimental. Give a reference for known compounds.

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COMPOUND DATA SHEET Compound data sheets are needed for all compounds

STRUCTURE Compound No.

Molecular formula

Stereochem Assignment

Molecular weight

CHECK LIST 1H

13C

mass

micro

i.r.

RF

m.p. app.

+ []D

NEW

high-res or micro

if opt. active

OLD

low-res

if opt. active

DATA 1H:

13C:

mass:

micro:

i.r.:

RF (with solvent system)

m.p. + app.

[]D (with c and solvent)

43

Information for students in the Physical Chemistry Section and Colour Science Section

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Guidelines for PhD students in the Physical Chemistry & Colour Science Sections 1. Keeping a laboratory notebook 1.1. Experimental projects Laboratory notebooks are formal documents, and remain the property of the University after submission of your PhD. It is expected that you adhere to the following guidelines on the maintenance of your notebooks:  



 



They should be kept neat and tidy. Label the volume number and the start and end dates clearly. They should contain all the necessary information to enable someone else to repeat your experiments after you have left. The experimental conditions should be very clearly stated. For example, the signal observed for a particular process may depend on many parameters (laser power, input range settings on amplifiers etc.), and in order to be able to return to optimum conditions, perhaps after a break in the experiment, the values of all parameters should be written down. Log books should be kept of the performance of major pieces of equipment (e.g. lasers), to facilitate diagnosis of faults. Details should be written directly into your laboratory notebook, not on scraps of paper to be transferred at a later date. Diagrams of the set up of the apparatus, or drawings submitted to the workshops, perhaps prepared on computer drawing packages, should either be affixed in the notebook, or cross-referenced to a ring-binder where these are kept. You should not use pencil nor obliterate any details As most results/data are written to computer disk, it is very important to clearly identify the filename used (a naming convention should be adhered to), indicate where the file is stored, and carefully note the conditions used for a given file (perhaps using a table). It is important to back the data up regularly, at least at the end of each working day. It may be sensible to automatically write the data to a second storage medium so that no data are lost if a computer crashes. Hard copies of key results should be kept in a ring-binder folder (or similar), carefully cross-referenced to the original experimental details in the lab. book. You should reference each experiment to a COSHH assessment (and reference each COSHH assessment back to an experiment number). COSHH assessments should be completed and signed (by you and your supervisor) before attempting new experiments. Risk assessments should be completed for each new experiment, making use, where relevant, of School approved safety protocols which are available on the Safety Web pages.

1.2. Theoretical projects. Although a laboratory notebook is not applicable, it is important to maintain a record of your activity, the precise form of which should be discussed with your supervisor. You should ensure that computer programs, data files, etc. and backed up regularly (daily). 2. Keeping up with the literature Being well informed of the latest advances in your field of study is of paramount importance. At the beginning of your PhD you will have discussed and agreed a Training Program / 45

Reading plan with your supervisor, and this will include those journals for which you should check the current contents (these can be emailed to you directly from the journal). You should reserve some time each week for reading the latest issues of journals in order to get into the habit of keeping up with current work. For highly relevant papers that you may wish to refer to in your written documents, the details should be entered into Endnote © or similar software. The Edward Boyle library still stocks print copies of the major journals, and you are encouraged to browse the current issues, it is amazing how you pick things up in this way. 3. Postgraduate lectures A series of postgraduate lectures is offered within the School, and you should agree with your supervisor which ones you should attend, in addition to any undergraduate lecture courses identified in your Reading and Training Plan, that you should attend. You should include a list of postgraduate lectures attended with your first year transfer report. 4. Departmental seminars It is expected that you attend departmental research seminars, and any ad hoc seminars by visiting scientists in your area. The aim of the seminars is to broaden your scientific knowledge by exposing you to work outside your expert area. Supervisors may wish to discuss with you the content of a recent seminar at the monthly supervisor meetings. Seminars you have attended may also be discussed at the First Year Transfer viva voce examination. 5. Reports Please see the School guidelines about the number of hard copies of each report that need to be submitted. All reports will be read by your supervisor and your internal assessor. You will be required to submit a revised version if reports are judged to be below an acceptable standard. Electronic copies of all reports must be handed in to Room G30 along with 2 or 3 hard copies, determined by the number of supervisors. Feedback will be given and recorded, and can be discussed in subsequent monthly supervisor meetings. Before embarking on a report you should consult with your supervisor, particularly with regard to length, and the time you are expected to spend on the report. It is important that the reports are well written and care is taken with your writing style, spelling and grammar. Do consult “Eats, Shoots and Leaves” by Truss or “Elements of Style” by Strunk and White, and refer to notes from your Scientific Writing course. Make sure due credit is given when you use the work of others, for example, if you use a diagram or modify it. 5.1. Four month report The report should primarily be a literature review summarizing the background to your project (ca. 20 pages). You should consult your supervisor on the content of the literature review, for example as to the fraction of material to include from the primary literature compared with from textbooks (the language of your project may be new and challenging, and so reading journal papers may at first not be appropriate). You should provide a short commentary (1-2 pages) on the initial goals of your project, and your plans over the next 3 months.

5.2. PhD Transfer report and viva At the end of your first year, you will be assessed to determine whether you have made enough progress and have the potential to complete a PhD. The assessment will be based be on the three reports submitted, progress in the laboratory or on specific theoretical/computational tasks, as well as on your knowledge of your specialist area and 46

more general topics in physical chemistry (e.g. thermodynamics, spectroscopy, kinetics), which will be probed during the viva. You will also need to bring your laboratory notebooks, your Training/Reading Plan, COSHH and risk assessments to the viva (they will be examined by the Head of Section), and a list of the seminars you have attended during your first year. This first year viva is very important - your PhD transfer could be deferred, or in extreme cases, your studentship terminated if progress in any of these areas is unsatisfactory. Your supervisor(s), internal assessor and Head of Research Section will be present at your transfer viva. If the Head of Section is either your supervisor or your internal assessor, then another member of staff will be present. You may be asked questions on the postgraduate lectures and research colloquia that you have attended. It is expected that the transfer report will contain (a) A one-page abstract, (b) A list of contents, (c) An introduction to your area of research, with appropriate reference to the primary literature, (d) A summary of the goals for your PhD project and how this will advance the field, (e) An experimental section which describes the apparatus you have used/constructed/developed, or the theoretical/computational methodologies used, (f) A results and discussion section, (g) Future plans for the remainder of the PhD project, and (h) a comprehensive list of references. The report should be substantive. The length of the report should be discussed with your supervisor, but is expected to be about 50 pages in length. 5.3. 21 month report The format of this report is similar in nature to that of the First Year report. The report will be read by the supervisor and internal assessor, and feedback will be given by your supervisor. The report should not repeat the introductory material or review of the literature, but should focus on results obtained during the 2nd year. The report could be based on a research paper that you have written based on your results (it should not be a paper that someone else has written but on which you are an author) – again this should be discussed with your supervisor. The length should be similar to that of the First Year report, namely ~ 50 pages. You will also present a poster at the end of the 2 nd year during the Postgraduate Conference, and this provides an opportunity for you to orally defend your work.

5.4. 30 month report You are not required to prepare a progress report or an update on your experimental work at this stage. Rather the report will involve writing a first draft of a full thesis Chapter. You should discuss with your supervisor the nature of this, but it is likely to be the experimental or introductory chapter. It may also be appropriate to submit a paper that you have written based on the results from your thesis work – again discuss with your supervisor. Feedback will again be given.

6. End of Year Three - Oral presentation at the Postgraduate Conference During your third year you will be required to give a 30 minute presentation at the Postgraduate Conference in front of staff and students.

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APPENDIX NOTES ON PREPARING YOUR REPORT Word Processing Use MS Word where possible. Customise this programme to make it quicker to use by adding icons onto the screen using the tools, customise commands and searching for what you want. Turn on the ‘spelling as you type’ and grammar checker. Make the default language UK English. Whilst the grammar checker is not perfect it does alert you to times when you miss verbs out of sentences or need to add commas. Set up a style for the main text and choose a suitable font and set paragraph spacing and tabs etc. To set up a style go to the menu bar then tools ,customise, commands, then locate styles in the format menu. Drag the style icon from the box and place into a menu bar. Close the customise dialog box. When you click on the style icon you can now modify whatever style you are using, say to ‘body text’ rather than ‘normal’. You can then define several different styles, one for figures, or for headings etc. To use numbering for figures, define a style with ‘numbering’ in the style dialog box its reference will appear in the cross-reference box under insert, reference, cross-reference. Next go to a place in the text where you want to insert a reference to a figure and click on the fig number in the cross-reference box and it will be inserted. The figure numbers will be undated automatically and kept in order. References The style of the reference should be that of one of the major journals such as JACS or Angewante Chemie. The references should be numbered in the text either as square brackets [2] or, preferably, as superscripts, Bloggs et al.2 The references should be numbered in order throughout the text and included at the end of the report. Use Endnote to keep consistent sequential numbering and accuracy of page numbers and so forth. Variables, Equations and Units (a) Variables are italicised in the text and in equations. Units are not italicised. “Assume the bond extends as an harmonic oscillator and use Hooke’s law; force  extension or f  k (r  re ) , where k is the bond force constant in Nm .” (b) Always use SI units. All measurable quantities have units so always include them. A unit is written with a space after the quantity 12.3 J or  1.0544  1034 Js . The unit is not italicised and spaces are not left between units. Reciprocal units are written as ms or K not m/s or 1/K. Degrees have the superscript circle ‘degrees symbol’ immediately after the number, and are only used for centigrade: as you are using SI units you didn’t need to know this because degrees Kelvin do not have a superscript circle after the number. (c) To insert equations use MathType. This allows you to rapidly construct equations and insert references on the same line as the equation as if in a journal or book. You can also insert equation references into the text and the numbering is automatically updated. If you only have a couple of equations use the MS equation editor provided with word, it is a cut down version of MathType. 48

eg “ if k1 and k2 are rate coefficients at temperatures T1 and T2 respectively show that  k  E T T  ln  2   a  2 1  .  k1  R  T2T1  Using equation (0.1) plot a graph …….”

(0.2)

Diagrams, Reaction Schemes, Graphs and Tables If you import diagrams from elsewhere do not to forget to reference where they came from. If they are not of a good enough quality redraw them using a drawing package. For simple line drawings the Word drawing package is suitable and easy to use. Reaction schemes Reaction schemes or structures should be imported from IsisDraw, Chemdraw and so forth and scaled to fit the text. The method of labelling of molecules and reaction conditions should be discussed with your supervisor or taken from JACS or other high quality journals. The scheme should be labelled in a similar way to figures to allow easy reference from the text. Graphs Graphs should not be produced using Excel; the quality of these graphs is almost never good enough for a professional document and you will normally be asked to redraw them. Use Origin, which is freely available on all computers in the University, or other commercial graphics / data analysis packages. Label both axes so that the axis is dimensionless, this means that the label is written as shown below. The temperature is divided by the unit to make the axis dimensionless, similarly for the pressure. Adjust the number of tick marks on the scale to suite the purpose of the graph and label the graph as appropriate. Do not use different colours to differentiate lines as these are often indistinguishable when reproduced and also fade with time. Use different line styles, dots, dashes, and labels to distinguish where there is ambiguity. There are plenty of examples in the literature, choose a style that you find clear. liquid solid

vapour

Tables The contents of tables are numbers and are dimensionless, as with graphs, so that the headings are divided by the units. For an example see experiment 0 in the first year physical chemistry lab.

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Grammar Get hold of a copy of Strunk and White “elements of Style” (£5), an invaluable book which includes some gems on how to write. You can easily look up points of grammar. “Eats, Shoots and Leaves” by Truss is a good rant about grammar and also an amusing book to read. Additionally, read the notes from your Scientific Writing course. When you have finished a section of writing, read it through and remove unnecessary words. Leave it for a day and re-read; you will usually find many things to clarify that you did not originally see. Avoid the first person, “I did this” or “I did that”, for example “I did these experiments using an FTIR spectrometer and then I did other experiments on the 400 MHz NMR instrument”, does not read well. “We did this“ and “we did that” sounds better but is odd as it is only you who has done the work. It is better to write something along the lines of “The experiments were performed using an FTIR spectrometer and the 400 MHz NMR”. Summary (a) ”system”: this word can always be changed to “reaction”, “instrument” or something more specific. (b) “In order to”: Avoid this and rewrite the sentence. (c) “so that”: Remove completely and rewrite. Change “So that the reaction could be completed acid was added” to “The reaction was completed by adding acid”. (d) “since” and “as”: Remove “since” and replace with “because” unless “since” refers to something happening in time. “As” is used colloquially but it is usually better to replace it with “because”. “It has been a long time since I saw you”. “Since the solution was acidic, base was added” or “As the solution was acidic, base was added”, should be changed to “Because the solution was acidic…”. (e) Semicolon “;” and colon “:” Use the semicolon to emphasise a phrase that is a consequence of the first part of the sentence. Use a colon in a similar way when the two statements do not need separating into two sentences with a full stop. “Critically evaluate you work; include weak points as well as successes”. “Tuberculosis is still a major killer in the world; between 1990 and 1999 approximately 30 million people have died from the disease” [1].

(f) That vs. which Use that' for restrictive clauses, e.g. "the grass that grows in your garden"; Use 'which' for descriptive clauses, e.g. "The grass, which is green, grows in your garden". 50

(g) However. “however” is surrounded by commas when used for emphasis: but see the next section. “There have, however, been a few cases of instant death from diphtheria and tetanus vaccines and there is much controversy about the vaccine for Anthrax for the military” [1]. (h) Avoid repeating a word in a sentence; it usually reads awkwardly. “However, although vaccines are generally extremely safe, no medicine is totally riskfree, however small the risk may be” [1]. Notice also the different meanings of however. (i) Lists. These are usually separated by commas. “As people in the west forget the ravages of polio, measles, diphtheria, rubella and so on, many will become less keen to have their children vaccinated because of the risk even if it is very small” [1]. “The symptoms of the progression of the disease are, among others, high temperatures, body filling with fluid, particularly the lungs, the apparent wellbeing of a person in the morning and death the same day or within a day or two”. [1] Notice here the use of the phase “particularly the lungs”, see below. (j) Commas. These cause more annoyance to some readers than almost anything else. As a rule of thumb use a comma to break up a sentence so that when spoken out loud it sounds correct. o Place a comma before the conjunction in an independent clause. “Our fuel was running out, but there was still enough left to finish the race”. o Phrases. Separate a phrase within a sentence by placing it between two commas. The phrase can be omitted and the sentence should still make sense. “The appearance of new diseases, and the resurgence of old ones, makes the case for interdisciplinary involvement even more pressing”[1]. o Commas or not before “and”. As a rule of thumb add a comma if the “and” introduces a new topic. “I played football this afternoon and scored a goal” “I played football this afternoon, and had a lift home” o Too many commas tend to confuse. Consider the sentence which discusses Tuberculosis in New York; “Control of the W-strain of the disease, which first appeared in the city in 1992, is resistant to every available drug and kills over half of its victims, has already cost more than $1 billion.” [1] This is hard to follow on first reading and should probably be split into two. An alternative could be, “Control of the W-strain of the disease has already cost more than $1 billion. It first appeared in the city in 1992, kills over half of its victims, and is resistant to every available drug”. (k) Set formats: Some words almost invariably come in pairs. either … or , neither … nor , not only… but also. (l) Plurals 51

o The word “data” is plural, “datum” is singular. o Plural-singular subject – verb agreement. Sometimes the correct version seems to read awkwardly. “The number of possible mistakes is large” is correct, whereas writing “are large” is not because number is singular. o Apostrophe “s”. If the word does not end in “s”, not only is the apostrophe added but also the “s”. If the word already ends in ”s” only the apostrophe is added. “Peter’s hat is red”. “The government has wasted £150m of taxpayers’ money” (m) Split infinitives. The most famous is the Star Trek “to boldly go”; this expression seems more natural nowadays than not splitting the infinitive by writing either “to go boldly” or “boldly to go”.

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Introduction to Intellectual Property Rights What is intellectual property (IP)? A rather grand definition given to inventions (whether patentable or not), registered designs, design rights, test results, reports and copyright material (written computer software) and technical know-how arising from any work you do. Basically, your work may be far more valuable than you think. You may have found a quicker, cheaper or more effective way of doing something or produced a set of results which, although you might not find that exciting, someone else may find invaluable. So, in order to protect this new found knowledge or idea (your IP) you can obtain protection, giving you the right to stop others exploiting it and making money or taking the credit themselves for your work. Types of protection available:     

patents - machines, products and processes designs - the outward shape or decorative appearance of a product trade marks - identification symbols/ words copyright - written work, music, art, sound recordings, films and computer programs confidentiality

Patents and Trade Marks cost money to file BUT Copyright, Design Right and Confidentiality are FREE!

Patents There are three questions which are always asked about an invention and if you can answer "yes" to all three, your invention is patentable:   

Is it a new idea? Is it inventive? (and not discovered) Is it capable of industrial application?

Designs The outward shape or decorative appearance of products can be protected by design rights or registered design depending on how valuable the design is:  

registered design - gives stronger protection and must be filed at the patent office design right - weaker but automatic protection, no need for registration

Trade Marks Provide protection for the goodwill and reputation of your firm in its products and services by way of an identification symbol or words. These trademarks prevent any other party from selling a product under your name. Copyright 53

Gives you the right to control exploitation and cover copying and any type of publishing and performing of your work although some invariably slip through the net. Confidentiality You may not wish to protect your IP using the above methods, but can you keep it confidential by requesting that any party wishing to talk to you about it must sign a confidentiality agreement which allows them to find out what it is but preventing them from using it without an agreement. This may lead to the party providing additional funding to further develop your IP. It is difficult however if that confidential information leaks out, to prove who the guilty party is, but it does provide an adequate barrier. Exploiting your ideas Once you have protection you should map out an exploitation plan, so you can make the best use (and the most money) out of your invention. Ask yourself these questions:      

Can I effectively exploit this idea on my own? Have I got the time, money and facilities to effectively exploit it? How much will it cost? Where am I going to find the money? Can I afford it? Who am I going to sell/licence it it?

The most likely option for you is to find an interested party, probably from industry who could profit/benefit from your invention. Under licence or assignment of the invention, they could fund further research and pay all the fees! (for a cut in the profits). Your position as an employee or student at the University of Leeds Any IP generated whilst carrying out your duties or during your employment at the University is legally owned by the University although by law you are the named inventor. The University can provide protection for your idea and will negotiate with interested parties for you and give valuable advice on how to make you millions ... or at least hundreds! We initially take on all the costs with the assumption that once you find an interested party(s) and commerical exploitation is successful, those costs will be reimbursed and the royalties divided amongst the inventor(s), your School and the University.

“Your IP will only work for you if you work for it.” Frances V Cameron, Research Support Unit

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Use of Computer Systems University and School IS/IT facilities are provided for operational and research purposes. Occasional and reasonable personal use of these facilities is permitted provided that such use does not interfere with the work performance of the employee or the productivity of other staff, and is wholly compliant with legislative requirements and all institutional IT and IS rules and regulations. See University of Leeds IT for further details. Getting help IT staff are based in room G.52b. Please note that all IT jobs should be submitted via the form which can be found at www.maps.leeds.ac.uk/ITsupport. Staff are happy to discuss issues and provide advice however users will be asked to submit jobs for tasks arising from discussions. Appropriate use Departmental IS/IT facilities must not be used in an illegal or malicious manner, including, but not exhaustively, the following activities, many of which could result in legal action or civil proceedings being mounted against either the individual, The University, or both:  the creation or transmission of any offensive, obscene or indecent images, data or other material, or any data capable of being resolved into obscene or indecent images or material;  the transmission or downloading of material, including music, games and software, which infringes the copyright of another person or causes undue traffic on the University network;  attempting to gain deliberate access to facilities or services which they are unauthorised to access;  initiating or participating in the sending of chain letters, ‘junk mail’, ‘spamming’ or other similar mailings. The following conditions apply specifically to computing facilities supported by the Faculty IT team.  All computers and peripherals should be purchased through the IT team or with their approval following discussion.  Users must not change settings in their operating system or PC BIOS without consultation with the IT team. In particular, system passwords should not be set in BIOS. Any non-standard settings which affect the running of the machine may prevent the IT team from supporting it.  Unlicensed software must not be installed. Users are responsible for ensuring that all software on their machines is licensed.  Users should not install or change hardware or peripherals without seeking advice from the IT team.  Access by the IT team to PCs in staff offices will normally be by arrangement with the member of staff concerned. However, the IT team have the right to access any machine at any time should the need arise.  Users are responsible for ensuring that all user files on their machine are organised in such a way as to be obvious to IT team personnel.

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Electronics Support in Chemistry Information on the Services Offered by the Electronics Workshop

Research in the School of Chemistry, as in many areas of science, is becoming increasingly dependent on specialised electronic equipment. There are many pieces of electronic equipment such as NMR spectrometers, mass spectrometers, X-ray diffractometers and many computers being used in the School of Chemistry. Many are used for controlling experimental apparatus and others are used for capturing and analyzing experimental data. We provide electronic support for this equipment in research and in teaching. Services Provided 1. Design and construction of specialised electronic equipment. Examples are: Hardware for computer controlled data acquisition systems, interfacing to PC's, temperature control systems, amplifiers, low and high voltage power supplies, stepper motor positioning systems, electronic safety systems, signal conditioning electronics etc. 2. Software Software is developed for computer controlled data acquisition systems. 3. Repairs We provide a repair service for most electronic laboratory equipment, computers, computer peripherals etc. 4. Electronic Components Stores We stock a variety of electrical and electronic consumables such as batteries, plugs, fuses, cables, thermocouples, meters, resistors, capacitors, semiconductors, PC keyboards, mice, power supplies, fans, various PC cards, printers, scanners, monitors and PC upgrades Staff Mr Richard Oliver, [email protected] Mr Andrew Price, [email protected] Mr Phil Thornton, [email protected] Mr Steven Teesdale, [email protected] Room number B37j Phone number 36556

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Mass Spectrometry Services

Welcome to the Mass Spectrometry Facility in the School of Chemistry at the University of Leeds. Our service can provide the analysis variety of compounds including organics, organometallics, oils, fuels, small polymers, sugars and dyes. The following techniques are available for routine analysis: Production of Low Resolution Mass Spectra using the following ionisation techniques: 3. LC-MS[Coupled Liquid Chromatography-Mass Spectrometry] 4. Electrospray Ionisation [ESI] (positive and negative ions, mass range 200 to 3000 Daltons) Accurate Mass Measurement of selected ions with