Department of ChemistryTraining and Courses

Handbook for Postgraduate Research Students

September 2016

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CONTENTS

Page

1. iDTC training programme 3

2. Core Skills Training 4

3. Theme Specific Training 9

4. Techniques Training 14

5. Concepts: Level 1 21

6. Concepts: Level 2 31

7. Hot Topics 37

8. University of York Training 47

9. National Training 48

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Innovative Doctoral Training in Chemistry Programme

Year 1 Year 2 Year 3 Extended Registration

1-3 months

Becoming an Effective Research Chemist

Up to 2 Techniques courses as required for your project

Research project

Essential Chemistry Research Skills

Developing as a Professional Chemist

Level 2 Concepts Course

2 Hot Topics

Research project

Write PhD Thesis

4-12 months

Level 1 Concepts Course

Next stage

Write MSc by research thesis or continue to Year 2 of PhD / MPhil

Write MPhil thesis or continue to Year 3 of PhD

Write PhD thesis Submit PhD Thesis

This framework is a guide that spreads the course requirements throughout your programme. However, if you wish to complete your courses sooner, you may do so.

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INNOVATIVE DOCTORAL TRAINING IN CHEMISTRY (iDTC)

Through the iDTC, the Department of Chemistry offers a comprehensive programme of training for graduate research students. In addition to the theme specific courses available to you, you are also required to complete training in a variety of core Chemistry skills. A training package that incorporates both specific research skills as well as transferable skills will enable you to fulfil you full potential during your research degree, and enhance your employability.

1. CORE SKILLS TRAINING

Core training will continue throughout your research degree and under three main headings:

1. Becoming an Effective Research Chemist;2. Essential Chemistry Research Skills;3. Developing as a Professional Chemist.

Some of this training will be delivered in specific sessions, but a large part of it is inherent in your research degree so you will complete it as you progress through your studies. All PGR students are expected to complete Core iDTC activities.

Becoming an Effective Research Chemist

Topic Year Details

Health and Safety: Responsible Research and Chemical Ethics

1 Compulsory safety training for all students outlined on page 7

Introduction to your research degree

1 Delivered by the Chair of the Chemistry Graduate School, this session will explain the structure of your higher degree course

Research Integrity: parts 1 and 2

1 All new research students are required to complete the Research Integrity Tutorial. These compulsory sessions will provide advice and guidance.

Employability and Professionalism

1 Induction session for all students. A high standard of professional conduct is expected from students during their studies and future career. This session will look at opportunities to develop those skills essential to a successful career and how to record your experiences

Searching scientific Literature and Databases

1 Induction session introducing you to the library and database facilities.

Time Management, Planning and Motivation

1 Induction session. A research degree is very different to your undergraduate degree. This session will provide advice on managing your time, juggling the many demands of carrying out research, as well as motivational tips to help you through those times when things may not go to plan.

IT Skills Awareness 1 The University offers a comprehensive range of training on a variety of IT programmes. This session will introduce you to the tools and training that may be of most use to you during your research degree.

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Research Data Management

1 Research data management is an increasing important skill as science becomes more data driven. It is also required by the university and most funders. In this session you will learn how to plan your data management through the course of your project.

Graduate Teaching Assistant Training

1 The GTA training course focuses on training you to teach practical chemistry to undergraduate students. The training aims to develop skills aligned with the Researcher Development Framework. Such skills include communication, consistent assessment and providing excellent feedback (both verbal and written) allowing our undergraduate students to continually improve their skills in chemistry. This course utilises methods to promote active learning, which we encourage you to apply to your own teaching practice. Further details on page 8

Preparing TAP reports 1 TAP meetings should take place every six months and you will be required to pass annual progression points at the end of each year of your programme. You will need to provide a report on your work for each meeting and this session provides advice and guidance what you need to include.

Equality and Diversity 1 The Department of Chemistry strives to promote a culture of equality which allows all staff and students to contribute fully, to flourish, and to excel. This session provides an introduction to equality and diversity issues, in particular the underrepresentation of women in STEM subjects, the role that unconscious bias plays in our decision making and ways that we can all contribute to create a supportive and egalitarian environment.

Outreach Opportunities 1 As scientists, we have a responsibility to share our enthusiasm and knowledge with an interested and engaged public through the written and spoken word. However, conveying complex ideas to audiences of non-specialists can be challenging; this session will look at how to overcome these challenges, and the outreach opportunities available at York.

Becoming An Effective Researcher – online tutorial

1 Research students are expected to complete this tutorial which provides information on the skills training and support available at University level. It is intended to encourage research students to reflect on their development as professional researchers.

Sections seminars, departmental seminars and graduate seminars

All Seminars are an excellent means of broadening your scientific knowledge and awareness. The Departmental seminar programme includes prominent speakers with acknowledged expertise in their area. You should aim to attend all departmental seminars, as well as those seminars that are specifically for your group/area. The Graduate Research Seminars provide an opportunity for research students to present their work to fellow students.

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Essential Chemistry Research Skills

Topic Year Details

Poster preparation / presentations skills

1 Posters are an essential mechanism of communicating your research as well as being a great aid to networking at conferences. This session will look at what makes a successful poster and will help prepare you for departmental poster events as well as external opportunities

Preparing Scientific Papers

2 You will write a publication based on your research in the style of Chem.Comm. These papers are reviewed by another student then by a member of staff to comment on English, style and scientific content.

Oral presentation skills 2 It is important that you are able to communicate your work to a range of audiences. This session will look at some of the key skills required to present your work effectively.

Preparing to write your thesis

3 Producing a thesis is a significant part of a research project and it is essential to follow the University guidelines. This departmental session aims to advise you on the process of preparing your thesis and how to manage your time during this period.

There are also other University course available:Creating Your Thesis Using Word is run by RETT and provides some general guidance on thesis writing.

Thesis Essentials with Word is run by IT services (http://www.york.ac.uk/it-services/training/ ) and provides hands-on training on the features of Word that are most important when writing a thesis. Even if you cannot attend the course, the workbook is available online: http://www.york.ac.uk/it-services/training/materials/thesis/

Developing As a Professional Chemist

Topic Year Details

Presenting Posters 2/3 In addition to presenting posters at conferences, there are also opportunities in the Department. At the start of Year 2, you will be required to prepare a poster about the first year of your research for an informal poster session. In Year 3, you will also be required to participate in a more formal poster competition.

Career Planning and Opportunities

2 The Department runs a number of careers events focussing on both academic and non-academic careers. This workshop provides an opportunity to think about future career plans and what steps you might take to develop the necessary skills and experience

Finding and Applying for Jobs:Part 1: CV GuidancePart 2: Interviews

3 To help you prepare for applying for jobs at the end of your course, there are sessions on finding and applying for jobs, CV preparation and interview techniques.

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Networking 3 Networking is an important skill for a variety of career paths. This event will provide you with some advice and tips, and give you an opportunity to practice your networking skills.

Prepare a Grant Proposal 3 Advice and guidance will be given on how to construct a grant proposal including tips on information to include and how to tailor your proposal to suit the funder.

Attending and Presenting at Conferences

2/3 Conferences provide opportunities for you to develop a number of vital skills such as networking and presenting. The Department can provide some financial support for students to attend conferences in order to develop these skills and gain experience of presenting your work to a large audience.

Supervising undergraduate projects

3 It is likely that undergraduate project students may be based in your supervisor’s lab. Mentoring and supervising an undergraduate student can provide you with valuable transferable skills.

Presenting your Research All There are numerous opportunities throughout your degree for you to present your work to others. This can be internally at Graduate Research seminars or group meetings, or on a larger scale at conferences.

Health & Safety: Responsible Research and Chemical Ethics

The aim of this course is to help students develop their ability to work in a responsible, ethical and professional manner, both during their studies and in later scientific careers. Topics to be addressed include:

Preventing Harm to You and Your Lab Colleagues Good Health and Safety

o Understanding and minimizing chemical riskso Being prepared for accidents and emergencies

Preventing Harm to People Beyond the Lab and the Wider Environment Good management of chemical waste Carbon footprint of lab workers Health & Safety, Green Chemistry and Green Toxicity

Preventing Harm to the Scientific Endeavour and the Wider Community Good Professional Academic Conduct by Minimising, for example:

o Plagiarism o Falsification o Fabrication

Good Lab Security and Dual Use of ChemicalsCourse outline

Health & Safety Understanding & minimizing chemical risks 5 lectures

o Fire Hazardso Explosion Hazardso Runaway Reactions Hazardso Toxicity Hazardso Protective Measures & Managing Risk

Departmental Health & Safety procedures 1 lectures Fire management and extinguishers 2 lectures & practical Demonstrating for Safety 1 lecture

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Environmental issues 1 lecture Chemical waste & carbon footprints Green Chemistry & Green ToxicityEthics Professional Academic Conduct 1 lecture & online tutorial Dual Use of Chemicals and Lab Security 1 lecture

ReferencesThe Hague Ethical Guidelineshttps://www.opcw.org/special-sections/science-technology/the-hague-ethical-guidelines/ Global code of ethics planned for chemists, E. Stoye, Chemistry World, 23 May 2016http://www.rsc.org/chemistryworld/2016/05/global-ethics-code-chemists-safety-conduct-sustainabilityGlobal Chemists’ Code of Ethicshttps://www.acs.org/content/dam/acsorg/global/international/scifreedom/global-chemists-code-of-ethics-fi-2016.pdf Scientific misconduct: a new approach to prevention, M. Nylennaemail, S. Simonsen, Lancet, 367, No. 9526, p1882–1884, 2006 DOI: http://dx.doi.org/10.1016/S0140-6736(06)68821-1

http://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(06)68821-1.pdf

Graduate Teaching Assistant (GTA) Training

The GTA training course focuses on training you to teach practical chemistry to undergraduate students. The training aims to develop skills aligned with the Researcher Development Framework. Such skills include communication, consistent assessment and providing excellent feedback. The programme includes:

Introduction to GTA training, Safety lecture, tour of the laboratories Communications workshop Assessment and Feedback workshop Reflections Workshop Hands-on sessions in the lab – two with your allocated mentor and two independent

For those students whose first language is not English, you may also be interested in a course run by our Researcher Excellence Training Team on English language and communications workshops for internationally recruited Postgraduates Who Teach.

This course is intended for internationally recruited postgraduates who are preparing to teach university students. The course aims to increase participants’ spoken confidence levels and to enhance interactions between participants and the students they teach.Further details can be found on Skills Forge: www.skillsforge.york.ac.uk The course number is RDT2100.

Resources on the Virtual Learning Environment (VLE)

The will be some additional materials available on the VLE for some of the courses available. All students have access to the VLE: https://vle.york.ac.uk/ Look at the left hand menu and select Chemistry Postgraduate Training and Courses.

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2. THEME-SPECIFIC TRAINING

In addition to the Core Chemistry Training that all graduate students are required to complete, there is more specific training available that aims to enhance your skills in your own research area. The courses are theme specific, but you can choose to take courses from outside of your theme if they are more relevant to your research. This section of the Handbook will explain the courses that are available and the themes they fall under – some courses are appropriate to multiple themes.

Research themes:

Healthcare and Medicinal Synthetic Chemistry (HMSC) Sustainability and Green Technologies (SGT) Functional Materials (FM) Atmospheric Chemistry (AC) Analytical and Data Analysis (ADA) Spectroscopy, Computation and Simulation (SCS)

Although some courses are more suited to particular themes, you should not feel restricted by your theme. You should discuss the courses with your supervisor and agree which courses are most relevant to you. You can then sign up for courses you wish to attend using Skills Forge: https://www.skillsforge.york.ac.uk/york/index.jsf

Timetables for graduate courses can be found on the Google Drive, accessible from your University email account.

Some courses are organised by other departments and will therefore need the agreement of both your supervisor and the course organiser for you to attend.

Techniques Training: usually taken in Year 1, techniques training is to familiarise you with the theory and operation of equipment that you will need to use in order to carry out your research. You should attend any techniques training required for your research project.

Concepts courses:Level 1: Underpinning Research: these courses are usually taken in Year 1 and provide a general knowledge for non-specialists in that area. All students should aim to take at least one of these courses.

Level 2: Advanced concepts: these courses are usually taken in Years 2 as they will delve deeper into a subject to a more advanced, specialist level. PhD students should aim to take one of these courses in year 2 or 3.

Hot Topics:These courses are taken in Years 2 or 3. They aim to discuss cutting edge chemistry research in a number of important areas and help to broaden your knowledge of the latest significant advances in literature. Students should aim to take two of these courses over these courses of their PhD.

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The iDTC research themes are:

(a) Healthcare and Medicinal Synthetic Chemistry (HMSC)

The interface between chemistry and biology is one of the most important areas of science in the 21st century. Established technologies such as pharmaceutical and medicinal chemistry are being joined by emerging areas such as chemical and synthetic biology in the search for effective and sustainable solutions to challenges in healthcare, energy and materials science. The Healthcare and Medicinal Synthetic Chemistry theme brings together Departmental research strengths in organic and inorganic synthesis, their application to pharmaceutical chemistry, and the knowledge and techniques involved in the preparation and study of biological molecules. It is therefore designed to provide a broad, interdisciplinary background for all students working at the chemistry-biology interface, with the flexibility to allow students to focus on one or more aspects within the lifetime of their PhD.

In addition to the number of courses offered within Chemistry, students interested in biological topics may also like to investigate the possibility of further graduate courses offered within the biology department. Attendance at such course would need to be done in consultation with both your supervisor and the course organiser:

http://www.york.ac.uk/biology/postgraduate/

(b) Sustainability and Green Technologies (SGT)

There is increasing pressure in industry for companies to become more sustainable by developing environmentally friendly products, minimising waste, using renewable resources, and to maintain cleaner processes throughout. This focus on “Green Chemistry” is a key feature of the Sustainability and Green Technologies theme. The Department runs a taught MSc in Green Chemistry and Sustainable Industrial Technology. Lectures are delivered by academics at York, as well as experts from other institutions; PhD students will have the opportunity to attend these lectures and enhance their knowledge of this exciting and rapidly developing area. Level 1 lectures will provide an introduction to the key principles of green chemistry before considering other factors such as the control of environmental impact, alternative reaction media as well as catalysis in green chemistry. Level 2 lectures will cover topics such as clean synthesis, renewable resources, energy efficiency, and clean chemical technology.

(c) Functional Materials (FM)

On the Functional Materials theme students will acquire knowledge in Materials Chemistry, including the areas of Soft Matter, Inorganic Materials and Nanoparticles, underpinned by the general concepts of Self-assembly, Supramolecular Chemistry, Physical properties and Nanochemistry. This area of the iDTC will encompass courses in Thermotropic Liquid Crystals (synthesis, characterization and thermal behaviour), Lyotropic Liquid Crystals, Inorganic nanoparticles, Gels, polymers and dendrimers. Students will learn about the characterization techniques that support knowledge in this area, including thermal behaviour, spectroscopic characterization and imaging techniques.

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(d) Atmospheric Chemistry (AC)

Air pollution is a serious health issue in the UK, with an estimated 2.5 - 8 % of deaths linked to air pollution, reducing the average person’s life expectancy by ~7 months and costing the UK economy around £16 billion per annum (AQEG). The key drivers of health effects in humans are exposure to particles and ozone. The levels of these species are in part controlled by emissions of nitrogen oxides (NOx) and volatile organic compounds (VOCs). In the Atmospheric Chemistry theme you will develop the skills required to identify, quantify, monitor and record the levels of these compounds in the laboratory or out in the field.

One of the key instruments used to measure VOCs is gas chromatography (GC). This technique is used widely across all areas of chemistry, for example in fuel analysis, reaction product yield determination or identification of unknown compounds. To get the best results, it is vital that students understand the theory behind GC but also develop the skills to allow them to maintain instruments and develop new methods. In this course you will learn about the day to day maintenance needed to successfully run a GC.

(e) Analytical and Data Analysis (ADA)

As a student on the Analytical Chemistry and Data Analysis theme, you will be introduced to the analytical chemistry facilities available in the Department and receive training on the submission of samples, data processing and interpretation. For those students using mass spectrometry as a central technique, a more in-depth study of instrument design and function will be available as a taught course. In addition to experimental techniques, students will receive training in experimental design, data pre-processing and error analysis and practice in the use of basic statistics within the R programming environment. More advanced multivariate statistical methods will also be taught using R and there will be opportunities for further programming, database and web application development courses.

(f) Spectroscopy, Computation and Simulation (SCS)

This theme provides training and background knowledge in several areas of contemporary chemistry which rely on the use of computers and theory. It involves courses that range from "hands-on" training on the Linux operating system, Python programming, experimental design, data pre-processing, error analysis and the practical use of quantum-chemical packages to advanced coverage of the most important aspects of quantum chemistry, electronic and vibrational spectroscopy, solid-state NMR and chemical thermodynamics.

International students

Another unique aspect of the iDTC is the support offered to international students. The international theme is a cross-theme training package designed to address the specific needs of international non-EU students. The training packages in this theme will be closely associated with supporting language and communication skills as well as fundamental chemistry knowledge. This is achieved through tailored courses delivered by the Centre for English Language Teaching (CELT) on pronunciation, presentations and scientific writing; report writing sessions; and by providing access to appropriate undergraduate courses, via lecture capture and lecture course handouts.

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Theme-specific Training

Course Type Healthcare and Medicinal Synthetic Chemistry (HMSC)

Sustainability and Green

Technologies (SGT)

Functional Materials (FM)

Atmospheric Chemistry (AC)

Analytical and Data Analysis (ADA)

Spectroscopy, Computation and Simulation (SCS)

Techniques Advanced Practical Techniques

Students to choose from other themes

Students to choose from other themes

Practical Gas Chromotography

Introduction to NMR & Mass

Spectrometry

Electronic and Vibrational

SpectroscopyGas Cylinder Training Experimental

Design, Data Processing and Error

Analysis

Introduction to Linux ComputingIntroduction to the

Chromotography Service

Introduction to Practical Quantum

ChemistrySingle Crystal X-ray Diffraction

Introduction to Programming

ConceptsLevel 1

Problem Solving in Organic Chemistry

Introduction to Green Chemistry and

Control of Environmental

Impact

British Liquid Crystal Society Winter

Workshop

Air Quality Measurement Techniques

Basic Statistics for Chemical and

Biological Analyses

Gaussian for Beginners

Quantum ChemistryNMR Spectra and

InterpretationCharacterisation of

Solid State Materials Solid State NMR

Alternative Reaction Media and Catalysis in Green Chemistry

Material: Soft Matter

CHEM 21 Online Platform: green and

sustainable methodologies

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Concepts Level 2 Problem Solving in Organic Chemistry

Clean Synthesis and Renewable Resources

Students to choose from other themes

Students to choose from other themes

Modern Mass Spectrometry:

Fundamentals of Instrument Design

and Function

Database and Web Applications in

Python

Contemporary Organic Synthesis

Energy Efficient Synthesis and Clean

Technology

Multivariate Statistics for Data Analysis

Drug Discovery

Hot Topics Proteins Technology and Business Strategy

within the Chemical Industry

Advanced Materials Environmental & Analytical Chemistry

Environmental & Analytical Chemistry

Photochemistry

Catalysis in Synthesis

Supramolecular and Nanoscale Chemistry

Lasers in Chemistry

Activation of Small Molecules and

Catalysis of Transition Metals

Chemical BiologyRENEWCHEM:

Sustainable Manufacturing for

the Chemical Industry

Depending on your research area, you may find that other departments offer courses that would be appropriate for you. If you find a course outside of the department that you wish to take, you can do so as long as your supervisor and the course organiser agree. The course may be used to fulfil the iDTC requirements.

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TECHNIQUES Training

The following courses will provide you with the necessary training to use a variety of departmental equipment proficiently and safely. You should discuss your requirements with your supervisor and sign up for the training on the equipment that you will need to use for your research.

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TECHNIQUES: Introduction to NMR Spectroscopy and Mass SpectrometryProfessor Peter O’Brien, Heather Fish and Dr Pedro Aguiar for NMR and Dr Ed Bergstrom and Mr Karl Heaton for MSAutumn 2016

The course will consist of four sessions, two on NMR spectroscopy and two on mass spectrometry. There will also be two optional NMR workshops.

Introduction to NMR spectroscopy Professor Peter O’Brien, Heather Fish and Dr Pedro AguiarAll students expecting to use the Departmental NMR Service should attend.

There are three compulsory parts:

Introductory Session (1 hour) given by Heather Fish: Introduction to the facilities and services available for NMR spectroscopy in the Department. There will be an opportunity to meet the NMR staff, including a tour of the various NMR facilities.

Training Session on submission of NMR samples: All users of the Department’s NMR facilities must attend a training session run by one of the NMR staff.

Lecture on NMR Experiments (1 hour) given by Dr Pedro Aguiar: This lecture will focus on the different types of NMR experiments that can be carried out and examples will be illustrated with suitable case studies.

There are two optional workshops (you can attend neither, just one or both sessions):

Workshop on Spectra Interpretation of Inorganic Complexes (2 hours) given by Dr Pedro Aguiar: A set of problems will be worked through in the workshop. This session is primarily for PhD students in the area of inorganic chemistry.

Workshop on Spectra Interpretation of Organic Compounds (2 hours) given by Professor Peter O’Brien: A set of problems will be worked through in the workshop. This session is primarily for PhD students in the area of organic chemistry.

Students are expected to attend the three compulsory parts of the NMR course.

Pre-requisites: Undergraduate degree in Chemistry, including appropriate Year 1-3 Courses on NMR spectroscopy.

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Introduction to Mass Spectrometry Mr Karl Heaton and Dr Ed Bergstrom

The MS part of the course will be divided into two parts:Mr Karl Heaton will provide a brief introduction to the equipment and facilities for MS in the department, and will explain how to access and make effective use of the services he provides.There will also be one half-day session which will cover the theoretical background to our service instrumentation, the sort of data obtainable from our instruments and data interpretation. This will be run by Dr Ed Bergstrom.

Students are expected to attend both sessions of the MS course.

THEMES: Relevant to all themes

TECHNIQUES: Advanced Practical Techniques (APT)Dr Paul Clarke, Dr John Slattery and Professor Ian FairlambAutumn 2016

This techniques course is in several different sections and you should sign up to the ones that are most appropriate to you. By the end of the course, students should be able to demonstrate that they can use the relevant equipment safely. The course is intended for those working in synthetic chemistry, requiring inert atmosphere conditions and techniques.

The courses are listed separately on Skills Forge as follows:

APT 1a+b: Safe Use of Air Sensitive and Potentially Explosive ChemicalsThis course runs over two sessions (one lecture and one practical session) and covers safety aspects of air sensitive reagents and Schlenk lines, Vacuum lines etc. Any student who will be using these techniques should attend.

APT 2a+b: Schlenk Techniques for organic and organometallic chemistsConsisting of two practical sessions, this course looks at the generation of an organolithium species, transmetallation at Zn and its Negishi cross-coupling reaction with a brominated 2-pyrone. This course is limited to 14 students and is only intended for those who will be specifically using these techniques.

APT 3a+b+c: Practical Chromatography for Synthetic ChemistsThis course involves a lecture on general concepts and tips, followed by two practical sessions covering TLC, GC, HPLC and flash column chromatography. This course is limited to 20 students and is only intended for those who will be specifically using these techniques.

APT 4: How to write-up experimental procedures and characterisation for organic and organometallic chemistsCovering experimental write-up, spectroscopic analysis and characterisation data, this session is open to anyone who wishes to attend.

THEMES: Most relevant to HMSC, SGT and FM

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TECHNIQUES: Introduction to ChromatographyMs Amanda DixonAutumn 2016

The course will consist of two sessions, an introduction to the facilities and services available for graduate students, followed by in depth training on the technique(s) relevant to the research project. All students considering using the Departmental Chromatography Service should attend.

This course is divided into two parts:Chromatography Centre Introductory Training (1 hour): Ms Amanda Dixon will provide an introduction to the instruments and services available for GC, HPLC and prep-LCMS chromatography in the Department. The session will cover how to access and make effective use of the facilities the Chromatography Centre provides, including sample preparation and submission. Users of the service must sign up to attend a training session on one or both of the chromatography techniques they will be using (times tbc). The training session will include effective use of the instrument and relevant software packages.

Assessment: Students are expected to attend both sessions of the course.Course pre-requisites: Undergraduate degree in Chemistry.

THEMES: Most relevant to HMSC, SGT, FM, AC and ADA

TECHNIQUES: Experimental Design, data pre-processing and error analysis Dr Julie WilsonSpring 2016

This course will consist of two one-hour lectures and a two-hour workshop and will cover:

The importance of good experimental design, appropriate controls and confounding factors.

Summary statistics and data visualization in exploratory analysis. Issues in chemical data analysis and pre-processing methods (baseline removal, de-

noising, peak alignment/binning). Error analysis, including propagation of errors. Hypothesis testing: what a p-value means (and does not mean).

Assessment: Lectures and workshop must be attended.Course pre-requisites: Basic mathematical understanding.

THEMES: Relevant to all themes

TECHNIQUES: Electronic and Vibrational Spectroscopy Professor Robin Perutz & Dr Laurence AbbottAutumn 2016

This course will provide a basic introduction to the spectroscopic techniques available in the Department and point the way towards a selection of more advanced applications. The emphasis will be on familiarising the student with the instrumentation available. Emphasis will be placed on understanding how to obtain the optimum spectra. There will be opportunities to run spectra of a variety of samples as well as to discuss the strengths and

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weaknesses of the different techniques, both from the practical point of view and in terms of their inherent theoretical features.

There will be four half day sessions as follows:

(1) (2) (3) Infrared spectroscopy. Equipment available. Choice of sampling methods and window materials. Principles of FTIR spectroscopy. Demonstrations and practical work on gas, solid- and solution-phase spectra. Spectrometer controls: spectroscopic and digital resolution. Single beam and ratioing. Interferograms.

(4) UV-visible absorption spectroscopy; fluorescence and Raman spectroscopy. Practical work with UV-visible and fluorescence spectrometers: sensitivities of techniques; experimental conditions and possible artefacts in fluorescence spectra. Introduction to Raman equipment available.

Assessment Full attendance and active participation in all four sessions is required to complete the

course satisfactorily.

THEMES: Most relevant to SCS and FM

Introduction to Linux for Postgraduate ChemistsDr John SlatteryAutumn 2016

This course will provide a general introduction to using, and making the most of, Linux as an operating system and is primarily aimed at students who have not used Linux before, or who would like to become more confident and efficient at using command-line Linux. The course will start by covering the basic principles required to navigate around using the command line. It will then cover various approaches to working with different files and using the Shell. We will finish by introducing some of the basic concepts of programming in Linux that may be encountered during a chemistry PhD. The course will start with an introductory lecture outlining the scope, aims and approach to be taken. This will be followed by a series of self-study exercises that are supported by a drop-in question and answer session and three workshops, where concepts encountered during self-study will be explored in more detail.

Thursday 20 Oct4-5pm A128

Introductory lecture – Introduction to the course, learning objectives, course structure, a general overview of Linux and a question and answer session identifying key learning targets for those on the course.

Week 5 Self-Study – Work through Chapter 1 – General Introduction to Linux and the associated activities. Ensure this is completed before the following drop-in session.

Thursday 27 Oct2-3 Location to be confirmed

Chapter 1 Drop-in Session – A 1 hour drop-in session with demonstrator(s) available to help with any problems encountered while working through Chapter 1 – General Introduction to Linux. It is essential that any problems so far are solved before moving on to more complex material. (Attendance is not compulsory)

Week 6 Self-Study – Work through Chapter 2 – Working with Files and the associated activities. Ensure this is completed before the following workshop.

Monday 7 Nov2-5pm D114 Derwent PC room

Chapter 2 Workshop – A 3 hour workshop covering material from Chapter 2 –Working with Files. Will contain additional, more complicated problems to work through with the help of demonstrator(s).

Week 7 Self-Study – Work through Chapter 3 – Advanced Linux and the associated activities. Ensure this is completed before the following workshop.

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Monday 14 Nov3-4pm D114 Derwent PC room

Chapter 3 Workshop – A 1 hour workshop covering material from Chapter 3 –Advanced Linux. Will contain additional, more complicated problems to work through with the help of demonstrator(s).

Weeks 8 and 9 Self-Study – Work through Chapter 4 – Basics of Programming/Scripting and the associated activities. Ensure this is completed before the following workshop.

Monday 28 Nov9am-12pm D114 Derwent PC room

Chapter 4/Consolidation Workshop – A 3 hour workshop covering material from Chapter 4-Basics of Programming/Scripting as well as consolidation of previously learnt material. Will contain complicated problems to work through with the help of demonstrator(s). Programming languages such as Python and Fortran will not be compulsory. Instead the workshop will focus on general problems solving with skills learnt so far, a few new skills and basic bash scripting.

Assessment Full attendance and active participation in all three workshops, along with the associated

self-study, is required to complete the course satisfactorily. Attendance at the chapter 1 drop-in session is not compulsory. This is intended as a support session to help with any initial problems.

THEMES: Relevant to all themes

TECHNIQUES: Introduction to Practical Quantum ChemistryDr John SlatteryAutumn 2016

This module provides an introduction to the most popular computational methods for studying the electronic structure and properties of molecules. Such computational work has become an essential part of academic and industrial research. A look at a recent issue of the Journal of the American Chemical Society will reveal that experimentalists often use quantum-chemical calculations to explain results obtained in the lab, as well as to make predictions to be verified by further experiments.

Applications of Ab Initio and DFT calculations : 4 lectures

Introduction to an ab initio program package (TURBOMOLE or GAUSSIAN). Practical aspects of single-point calculations and geometry optimizations.

Determination of transition structures and reaction coordinates. Calculation of thermochemical data and dipole moments. Examples of current applications of DFT.

Workshops on ab initio and DFT calculations: 2 x 3hr workshops

Two workshops will focus on 'hands on' ab initio and DFT calculations, including optimisation of ground and transition state geometries for a “real life” organometallic reaction mechanism.

Pre-requisites: There are no pre-requisites for this course, but some students may find it advantageous to also attend Dr Peter Karadakov’s part of the module earlier in Autumn term. This is CONCEPTS: Level 1: Introduction to Practical Quantum Chemistry. Both of these courses are part of an MChem module.

THEMES: Relevant to all themes

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TECHNIQUES: Introduction to Programming Dr Kevin CowtanSpring 2017

This module introduces students to computer programming. Students will learn the principles of programming, in particular object-oriented methods. The Python programming language will be used throughout. Bioinformatics tasks, simulations, numerical problems and puzzles will be used as examples of problems soluble by writing computer programs.

Topics:Basic Python Programming1. Introduction to computer programming2. Variables, expressions and statements3. Conditions and iteration4. Functions5. Strings and lists6. Tuples and dictionaries7. Files and exceptions8. Classes and objects9. Recursion10. Graphics

Special Topics1. Regular expressions2. Plotting with matplotlib3. Arrays and matrices with NumPy4. GUI programming with Tkinter

There will be 12 x 1 hr lectures, a 2-hour compulsory workshop and 8 optional 1-hour workshops. Students should attend all lectures and complete the workshop problems. Attendance at the workshop sessions is optional depending on whether assistance is required with the problems that have been set.

THEMES: Relevant to all themes

TECHNIQUES: Practical Gas Chromatography (GC) Dr Rachel DunmoreAutumn 2016

This 2 hour session will provide practical based learning, looking at the details of how to set up and maintain good separation in GC. The specific content is outlined below:

Introduction to GC and how it works Injectors – split-splitless, headspace, thermal desorption Columns – PLOT versus WCOT Detectors – TCD, FID, MS, other How to guide – ferrules, unions, press fits, maintenance

THEMES: Most relevant to AC and ADA

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TECHNIQUES: Single Crystal X-Ray DiffractionProfessor Keith Wilson, Dr Johan Turkenburg and Dr Adrian WhitwoodSummer 2017

This course will cover the principles and methods of single crystal X-ray diffraction. The aim is to give students a working knowledge of basic diffraction theory and appreciate the content of publications reporting single crystal structures.

The following topics will be covered:

Scattering and microscopy versus spectroscopy Why use X-rays Scattering from a single slit Diffraction from repeating slits The molecular transform The need for crystals The phase problem: Patterson maps and direct methods, Least-squares and Fourier

based refinement methods Statistics and reliability indices The final model

There will be two workshops:

The representation of the electron density as a sum of waves The Patterson synthesis for locating atoms, including space group symmetry

The final session will include a tour of the Departmental small molecule facility and a demonstration of structure solution by Adrian Whitwood.

Students must attend all sessions of the course.

THEMES: Mainly relevant to HMSC, FM

TECHNIQUES: Gas CylindersDr Graeme McAllisterAutumn 2016

This half day session is a requirement for anyone who will need to use gas cylinders for their research. The training will take place in the YSOC labs in B-block

CONCEPTS: Level 1 courses

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These courses are designed to underpin some of your research knowledge and are general courses for non-specialists. All students should aim to take at least one of these courses.

Some courses require a minimum number of students to run. If numbers are too low, a course may be postponed to the following academic year.

CONCEPTS Level 1 and 2: Problem Solving in Organic ChemistryProfessors Peter O’Brien and Ian Fairlamb, Dr Paul ClarkeSpring and Summer 2017

The ability to apply organic chemistry knowledge to unseen problems is a key skill that should be practised throughout your PhD and therefore represents a key training element. In this course, organic chemistry problems will focus in the areas of synthesis, named-reactions, mechanisms, spectroscopy and physical organic chemistry. The training will be achieved through problem-based workshops and working through problems in your own time before or after the workshops.

The Problem Solving in Organic Chemistry will run in Years 1-3 of the PhD and attendance in all years is required. Each course is 8 x 1 hour workshops (4 in spring term and 4 in summer term). Time spent outside workshop: ca 16 hours

There will be two strands you can follow, depending on your level of expertise. You will be assigned to a Strand at the start of the course:

Strand 1Year 1: Level 0 course – Professor Peter O’BrienYear 2: Level 1 course – Professor Ian FairlambYear 3: Level 2 course – run by Dr Paul Clarke. This is a Concepts Level 2 course

Strand 2Year 1: Level 1 course – run by Professor Ian FairlambYear 2: Level 2 course – run by Dr Paul Clarke. This is a Concepts Level 2 courseYear 3: Level 3 course – informal workshop sessions.

In Spring/Summer terms 2017, the Level 0 and Level 1 courses will usually run at the same time. You then progress into the next course level in the following year of your PhD i.e. following strands 1 or 2.

Spring/Summer 2017Level 0 course – run by Professor Peter O’Brien

This course is aimed at students who will need to be aware of organic chemistry topics as part of their PhD. Students with limited experience of curly arrow mechanisms should attend. Topics covered will include curly arrow mechanisms and selected parts of the organic chemistry York undergraduate course.

Spring/Summer 2017Level 1 course – run by Professor Ian Fairlamb

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The course is aimed at students who will be carrying out an organic chemistry-based PhD. The course will assume knowledge of a typical UK undergraduate chemistry course. You should have carried out a MChem research project in organic chemistry.

Spring/Summer 2017Level 2 course – run by Dr Paul Clarke (NB this level is a Concepts Level 2 course)

This course will build on the concepts presented in Organic Problem solving Level 1 and will be suitable for students who have completed that course. It will deal with advanced retrosynthetic and synthetic strategy using examples from the recent literature. Students will be provided with synthetic problems to work through and present in a workshop environment.

Students must attend all sessions of the course, over the three years (Strand 1 or 2).Student contribution to the workshops is also assessed and feedback will be given.

Spring/Summer 2017Level 3 workshop sessions

These are informal weekly sessions on natural product total synthesis. Open to all PhD students, particularly those who wish to progress after the Level 2 Problem Solving in Organic Chemistry. The information nature of these sessions means that a separate timetable is prepared via an email list.

Pre-requisites: MChem / MSc (or equivalent) undergraduate degree in Chemistry.

THEMES: Most relevant to HMSC, SGT and FM

Concept Level 1: NMR Spectra and InterpretationProfessor Simon DuckettSummer 2016

The course aims to teach graduate students about NMR spectroscopy in a format that will allow them to understand and specify their own experiments. The first part of the course will consist of four lectures that deal with practical aspects of NMR spectroscopy. Every effort will be made to exemplify available techniques through the use of case studies. Both 1 and 2 dimensional methods will be covered.

Workload: 4 x 2 hour sessions.

Assessment: Students must attend all sessions of the course. Students will see how a range of complex experiments can be set-up and their data

analysed

Course pre-requisites: The NMR component of the Techniques Course (or its equivalent elsewhere) is a

prerequisite for this course.

THEMES: Most relevant to HMSC, FM, ADA

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CONCEPTS Level 1: 1a: Introduction to Green Chemistry & Control of Environmental ImpactVarious Green Chemistry staffAutumn 2016

Green chemistry can be considered as the design and application of processes and products that do not harm the environment. The application of green chemical technology is becoming increasingly important as traditional raw materials become scarcer, the costs of waste disposal and fines from pollution escalate, and energy costs increase. Green chemistry principles and tools are available to aid environmentally friendly process and product design.

Lectures on this topic cover:

The costs of waste and the changing chemical industry, principles and terminology of green chemistry, greening chemical synthesis, green chemistry metrics

Green chemical technologies, life cycle considerations Product and process design for sustainability; chemical product legislation Atom economy and experimental design; Green Metrics Use of Renewable Resources

Control of Environmental Impact: Increasingly tight legislation and improving awareness of the effect chemicals have on the environment have led to stringent control of chemical releases to the environment. In order to minimize the environmental impact of products and process a whole range of technologies aimed at reducing waste at source, recovery and reuse of by-products and recycling of products at the end of their useful life have been developed. This module explores the drivers and options for reducing the environmental impact of both products and processes.

Lectures cover:

Waste: A problem in so many ways but also an opportunity Environmental management systems, reporting and the influence of legislation Waste valorisation Recycling, reuse and recovery Life Cycle Assessment Measuring 'Greenness'

This course is part of the MSc in Green Chemistry & Sustainable Industrial Technology. This course consists of 15 lectures

THEMES: Most relevant to SGT, FM, HMSC

CONCEPTS Level 1: 1b: Catalysis in Green Chemistry & Alternative Reaction MediaVarious Green Chemistry StaffAutumn 2016

Catalysis is probably the most important technology for green chemistry. Heterogeneous catalysis offers an additional advantage in facilitating separation at the end of the reaction, and increasing catalyst life-time. Heterogenisation chemistry is an art as well as a science

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and requires careful choice of support as well as catalyst preparation methodology. Supported Reagents is a general term that can be used to describe the use of typically high surface area carrier materials to deliver a catalytic species or “reagent” to a “location” where it is meant to achieve an effect. The methodology can also be extended to other applications including drug delivery. In all cases good characterisation of the active solid material is important.

Lectures on Catalysis include:

Introduction to Catalysis – Applications - Heterogenisation Heterogeneous catalysis Biocatalysis Catalysis in Ionic Liquids Homogeneous Catalysis Phase Transfer Catalysts

Solvents are widely used in chemical processes, formulation chemistry and cleaning. Traditional solvents present numerous health and safety, and environmental problems; many have been banned or severely restricted while others are under threat from increasingly restrictive and punitive legislation. This has led to an enormous research and development effort on greener alternatives including water, low volatility solvents and supercritical carbon dioxide. The relative advantages and disadvantages of different solvents requires careful assessment.

Lectures on Alternative Reaction Media cover:

Solvents Properties – General Overview Water as a solvent Fluorous biphasic solvent systems Bio-derived solvents and the importance of solvent development Supercritical Fluids Introduction & Applications Carbonates as solvents Gas expanded liquids as solvents Super-heated water extraction

This module is part of the MSc in Green Chemistry and Sustainable Industrial Technology. This course consists of 17 lectures

Pre-requisites: Ideally Concepts Level 1a Introduction to Green Chemistry & Control of Environmental Impact before doing this course

THEMES: Most relevant to SGT, FM, HMSC

CONCEPTS Level 1: CHEM21 Online PlatformLouise SummertonRuns throughout the year

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The CHEM21 online learning platform* http://learning.chem21.eu comprises a range of free, shareable and interactive educational and training materials that have been created in collaboration with industry to promote the uptake of green and sustainable methodologies, with a particular focus on the synthesis of pharmaceuticals.

The platform covers a broad range of topics, both at an introductory level and in-depth under the following topics:

Foundation Guides and Metrics Solvents Synthetic Toolbox Process Design Life Cycle Impacts and the Environmental Fate of Pharmaceuticals

The platform also incorporates new cutting-edge methodologies for greening the synthesis of APIs (active pharmaceutical ingredients) and intermediates, with associated case studies arising from CHEM21 research. This information encompasses the ‘Synthetic Toolbox’ module, which describes a range of synthetic approaches that are more sustainable and efficient than existing ones including:

Base metal catalysis; Biocatalysis; Multicomponent reactions; C-H activation; Carbonylation; C-F bond formation; Flow chemistry; Amidation; Synthetic biology.

Each learning module stands alone, so the user can pick and choose from a wealth of resources to create a learning path appropriate to their needs. Embedded references and further reading also allow easy access to more information for those that are interested in learning more on a particular subject area.

For more information on the CHEM21 project visit www.chem21.eu or contact Louise Summerton (louise.summerton@york.ac.uk).

*The CHEM21 online platform has been created as part of the IMI funded CHEM21 project (Chemical Manufacturing Methods for the 21st Century Pharmaceutical Industries). CHEM21 has received funding from the Innovative Medicines Initiative Joint Undertaking under grant agreement n°115360, resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in kind contribution.

CONCEPTS: Level 1British Liquid Crystal Society Winter WorkshopUniversity of Hull

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Every year, the British Liquid Crystal Society runs a Winter Workshop at the University of Hull, funded by the EPSRC. Taking place in December / January, the workshop runs over two full days and involved internationally leading specialists in the field covering topics such as:

Synthesis Mesophase characterisation (POM, DSC) Electro-optic properties Devices Computer simulation of condensed phases.

Further information about the workshop will be available in due course and students are advised to check the website: http://blcs.eng.cam.ac.uk/ and speak to their supervisor. Attendance and accommodation are funded by the EPSRC. Travel expenses can be claimed from students’ conference funding allowance.

THEMES: Most relevant to FM

CONCEPTS Level 1: Air Quality Measurement TechniquesVarious members of Atmospheric Chemistry – part of the NERC SPHERES DTP training but open to other students as wellSpring/Summer 2017

Nitrogen oxides (NOx), ozone and CO are measured across the UK by automated monitoring networks. In the Air Quality Measurement Techniques course you will learn about the impact of air pollution on human health and the procedures put in place to monitor regulated pollutants. It is only through accurate and precise measurements that the data collected can be used to inform policy makers. This course is a combination of lecture based material and practical demonstrations of the key techniques used to detect compounds in the atmosphere.

4 hours practical/lectures + additional reading: This course will be taught through a combination of lectures, practical demonstrations and additional reading to provide an introduction to air pollution, measurements and public health.

The structure of the course is laid out below:

Introduction to air pollution: 50 mins (JFH) 1. An overview of the key pollutants in urban air2. What are the health effects of these pollutants3. Some chemistry of O3 – example of atmospheric reactions. Material ties in to the following lab experiments.

Sampling in the field. 40 mins (JRH)Intro to tube, bag, filter head, and canister methods; Collect samples outside in two groups each has one of each; Groups take bags / canisters to labs for subsequent analysis].

Lab experiment 1.Principles of trace gas analysis TOTAL of 45 mins (JRH, KR, SM)

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Presentation given in the lab alongside the demonstrations.Introduction to instrumentation for O3, NOx and CO.Getting inside an ozone analyserMaking and measuring ozone as a demo.

Networks, measurements, forecasts. 30 mins (SM)Current Defra, Met office, NCAS forecasts

Lab experiment 2.Principles of GC-MS and VOC analysis 45 mins (ACL, RTL)

Talk with slides alongside instrument, measurement of canister sample in real time. Covering the following key steps in analysis

Sample drying.Thermal desorptionGC separation (including principles of GC)MS – use TOF as example. (basics of MS)Very basic explanation of what spectra tell you

THEMES: Most relevant to AC and ADA

CONCEPTS Level 1: NSCCS Gaussian Workshop for BeginnersExternal course held around September each year

http://www.gaussian.com/

This external workshop for beginners takes place in September each year at Imperial College London. The workshop is aimed at complete beginners and will consist of a mixture of lectures and problem-oriented practical sessions. Further details on the workshop and how to register can be found: http://www.nsccs.ac.uk/

Registration is usually free, but accommodation and food costs will need to be covered. Students can speak to their supervisor about this and if necessary, request some of their conference funding allocation to cover the costs.

THEMES: Most relevant to SCS

CONCEPTS: Level 1Introduction to Practical Quantum ChemistryDr Peter KaradakovAutumn 2016

This module provides an introduction to the most popular computational methods for studying the electronic structure and properties of molecules. Such computational work has become an essential part of academic and industrial research. A look at a recent issue of the Journal of the American Chemical Society will reveal that experimentalists often use quantum-chemical calculations to explain results obtained in the lab, as well as to make predictions to be verified by further experiments.

12 lectures and 1 x 2hr theoretical workshop

Topics:

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General overview of electronic structure theoryBrief revision of quantum theory and its mathematical background. Schrödinger equation for a many-electron system. Born-Oppenheimer approximation. Electron spin. The simplest many-electron wavefunction: a Slater determinant.

The Hartree-Fock approachHartree-Fock equations. Occupied and virtual orbitals. Brillouin theorem. Koopmans theorem. Molecular orbitals, Hartree-Fock-Roothaan equations and the self-consistent field procedure. Interpretation of the results of Hartree-Fock calculations.

Practical aspects of Hartree-Fock CalculationsTypes and properties of atomic orbital basis sets used to construct molecular orbitals. Specifying molecular geometries through Z-matrices.

Electron correlation and post-Hartree-Fock methodsConfiguration interaction. Multi-configuration self-consistent field theory (MC SCF), complete-active space SCF (CAS SCF), many-body perturbation theory (MBPT).

Density-functional theory (DFT)The Hohenberg-Kohn theorem. Exchange functionals and correlation functionals. Specifics of DFT calculations.

THEMES: Most relevant to SCS

CONCEPTS LEVEL 1: Introduction to Solid-State NMR SpectroscopyDr Angelika Sebald Spring Term

The course is suitable for anybody planning to use solid-state NMR experiments in any area of chemistry. There are no pre-requisites but we request participants to let us know two weeks before the start of the course about their areas of interest / application areas (by email: angelika.sebald@york.ac.uk).

The course will be delivered in five 2-hour workshop-style sessions. The number of participants will be limited to 8.

The course will cover the anisotropic nuclear spin interactions relevant in solid-state NMR and explain basic and commonly used experiments on powder samples such as magic angle spinning (MAS), cross polarization (CP) and dipolar de- and recoupling experiments. The principles will be illustrated by a range of examples, including the preparation of samples, suitable experimental set-up procedures and interpretation of spectra.

THEMES: Most relevant to SCS and FM

CONCEPTS Level 1: Materials: Soft MatterDr Isabel Saez

The course is a Long Distance Learning Package accessed via the VLE. It is available throughout the year. Students will need to contact the Chemistry Graduate Office at the start of the year to arrange access.

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The central question that has fascinated materials chemists from the beginning has been how to design and control the molecular structure to achieve materials with a specific response. In nature numerous examples can be found in which function is determined by both the chemical nature of the material and its physical attributes such as molecular size and shape and the mechanical properties. The course covers advances at the forefront of materials chemistry in the development of Soft Matter, based on the principles of self-organisation and self-assembly, followed by some exciting new developments in materials chemistry.

The course covers a brief introduction to thermotropic and lyotropic behaviour and the techniques used in the characterisation of mesophases, followed by the study of a range of materials that form liquid crystal phases, from surfactants and amphiphiles to block co-polymers, dendrimers and nanoparticles. Finally it applies these concepts to the area of templating, in order to obtain ordered mesoporous structures. It will concentrate on how the manipulation of the chemical structure, for example through chirality and amphiphilicity, leads to specific supramolecular organization, which in turn imparts certain properties to the bulk material, including applications in a number of areas.

Examples of topics to be studied may include:

Mesoporous materials from liquid crystal templating. Discotic materials in organic electronics. Liquid crystal polymers in biomaterials. Carbon-based organized nanostructures.

The module is part of the MChem programme

THEMES: Most relevant to FM===================================================================

CONCEPTS Level 1: Characterisation of Solid State MaterialsDr Richard DouthwaiteSpring 2017

This course will focus on the most common methods used to characterise solid state compounds, principally metals and metal oxides. These will include common methods for structural and functional characterisation such as x-ray diffraction, electron microscopy, spectroscopies (NMR, XPS, UV-vis) and more specialised techniques such as transport measurements and electrochemistry. Some basic theory will be included but practicalities of each technique will be emphasised.

The format will be 5 x 2hr workshops. This course requires a minimum number of 6 students to run. If numbers are low, the course may be deferred to the following academic year.

THEMES: Most relevant to FM

CONCEPTS Level 1: Introduction to statistical analysis in RDr Julie WilsonAutumn 2016

This course will introduce students to R, a statistical environment for carrying out mathematical and statistical analyses. The course consists of 4 one-hour practical sessions

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in a computer room and provides a hands-on introduction to statistical analysis in R with the emphasis on choosing the correct test, interpreting the output and learning how to use R.

The module aims to:

familiarise students with fundamental ideas in statistical data analysis introduce the use of R for data manipulation, analysis and graphing teach students how to interpret the outputs of statistical tests teach students how to report the results of analysis including appropriate figure

choiceAfter completing the module the student will have an understanding of the following in general and in R:

the logic of hypothesis testing the normal distribution t-tests one-way ANOVA correlation and single linear regression presenting statistical results

THEMES: Most relevant to HMSC, ADA

CONCEPTS: Level 2 courses

Level 2 courses will allow you to enhance and develop skills and knowledge in specific areas and will delve deeper into a subject to a more advanced, specialist level. You should take one of these courses in either year 2 or 3 of your PhD.

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Some courses require a minimum number of students to run. If numbers are too low, a course may be postponed to the following academic year.====================================================================

CONCEPTS Level 2Problem Solving in Organic Chemistry – also extends to Concepts level 2. Please refer to the entry in the Concepts Level 1 section.

CONCEPTS LEVEL 2: Contemporary Organic Synthesis – Stereoselective Synthesis of Pharmaceuticals and Natural ProductsSpring and Summer 2017

Stereoselective Synthesis of Natural ProductsDr Paul Clarke (3 hours, Spring 2017)

In this part of the course we will discuss modern strategies for preparing biologically important natural products. The course will consist of (i) a lecture giving an overview of advanced retrosynthetic and synthetic strategies, with a particular emphasis on the control of absolute and relative stereochemistry; (ii) a problem solving workshop where the students will work in groups; (iii) a short group assignment will be completed after the workshop – and feedback will be provided.

Asymmetric Synthesis of PharmaceuticalsProfessor Peter O’Brien (3 hours, Summer 2017)This part of the course will focus on some of the most important and useful asymmetric reactions for synthesis. Reactions will include enolate -alkylation and aldol reactions, Ellman’s sufinamide, asymmetric reduction of ketones, Sharpless asymmetric dihydroxylation and epoxidation, Shi epoxidation and Jacobsen’s asymmetric epoxidation and hydrolytic kinetic resolution. These will be presented in an initial lecture. Then, in a workshop format, the use of these reactions in the synthesis of chiral pharmaceuticals will be explored. Synthetic problem solving skills will be developed in the interactive workshop. A short assignment will be completed after the workshop – and feedback will be provided.

Course pre-requisites: Organic Problem Solving Levels 0 and 1.

THEMES: Most relevant to HMSC, SGT, FM

CONCEPTS LEVEL 2: Modern Mass Spectrometry: Fundamentals of Instrument Design and Function Professor Jane Thomas-Oates, Dr Ed Bergström Spring 2017 – runs every other year

Four half-day sessions, in the Spring termTeaching method: lecture, workshop/discussion sessions, instrument visits if appropriate.

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This course will involve an in-depth study of the modern ionisation techniques electrospray (ES), atmospheric pressure chemical ionisation (APCI) and matrix-assisted laser desorption/ionisation (MALDI) and the design and optics of modern mass spectrometers. In this context we will examine the different mass spectrometric experiments that can be carried out, and how these may be achieved with the instruments being discussed in the course. These are likely to include:

quadrupoles quadrupole ion traps orbitraps time of flight (TOF) orthogonal time of flight (oTOF) tandem time of flight/time of flight (TOF/TOF) instruments ion cyclotron resonance (FT-ICR) instrumentation.

The instruments and ionisation methods covered will be tailored to the needs and interests of the course participants.

Please note: This course is NOT an introduction to mass spectrometry but an in-depth taught course aimed at students (probably Analytical or Physical Chemistry students) whose research will use modern mass spectrometric methods as one of the central techniques and who therefore need to understand in detail how these instruments are constructed and function. The ‘Introduction to NMR and MS’ techniques course is designed for students (probably those doing synthesis projects) who will use MS as a tool and so are interested in an overview of the techniques available in the department and how to apply and best use them, but who do not need an in depth understanding of the instrumentation itself. The modern mass spectrometry course is not a spectral interpretation course.

Students are expected to attend all four half-day sessions, and to contribute to them all by both chairing sessions as well as by making presentations. If you are not going to be able to attend all four sessions, you should arrange to sit the course another year.

THEMES: Most relevant to ADA

CONCEPTS Level 2: Databases and Web Applications in Python Dr Kevin CowtanSummer 2017

Building on Python, this course looks firstly at developing algorithmic and problem solving skills, and continuing to look at local and distributed data organisation and manipulation as applied to computational biology problems. As useful as word processors, databases and other tools might be, the one thing that makes computers so important is our ability to program them to perform a huge variety of tasks, from solving equations to processing and analysing data. In addition, the large databases produced today by genomics efforts present significant problems of data description and organisation, and are often distributed across local and external computing resources. This course develops programming skills though problems solving using the Python programming language, and will explore techniques for data organisation and methods for accessing local and remote databases through MySQLdb and web services portals.

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Topics include:

Scientific algorithms in Python DB design Basic web applications with mod_python Advanced web application with django Grid computing and web services, with examples

There will be 10 x 1 hr lectures, a 2-hour compulsory workshop and 6 1-hour optional workshops. Students should attend all lectures and complete the workshop problems. Attendance at the workshop sessions is optional depending on whether assistance is required with the problems that have been set.

Useful resources: Python DB API tutorial: http://www.kitebird.com/articles/pydbapi.htmlApache mod_python tutorial: http://webpython.codepoint.net/mod_python

Pre-requisites: students should have recently completed the Intro to Programming course, or have recent experience of using Python and have been doing some programming. If you are unsure about whether you have suitable experience for this course, please contact Dr Kevin Cowtan. It would also be beneficial if students have some knowledge / experience of Linux but this is not compulsory

The running of this course will depend on a minimum number of students so may only run in alternate years.

THEMES: Relevant to all themes

CONCEPTS Level 2: Multivariate Data AnalysisDr Julie WilsonSpring 2018 – runs every other year

Chemistry is undergoing a transformation, from predominantly small-scale hypothesis-driven science to large-scale data-driven science. Large multivariate data sets are being generated and analysis and interpretation of these data are key challenges to knowledge discovery and understanding. In this course, methods for handling multivariate data sets are introduced. The course involves practical analysis and although concepts and methods will be introduced in lectures, the focus is on practical applications rather than the theoretical background to the techniques.

In 4 X 1-hour lectures and 4 X 2-hour practical sessions, the course will cover:

Introduction to multivariate analysis and data pre-processing Exploratory data analysis Principal component analysis Classification and discriminant analysis

Reference texts:

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Krzanowski WJ and Marriout FHC. (1994) Multivariate analysis. Vol 1 and 2. Kendall’s library of statistics Mardia,KV, Kent, JT and Bibby, JM (2003) Multivariate analysis

Pre-requisites: Students should already have taken Concepts Level 1: Introduction to Statistical analysis in R

THEMES: Relevant to all themes, particularly ADA

CONCEPTS Level 2: 2a: Clean Synthesis & Renewable ResourcesVarious Green Chemistry Staff.

This course consists of 12 lectures that are part of the MSc in Green ChemistryAutumn 2016 – 5 lectures on Clean SynthesisSpring 2017 – 7 lectures on Renewable Resources

Clean Synthesis: The design and development of a chemical synthetic route should take into account, economic, societal and environmental factors. The integration of cleaner and efficient methods can achieve these goals.

Lectures cover:

Scale up and industrial application of clean synthesis including asymmetric synthesis High throughput synthesis

Renewable Resources: Diminishing fossil resources, increasing oil prices and numerous other drivers are rapidly forcing society to seek new, sustainable sources of carbon for future chemicals, energy and materials production. These will be based on biomass including crops, trees and food waste which will be the feedstocks for new biorefineries. Green chemical and bio-processing should be used to transform these raw materials into genuinely green products.

Lectures cover:

Renewable v Non-renewable feedstocks Biofuels v Conventional fuels The biorefinery, technologies and products Platform molecules from biomass

Pre-requisites: Ideally Concepts Level 1a: Introduction to Green Chemistry

THEMES: Most relevant to SGT, FM, HMSC

CONCEPTS Level 2: 2b: Energy Efficient Synthesis & Clean TechnologyVarious Green Chemistry StaffSpring 2017. This course consists of 20 lectures that are part of the MSc in Green Chemistry.10 lectures on Chemical Engineering and Clean Technology10 lectures on Energy Efficiency

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Green chemistry and energy efficiency can only be effectively applied to chemical processing through the use of appropriate chemical engineering. Thus green chemical technology requires the integration of efficient and selective chemical methods, highly efficient reactors, online monitoring, and rapid and low-waste separation processes. The use of microreaction and intensive processing is especially exciting and promises to revolutionise the industry through the use of small and flexible manufacturing plants.

Lectures cover:

Intro to chemical engineering Traditional reactors and process development Electrochemistry and clean technology; Membrane reactions Reactor design for improved efficiency; Process Intensification

Energy efficiency and the use of a wider range of feedstocks is an increasingly important part of clean technology as we move away from a fossil fuel-based energy industry. In the case of the chemical industry, energy input to a chemical process can represent a major contribution to the production of waste.

Lectures cover:

Carbon dioxide and fossil fuels Nuclear, wind, hydro power and solar power Critical elements in energy Fuel Cells Energy Efficiency in Chemistry through Microwave and Sonochemistry

Pre-requisites: Ideally Concepts Level 1a Introduction to Green Chemistry

THEMES: Most relevant to SGT, FM, HMSC

CONCEPTS Level 2: Drug DiscoveryProfessor Ian Fairlamb and Dr Anne RoutledgeSpring/Summer 2017

Biological and medicinal chemistry (Drug Discovery) has emerged as an exciting area, the results of which have had a tremendous positive effect on the whole of humanity. Being able to understand aspects underpinning the fundamental basis for life has been the main reason behind this. Our continued drive to finding cures for both old and new diseases is of critical importance to the world as a whole. Indeed, it is the combination of biological and medicinal chemistry that has led to newer, more efficient ways of targeting devastating diseases such as cancer, coronary heart disease and Parkinson’s disease, to name just a few.

New biological processes (finding new cellular targets) allow new therapeutic agents to be developed, while also enabling an understanding of the molecular basis of the disease, e.g. mutations of genes in cancer – the so-called “oncogenes”. Drug discovery plays a significant role in this context and humanity has benefited tremendously from the development of such agents, which improve the quality of life and increase life expectancy rates in both developing and developed nations.

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The course broadly covers a wide range of topics in drug discovery. It is intended to give an insight into drug design, detailing how one goes about choosing an appropriate enzyme/receptor target (Lecture 1), and then how to optimise a new drug in terms of biological activity and profile (availability) and selectivity (toxicology). We will also touch on the synthesis of drug compounds and show how sustainable synthetic routes are being developed, avoiding both toxic reagents and catalysts, where possible.

A few practical exercises will allow students to engage directly with the presented lecture material, specifically drug design concepts and rules. Lecture 2 focuses on the design of antibiotics, from classical organic compounds to metal-derived compounds. A particular emphasis is placed on current commercial antibiotics, as well as the antibiotic resistance problem which humanity needs to grapple with. We will highlight work on antibacterial silver compounds, carbon monoxide (CO) and transition metal-CO releasing molecules (CO-RMs). The latter are emerging as a unique class of interesting antibiotics, with quite different but complementary drug design principles to organic compounds.

This course may be part of the CIDCATS PhD programme and numbers may be limited to 5 research students.

THEMES: Mainly relevant to HMSC

There may be other learning opportunities outside of the Department that you and your supervisor feel would be beneficial for you to attend. Examples of these are given below and can be taken as a Concepts course if you wish.

Electronic Structure methods in Inorganic Chemistry- Dalton Summer School

NSCCS Workshops – Computational Software Training

Advanced Quantum Chemistry Summer School, Oxford

HOT TOPICS

These courses aim to discuss cutting edge chemistry research in a number of important areas and help to broaden your knowledge of the latest significant advances in literature. You should take two Hot Topics courses over years 2 or 3 (not year 1) of your PhD.

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Some of these courses only run in alternate years and may be subject to minimum numbers. Therefore please ensure you sign up in good time for the course you would like to take.

Most Hot Topics courses will require you to make a presentation to the rest of the group on a selected topic. You will be given guidance in advance of the session.

HOT TOPICS: PhotochemistrySpring 2018 – runs every other yearDr John Moore

The aim of this course is for you to prepare and deliver a presentation on a topic in photochemistry that is not directly related to you own research work, and to learn about current research in photochemistry from the full range of presentations delivered by the group. The topics below illustrate some of the options on which lead references will be provided; you can choose from a full list of ca. 20 such topics, or suggest a topic of your own in consultation with the course organiser.

Photoisomerisation of stilbene and azobenzene. Photochromic compounds. Photochemistry of charge-transfer states of transition metal complexes. Supramolecular photochemistry. Photochemically controlled ion complexation. Femtosecond photochemistry in the gas phase. Photodynamic therapy of cancer. Photochemistry of polyenes. Primary events in photosynthesis. Solar energy conversion.

Course pre-requisites:Some prior knowledge of photochemistry (e.g. an undergraduate degree in chemistry).

Advanced MaterialsSpring 2017 – runs every other yearDr Richard Douthwaite, Dr Isabel Saez

Many current technologies are underpinned by solid state chemistry and soft materials science. This course is designed to highlight some of the areas that have undergone recent advances that may contribute to the development of existing and new technologies.

Thermoelectric materials. Superconductors. Biomaterials and bioactive coatings. Photonic materials. Molecular framework solids. Materials for solar energy conversion. Colossal magnetoresistance. Shape-memory polymers. Biomineralisation and biomineral-inspired materials chemistry. Organic light emitting materials. Liquid crystals. Molecular engineering for display materials. Artificial muscle from polymers and elastomers. Block copolymers self-assembly. Micelles, vesicles and polymersomes.

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Carbon nanomaterials. Fullerenes, graphene, carbon nanotubes.

Course pre-requisites: None

HOT TOPICS: ProteinsProfessor Andrzej Marek Brzozowski and Dr Seishi ShimizuSummer 2018 – runs every other year

Proteins are responsible for almost all the chemistry in the cell and are the key elements of physiological processes. Understanding of their structure, function and complexity of their interactions is vital for the comprehension of fundamental issues in biology, medicine and chemistry. The main aim of the course will be a critical revision and deepening of the knowledge of the most important elements of protein structure and function. Although the topics proposed here concern rather fundamental problems of protein chemistry they will be revisited in the context of the most recent developments in structural biology and biomedical sciences. Several very broad key problems are suggested for further narrowing but you are encouraged to choose a topic of your own in agreement with the course organiser. However, it is expected that the topic you select is not similar to your current research project.

Organisation of protein structure: coexistence of simplicity and complexity Sequences and topologies: decades of genomes – personalised medicine Dynamic nature of proteins - the importance of simulations The nature and role of protein - protein interactions How to interpret a protein structure - validation of the protein model The nature and role of protein - RNA interactions Protein - metal partnership Proteins in human immune response - re-birth of monoclonal antibodies? Molecular control of protein folding: implications for brain-related diseases Pathological effects of protein misfolding: why anti-amyloid vaccine does not work? Inside out: proteins and membranes Protein interaction and metabolic networks Accidental miracle or a reason? - the crossroads of drug design SN1 or SN2? - the role of chemistry in the elucidation of mechanism of enzymes-

driven catalysis What can thermodynamics and statistical thermodynamics teach us about how

proteins work? The role of water in protein structure and function Denaturation or happiness? - life processes in extreme environments How does the crowding of macromolecules in the cell affect biochemical reactions?

Departure from Stoke's law Why enzymes work if we dip them into solvents other than water? Applications of physical chemistry in understanding of properties and functions of

macromolecules? Molecular traits and markers of disease Enzymes in bio-transformations and industry Proteins as drugs

HOT TOPICS: Technology and Business Strategy within the Chemical IndustryDr Brian GrievsonSpring 2018 – runs every other year

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This course aims to increase your awareness of issues of crucial importance to the success of the chemical industry. Working in teams, you will choose a topic of interest to you, either from general product areas such as ceramics, polymers, adhesives, surfactants, electronic materials, pharmaceuticals, agrochemicals, petrochemicals, biotechnology or from general process areas such as catalysis, hydrogenation, oxidation, energy generation, environmental protection. The topic should reflect an area of the chemical industry likely to grow rapidly in the near future.

The course will involve a literature search into the latest technology from your topic area, using both academic and industrial sources. A number of business strategy models, including the STEEP model and the Porter’s 5-forces model, will be introduced during the course. You will apply these models to your chosen topic area in an attempt to understand in greater depth the commercial and technological forces that generate competitive advantage for companies that will ultimately lead to long term business success.

HOT TOPICS: Catalysis in Synthesis: The Basics, Key Techniques and Cutting-Edge DevelopmentsSummer 2018 – runs every other year Professor Ian Fairlamb

Catalysis is of fundamental importance in many fields of study, from sustainable and clean synthetic chemistry through to biology. The ability to affect chemical transformations in a clean and efficient manner is of central importance in 21st century chemical processes, with both academia and industry relying heavily on catalytic methods.

This 1 day course begins with two 50 minute lectures detailing the cutting-edge of catalysis, the techniques commonly used to probe mechanistic aspects and the problems that need to be addressed (delivered by IJSF; you will receive a handout to accompany this part of the course). The catalysis field is cross-disciplinary, employing both homogeneous and heterogeneous processes. Therefore the course will reflect these differences and identify complementary themes. These latter themes are essential for the identification and development of new catalytic methods.

The lectures will be followed by a ‘literature critique’ session (lasting ca. 1.5 hours). You will be assigned to a group of 3 or 4 students, and asked to critique one specific paper (supported by related work in the field). This will be presented to the rest of the group and discussed in detail. A topic and paper will be assigned to a group students (by IJSF) a month before the course begins. It will be important to meet with your assigned group, to discuss the strengths and weaknesses of the paper, moreover come up with alternative methods / approaches for addressing the problem outlined in the paper or indeed where the work might head in the future. In the final part of the course (afternoon session; lasting ca. 1.5 hours), you will be given a series of synthetic targets (on the day) and asked to devise routes to these using the methods described in the introductory lectures, whilst also drawing on your own knowledge of chemical transformations. Your ideas will be presented to the rest of the group on the blackboard (using a ‘chalk n talk’ type presentation).

Pre-requisites:Some background training in synthetic chemistry (organic and inorganic) and instrumental methods (e.g. NMR, IR, MS, X-ray). Organic Chemistry or Inorganic Chemistry problem-solving (either desired, but not essential).

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Maximum of 15 students

HOT TOPICS: Activation of small Molecules and Catalysis of Transition MetalsProfessor Robin Perutz and Dr Jason LynamSummer 2017 – runs every other year

This topic has brought three Nobel Prizes in the last 10 years, the most recent in 2010. Transition metal complexes are capable of reacting with most small molecules regardless of their inertness towards other reagents. In the products of these reactions, the bonds of the small molecule may be cleaved as in a metal dihydride, or remain intact, as in a metal dihydrogen complex. These products will often transfer the small molecule to suitable organic substrates. Such reactions also underlie many key biological systems. The activation of small molecules in this way underlies extremely important developments in catalysis, especially stereoregular polymerisation. Participants will give talks on recent developments in one of the areas listed below:

1. Organometallics for water oxidation to O2 (Bernhardt, Crabtree)2. Activation of CF bonds (R. H. Crabtree, R. N. Perutz, T. G. Richmond, Torrens, T Braun, S. Johnson, P. Holland, Whittlesey)3. Formation of C-F bonds mediated by transition metals (Ritter, Sanford)4. Mechansitic aspects of transfer hydrogenation (R. Noyori, J. E. Backvall, S. Gladiali, C. P. Casey, R. H. Morris, A. J. Blacker, J. M. J. Williams)5. Interconversion of alkynes (RCºCR) and vinylidenes (C=CR2) through complexation (H. Werner, P. Dixneuf, J. Templeton, A. F. Hill, R. Beckhaus, D. B. Grotjahn, De Angelis, Ishii)6. Z-selective alkene metathesis (RH Grubbs, RR Schrock)7. Role of agostic complexes in catalysis in Groups 4 and 5: theory & experiment (R. H. Grubbs, H. H. Brintzinger, T. Ziegler, R. Meier, R. R. Schrock, M. Brookhart)8. Silation, hydrosilation catalysed by transition metal complexes and silyl migration at transition metal complexes (S. Sabo-Etienne, J. Y. Corey, J. Harrod, D. Tilley)

9. 2-Coordination of SiH bonds and related coordination modes (S. Sabo-Etienne, G. Kubas, J. Y. Corey)10. New CC activation processes (D. Milstein, G. van Koten, W. D. Jones, A. Weller)11. Oxidative addition of arene CH bonds: mechanism, stabilisation of intermediates and catalytic application (W. D. Jones, R. N. Perutz, E. Carmona, D. Milstein)12. (a) Activation of alkane CH bonds, especially recent developments at platinum complexes (J. E. Bercaw, K. I Goldberg, M. Tilset, Perez,) (b) Catalytic dehydrogenation and metathesis of alkanes (R. H. Crabtree, Jensen, A. Goldman, Brookhart)13. Iron catalysis – using an earth-abundant element for nobel metal catalysis (A Fürstner, R. B. Bedford, C Bolm, M. Beller)14. Evidence for alkane complexes (G. Ball, M. W. George, M. Brookhart, R. N. Perutz, A.S. Weller)15. Borane complexes and amine-borane complexes (Sabo-Etienne, Manners, Aldridge, Weller) 16. Catalytic borylation of hydrocarbons (J. F. Hartwig, M. R. Smith III, T. B. Marder, Miayura)17. Exploiting the cooperativity of ligands for activating alcohols (D. Milstein)

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18. Catalysis of amination and hydroamination by transition metal complexes (J. F. Hartwig, J. J. Brunet, R. Taube, T. Mueller, S. Buchwald, B. Messerle)19. Nitrogen reduction by early transition metal dinitrogen complexes (C. C. Cummins, M. Fryzuk, F. G. N. Cloke, Floriani, R. Schrock, Gambarotta, Chirik, Sita)20. Activation and derivatisation of elemental phosphorus and arsenic (C. C. Cummins, G. Bertrand, M Peruzzini)21. Enzymes with MC and MH bonds and their model complexes: hydrogenase, CO dehydrogenase (Fontecilla-Camps, M. Y. Darensbourg, S. W. Ragsdale, F Armstrong, Pickett, Rauchfuss)22. Are all M-C bonds equally strong and why does it matter? (W. D. Jones, R. N. Perutz, O.Eisenstein)23. Breaking C-H bonds with carbene and nitrene ligands (P. J. Perez, H. M. L. Davies)

Pre-requisites: A working knowledge of organometallic chemistry at an undergraduate level is essential

HOT TOPICS: Lasers in ChemistryDr Laurence AbbottSummer 2017 – runs every other year

In the past decade, there have been considerable developments in laser technology, methods and applications, particularly in the commercialisation of turn-key solid-state diode lasers and ultrashort laser systems, which can be used to generate extreme wavelengths. New technologies such as Free Electron Lasers can produce < 100 femtosecond pulses with ultrahigh intensities in regions from the far-infrared (THz) to the extreme ultraviolet, and even X-ray lasers are becoming a possibility. The ability to perform spectroscopic measurements, or transient structural determinations, on unprecedented timescales now exists. Participants of this course should give an overview of a laser-based technique of interest but that is not directly related to your own research. Any unique features of the laser system and any particular advantages or disadvantages of the technique (or two complimentary techniques) should be highlighted. Some general starter references and a list of modern review articles will be provided. Example topics include:

Transient absorption spectroscopy (X-ray, UV-vis, IR, THz) Fluorescence spectroscopy (transient, stimulated, multi-photon, FLIM, single

molecule) Raman spectroscopy (CW, transient, CARS, stimulated) Photothermal, photoacoustic spectroscopy Transient ESR, optically detected magnetic resonance Photodissociation, photoemission, photoelectron spectroscopy Hole burning spectroscopy Cavity ringdown spectroscopy Degenerate wave mixing, photon-/vibrational-echo spectroscopy Optical limiting, z-scan, sum-frequency generation Protein folding (T-jump) Laser ablation and laser desorption mass spectrometry

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HOT TOPICS: Supramolecular and Nanoscale ChemistryProfessor Dave Smith and Dr Victor ChechikSpring 2017 – runs every other year

This course will include an interactive session focussed on critical analysis of published work in a scientific debate. The papers for critique will be drawn from the following list of topics:

The use of small organic molecules to induce solvent gelation via supramolecular ordering.

Supramolecular chemistry on polymeric supports – new chromatography media. Design, synthesis and investigation of molecular scale sensors. Molecular recognition of large biomolecules – proteins, DNA. Supramolecular dendrimer chemistry – molecular recognition using branched

architectures. Designing components for molecular scale computing. Self-assembly – using supramolecular chemistry to generate larger ordered

architectures. Supramolecular catalysis – designing synthetic catalysts to stabilise transition states. Soluble inorganic nanoparticles in catalysis. Inorganic nanoparticles in biological diagnostics and imaging. Organic nanoparticles in drug delivery. Metal-Organic Frameworks. Bringing reactive sites together: catalysis by supramolecular and nanoscale

structures Nanoreactors

Pre-requisites: Undergraduate degree in Chemistry.

HOT TOPICS: Chemical BiologyProfessor Gideon DaviesSpring 2017 – runs every year subject to numbers

What is Chemical Biology? For some it is simply a cynical “re-branding” of techniques used for many years; the only combination of the words “chemistry” and “biology” that hasn’t been used previously! For others, it is a new found synergy between chemistry and biology that opens up whole new areas of biology to exploration – a field where classically-trained chemists are making huge insightful inroads into the study of cellular processes. That the Chemistry Department at Harvard has been renamed “Department of Chemistry and Chemical Biology” hints at the importance this area of science is having in mainstream Chemistry Departments.

We will consider chemical biology to be the harnessing of novel chemistries to study biology; predominantly ‘cell biology’. It is thus quite distinct from biological chemistry – the study of the (curly arrow) chemistry of biological reactions.

How is the use of ‘bio-orthogonal’ chemistry providing insight into previously challenging areas? How are novel reagents providing insight into reactions in living cells and organisms? How is activity-based proteomics allowing chemists to delve into living cell analytical chemistry in a way that has never previously been possible?

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Students will be given a few example areas, but are strongly encouraged to search out ideas, and original research papers, themselves. Presentations must focus on the goal, the chemistry and the subsequent biological insight.

HOT TOPICS: Analytical and Environmental ChemistryProfessor Brendan KeelySummer 2017

The aim of this course is for you to research a topic not directly related to your own research work and to deliver a presentation that achieves an appropriate balance between background information and the latest developments in the area. In particular, the presentation should emphasise and explain the chemistry related to the topic.

The following topics are suggested. You will be asked to make up to three selections in order of preference and, but will talk on only one of your choices. Alternatively you can choose a topic of your own, subject to agreement from the course organiser. You will be contacted in advance to make your choices.

Analytical:

Emerging Technologies for Analysis Strategies for Protein Sequence Determination by MS Characterisation of Pigments in Works of Art Detection of Adulteration of Foods Drugs Testing in Sport Chemistry in the Forensic Analysis of Firearms Isotope Ratio Monitoring Gas Chromatography Mass Spectrometry (basis and

approach) Single Molecule Detection Systems: Reality or Fiction? Lab on a Chip Systems Frontiers in the Analysis of DNA Metals determination by Inductively Coupled Plasma Techniques Chemical and Biological Sensors

Environmental:

Natural Climate-Forcing Factors Proxies for Estimation of Palaeoclimates Estimation of Variations in Atmospheric pCO2 on the Geological Timescale Stable Isotopes of C, N, H as Tracers of Biogeochemical Processes Life in Extreme Environments Application of Techniques from Molecular Biology as Probes of Natural Living

Communities Heterogeneous Atmospheric Chemistry in the Planetary Boundary Layer Production of Secondary Organic Aerosol in the Troposphere Spectroscopic Probes for the Measurement of NOx/NOy Species in the Atmosphere Strategies for Remediation of Contaminated Land Chemical Archaeology

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Arctic warming: Impact and feedbacks Geoengineering

HOT TOPICS: YSBL Journal ClubDr Sandra Greive and Dr Mahima SharmaRuns throughout the year

This course is based on a collaborative query-driven learning model provided by the presentation of a ‘cutting edge’ publication in Structure/Function followed by a group discussion. The YSBL Hot topics Journal club mainly focuses on training students for systematic evaluation/appraisal of the latest scientific literature. A self-directed component is facilitated by the individual choice in the manuscript to be presented and an open-ended Q&A discussion conducted in a supportive learning environment.Participation is open to all interested parties and currently is mostly composed of a mixture of graduate research students (masters and PhD), Post-Doctoral Research Associates from YSBL and Biochemistry/Biophysics research laboratories situated within Biology L-block. Other attendees and discussion participants often include senior scientists from these areas as well. This mixed participant group creates an environment where collective information and knowledge can be efficiently transferred between members.

The learning goals of this journal club are to:

increase exposure to cutting edge advances in concepts and techniques related to structural and functional Biology;

provide an opportunity to practice presentation skills; promote discussion of interesting science; provide an opportunity for developing critical analysis skills.

These are fortnightly half-hour meetings with a format where two participants each present the key data points and conclusions from their selected publication (7 minutes) followed by a short discussion (7 minutes). Further discussion after the meeting is encouraged. Publications selected for presentation can be on any topic related to structural and/or functional biology with the provision that it be less than 6 months since publication and be in a top-tier peer-reviewed journal with an impact factor 8 or greater. Selected publications will be disseminated to the group on Monday morning for presentation on Thursday morning.

While participation is always encouraged for all YSBL member postdoctoral and student researchers, we propose that students officially enrolled in this course as a “hot-topics” module have additional requirements. These are to present at least once and to read both selected papers prior to each meeting, equating to at least 6 h over the course of an academic year. Enrolled students are strongly encouraged to participate actively in the discussion to demonstrate that they have read the presented papers prior to the meeting. A form will need to be signed by one of the course organisers to confirm satisfactory completion.

The club meets at 11am on alternate Thursdays in term time. Usually in Biology M052. Details confirmed when papers are circulated. ===================================================================

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RENEWCHEM: Sustainable Manufacturing for the chemical industrySpring 2017

These workshops are part of the Green Chemistry RENEWCHEM programme and numbers are limited. For more information contact Dr Rob McElroy (rob.mcelroy@york.ac.uk ) or Louise Summerton (louise.summerton@york.ac.uk). If you do complete parts of this course, it can count towards your iDTC course requirements

Increasing demand for chemicals worldwide, depleting resources, stricter legislation and the rising cost of waste disposal are placing increasing pressure on the chemical and related industries. For any organisation to survive in the current climate, the issue of sustainability must be fundamental to the way it operates. A sustainable manufacturing approach will enable economic growth to be combined with environmental and social sustainability, and will be realised via collaboration between a multidisciplinary community including chemists, biologists, engineers, environmental scientists, economists and policy makers. Hence employees with new skills, knowledge and experience are needed.

After close consultation with industry this course has been designed to provide students with an insight into the issues surrounding sustainable manufacturing including change management, commercialisation, environmental impact, circular economy, legislation and bio-resources including the conversion of waste into valuable products. This multidisciplinary content will incorporate industrial case studies, providing access to real business issues, and will be delivered by experts from departments across campus as well as from industry. The course is open to all with an interest in the future of sustainable manufacturing.

Workload: 5 x 2 hour sessions each including an introductory lecture followed by interactive workshop. (Students may sign up for all or some of the course).

Content:• ‘What is green chemistry?’ Dr Rob McElroy, Chemistry Dept.• ‘Safer chemicals for healthy buildings’, Dr Nic Carslaw, Environment Dept.• ‘Business case for green’ Prof. Peter Ball, Management School• ‘Running a sustainable chemical company’ Dr Glenn Hurst, Chemistry Dept & Robert Brocklesby, MD, Brocklesby Ltd • ‘From academic to applied – bench to pilot scale’ (including a site tour) Dr Joe Ross, Biorenewables Development Centre

We also expect to hold a series of optional evening lectures from collaborating businesses and other local companies.

Please note that many of our courses require a certain number of students to run. Therefore, in some cases, a decision may be taken not to run a course in a particular year. Some of the courses offered are part of other programmes within the University – therefore numbers may be limited. Every effort will be made to ensure that students can attend their chosen course if possible.

Some courses are organised by other departments and will therefore need the agreement of both your supervisor and the course organiser for you to attend.

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Every effort is made to ensure that course information in this handbook is correct. However, in some circumstances, changes may be necessary.

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UNIVERSITY OF YORK TRAINING

In addition to training offered within the department, the University also offers training opportunities in a variety of areas to help you expand your own transferable skills.

I. Languages for All (LFA): You can improve you language skills by taking a foreign language course with LFA. Successful completion of the course means you can claim back the cost of the course from the Chemistry Graduate School – just keep your receipts. Further information can be found at: http://www.york.ac.uk/lfa/

II. Centre for English Language Teaching (CELT): The Centre for English Language Teaching run a range of courses to help students with both academic and general English language skills. Further information about the support available can be found at: http://www.york.ac.uk/celt/ CELT will also be running sessions within the Chemistry Department for International students to offer tuition in both writing and giving presentations.

III. Research Excellence Training Team (RETT): Throughout your research degree, you can access a range of training opportunities offered by RETT. Successful researchers think carefully and strategically not just about their research but about their skills, objectives and both personal and professional development. The Department and your supervisor will help develop your intellectual skills in your chosen subject area and RETT offers training and development opportunities which enable you to excel in your chosen field. In line with the principles of the Concordat to Support the Career Development of Researchers, the RETT are committed to providing all researchers with a supportive, stimulating and structured framework in which to develop your professional skills and career profile. Find out more at: http://www.york.ac.uk/admin/hr/researcher-development

IV. York Learning and Teaching Award (YLTA): This accredited nine month programme is for researchers wanting to develop their teaching skills ahead of an academic career in higher education. Find out more:https://www.york.ac.uk/staff/research/training-forums/research-excellence-training-team/postgraduates-who-teach/york-learning-and-teaching-award/

V. The Researcher Development Framework (RDF): This underpins the delivery plans of the Research Councils. It provides a framework of the knowledge, behaviour and attributes of successful researchers, enables self-assessment of strengths and areas for further development. The RDF has four main areas: Knowledge and Intellectual Abilities Personal Effectiveness Research Governance Engagement, Impact and Influence

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NATIONAL TRAINING

Vitae

Vitae is a national organisations championing the personal, professional and career development of researchers in higher education and research institutes. Their website provides a wealth of information on issues relating to postgraduates, career development, advice on motivation for doing postgraduate research, how to manage your research and how to develop: https://www.vitae.ac.uk/

Vitae GRADschool is a national workshop for PhD students in their 2nd and 3rd year which is designed to support you in making informed choices about what you would like to do after your PhD. The programme will help you understand the skills you have and to help broaden those skills to become a more effective researcher, as well as help you to plan and manage the next stage of your career. You will meet other researchers from a variety of disciplines and work with experiences tutors who will share their career experiences. Further information about GRADschools can be found on their website: www.vitae.ac.uk/events . Please note that there is a significant cost to this course so you should discuss attendance with your supervisor.

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