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Department of Chemistry

Department of Chemistry course timetable

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Tue 4 Feb – Tue 10 Mar

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February 2020

Tue 4
Chemistry: Machine Learning in Chemistry 101 new (8 of 8) Finished 13:00 - 14:00 Unilever Lecture Theatre

This graduate-level course gives an overview of machine learning (ML) techniques that are useful for solving problems in Chemistry, and particularly for the computational understanding and predictions of materials and molecules at the atomic level.

In the first part of the course, after taking a quick refresher of the basic concepts in probabilities and statistics, students will learn about basic and advanced ML methods including supervised learning and unsupervised learning.

During the second part, the connection between chemistry and mathematical tools of ML will be made and the concepts on the construction of loss functions, representations, descriptors and kernels will be introduced.

For the last part, experts who are actively using research methods to solve research problems in chemistry and materials will be invited to give real-world examples on how ML methods have transformed the way they perform research.

Chemistry: DD5 Medicinal Chemistry Game Workshop Finished 14:00 - 17:00 Todd-Hamied

A real drug discovery example will be used. After a brief introduction to the task and the chemical startpoint, we will split into teams and iteratively try to design improved analogues. Molecules will be marked “in real time” during the session to recreate the design-make-test-analysis cycle, then teams can compare their optimized molecules, and we can compare them to what happened in real life.

Please note: To take part in this session you will need to have attended DD1-DD4.

Wed 5
Chemistry: SC1-10 Statistics for Chemists (7 of 8) Finished 10:00 - 12:00 G30

This course is made up of 8 sessions which will be based around the topics below: unlike other courses in the Graduate Lecture Series, it is essential to attend all 8 sessions to benefit from this training. Places are limited so please be absolutely certain upon booking that you will commit to the entire course.

Thu 6
Chemistry: IS4 Research Data Management Finished 10:00 - 12:00 Todd-Hamied

This compulsory session introduces Research Data Management (RDM) to Chemistry PhD students. It is highly interactive and utilises practical activities throughout.

Key topics covered are:

  • Research Data Management (RDM) - what it is and what problems can occur with managing and sharing your data.
  • Data backup and file sharing - possible consequences of not backing up your data, strategies for backing up your data and sharing your data safely.
  • Data organisation - how to organise your files and folders, what is best practice.
  • Data sharing - obstacles to sharing your data, benefits and importance of sharing your data, the funder policy landscape, resources available in the University to help you share your data.
  • Data management planning - creating a roadmap for how not to get lost in your data!
Fri 7
Chemistry: DD6 Toxicity and Drug Safety Finished 14:00 - 15:00 Unilever Lecture Theatre

Drug safety remains the primary cause of compound attrition when developing new medicines and consequently the ability to understand and predict toxicity is regarded as high priority within the pharmaceutical sector. This lecture will describe some common safety liabilities and ongoing work to build a greater understanding of the relationships between chemical structure and toxicity risk that are being harnessed to guide the design of safer compounds.

Mon 10
Chemistry: SC1-10 Statistics for Chemists (8 of 8) Finished 10:00 - 12:00 G30

This course is made up of 8 sessions which will be based around the topics below: unlike other courses in the Graduate Lecture Series, it is essential to attend all 8 sessions to benefit from this training. Places are limited so please be absolutely certain upon booking that you will commit to the entire course.

Chemistry: Quantum Computing new (1 of 4) Finished 14:00 - 15:00 Todd-Hamied

Lecture 1 - Fundamentals of Quantum Computing A short summary of all the basic quantum computing knowledge needed to do quantum chemistry on a quantum computer.

Lecture 2 - Encoding chemistry systems in quantum computers

  • Second quantization
  • Jordan-Wigner and Bravyi-Kitaev transforms
  • Molecular orbital encoding
  • State Preparation

Lecture 3 - Quantum algorithms for energy calculations

  • NISQ: Variational quantum algorithms
  • Future: Phase Estimation algorithms

Lecture 4 - Advanced quantum chemistry quantum computing algorithms

  • Excited Algorithms: QSE, Constrained Minimisation, etc
  • Special Ansatz using symmetry
  • Imaginary time evolution
  • TBA
Wed 12
Chemistry: DD7 Kinase Inhibitor Case Studies Finished 14:00 - 15:00 Unilever Lecture Theatre

Kinase drug discovery remains to be an area of significant and growing interest across academia and in the pharmaceutical industry - there are approximately 30 FDA approved small molecule inhibitors which target kinases, half of which were approved in the last 3 years. This lecture will give an insight into the medicinal chemistry story behind one clinical candidate and 2 marketed drugs. Crystal structures will be used to explain general principles behind designing for kinase inhibition, and some more advanced topics will be covered such as prodrugs, covalent inhibition and consideration of mutation status in drug discovery

Thu 13

FS1 - Successful Completion of a Research Degree An hour devoted to a discussion of how to plan your time effectively on a day to day basis, how to produce a dissertation/thesis (from first year report to MPhil to PhD) and the essential requirements of an experimental section.

FS2 - Dignity@Study The University of Cambridge is committed to protecting the dignity of staff, students, visitors to the University, and all members of the University community in their work and their interactions with others. The University expects all members of the University community to treat each other with respect, courtesy and consideration at all times. All members of the University community have the right to expect professional behaviour from others, and a corresponding responsibility to behave professionally towards others. Nick will explore what this means for graduate students in this Department with an opportunity to ask questions more informally.

This is a compulsory session for 1st year postgraduates.

Fri 14
Chemistry: DD9 Process Chemistry Finished 13:00 - 15:30 Todd-Hamied

Two complementary lecture from industry experts on process chemistry from GSK and Syngenta will share their experiences and challenges gathered over many years of experience.

Mon 17
Chemistry: DD8 Agrochemical Discovery Finished 11:00 - 12:00 Todd-Hamied

As the world population continues to grow, so does the need to increase global food production sustainably with limited resources. Agrochemicals, in the form of herbicides, fungicides and insecticides, provide an important tool for farmers to combat the weeds, fungi and insect pests that target their crops and help to ensure reliable yields and quality produce. Resistance, emerging pests, abiotic stress and regulatory pressure all drive an ongoing search for new and more innovative crop protection products. This lecture will outline the process used to discover new agrochemicals, from lead generation through to development. It will show the critical roles that chemistry, biology and human & environmental safety play, illustrated with a number of recent examples.

Chemistry: Quantum Computing new (2 of 4) Finished 14:00 - 15:00 Todd-Hamied

Lecture 1 - Fundamentals of Quantum Computing A short summary of all the basic quantum computing knowledge needed to do quantum chemistry on a quantum computer.

Lecture 2 - Encoding chemistry systems in quantum computers

  • Second quantization
  • Jordan-Wigner and Bravyi-Kitaev transforms
  • Molecular orbital encoding
  • State Preparation

Lecture 3 - Quantum algorithms for energy calculations

  • NISQ: Variational quantum algorithms
  • Future: Phase Estimation algorithms

Lecture 4 - Advanced quantum chemistry quantum computing algorithms

  • Excited Algorithms: QSE, Constrained Minimisation, etc
  • Special Ansatz using symmetry
  • Imaginary time evolution
  • TBA
Tue 25
Chemistry: Quantum Computing new (3 of 4) Finished 14:00 - 15:00 Todd-Hamied

Lecture 1 - Fundamentals of Quantum Computing A short summary of all the basic quantum computing knowledge needed to do quantum chemistry on a quantum computer.

Lecture 2 - Encoding chemistry systems in quantum computers

  • Second quantization
  • Jordan-Wigner and Bravyi-Kitaev transforms
  • Molecular orbital encoding
  • State Preparation

Lecture 3 - Quantum algorithms for energy calculations

  • NISQ: Variational quantum algorithms
  • Future: Phase Estimation algorithms

Lecture 4 - Advanced quantum chemistry quantum computing algorithms

  • Excited Algorithms: QSE, Constrained Minimisation, etc
  • Special Ansatz using symmetry
  • Imaginary time evolution
  • TBA
Fri 28
Chemistry: Green Chemistry new (1 of 2) Finished 09:00 - 13:00 Todd-Hamied

This course will provide an overview of Sustainable Chemistry in the Pharmaceutical Industry: Motivation and Legislation It will cover the following in more detail;

  • Solvents - tools for analysing the merits and drawbacks of different solvents and tools for selecting the optimum solvent for chromatography, common reactions, work-ups and other purposes
  • Reagents - tools for analysing the merits and drawbacks of different reagents and substrate scope for some greener reagents for common transformations
  • Metrics: Yield, Atom Economy, Reaction Mass Efficiency, E-factor, Process Mass Intensity, Life Cycle Analysis and Carbon Footprinting
Chemistry: Green Chemistry new (2 of 2) Finished 13:00 - 17:00 Todd-Hamied

This course will provide an overview of Sustainable Chemistry in the Pharmaceutical Industry: Motivation and Legislation It will cover the following in more detail;

  • Solvents - tools for analysing the merits and drawbacks of different solvents and tools for selecting the optimum solvent for chromatography, common reactions, work-ups and other purposes
  • Reagents - tools for analysing the merits and drawbacks of different reagents and substrate scope for some greener reagents for common transformations
  • Metrics: Yield, Atom Economy, Reaction Mass Efficiency, E-factor, Process Mass Intensity, Life Cycle Analysis and Carbon Footprinting

March 2020

Mon 2
Chemistry: IS5 SciFinder and Reaxys Finished 11:30 - 13:00 U203

A ‘highly recommended’ optional course introducing electronic databases SciFinder and Reaxys presented by Professor Jonathan Goodman comprising of presentation followed by hands-on investigation.

SciFinder https://www.cas.org/products/scifinder provides access to biochemical, chemical, chemical engineering, medical and other related information in journal and patent literature. Bibliographic, substance and reaction information is available. SciFinder includes references from more than 10,000 scientific journals and patent information from 63 patent issuing authorities. Sources include journals, patents, conference proceedings, dissertations, technical reports and books. It is one of the world’s largest collections of organic and inorganic substance information.

It is possible to search by topic, author, company name, chemical structure, substructure, structure similarity and reaction. Personal registration is required for access to SciFinder on- and off-campus, please follow the instructions at: https://www-library.ch.cam.ac.uk/scifinder

Reaxys combines the content of CrossFire Beilstein, Gmelin and the Patent Chemistry Database in one search. Validated reaction and substance data are integrated with synthesis planning. Data from all three sources are merged into one substance record. Unlimited access on-campus via the web: https://www.reaxys.com/. Off-campus access via Raven password. (Personal registration is not required for access).

Please see the prerequisites. Please bring your own laptop for the practical element of the session.

Chemistry: Quantum Computing new (4 of 4) Finished 14:00 - 15:00 Todd-Hamied

Lecture 1 - Fundamentals of Quantum Computing A short summary of all the basic quantum computing knowledge needed to do quantum chemistry on a quantum computer.

Lecture 2 - Encoding chemistry systems in quantum computers

  • Second quantization
  • Jordan-Wigner and Bravyi-Kitaev transforms
  • Molecular orbital encoding
  • State Preparation

Lecture 3 - Quantum algorithms for energy calculations

  • NISQ: Variational quantum algorithms
  • Future: Phase Estimation algorithms

Lecture 4 - Advanced quantum chemistry quantum computing algorithms

  • Excited Algorithms: QSE, Constrained Minimisation, etc
  • Special Ansatz using symmetry
  • Imaginary time evolution
  • TBA
Single Cell RNA Sequencing new (1 of 4) Finished 16:00 - 18:00 Unilever Lecture Theatre

The course will outlay bioinformatic analysis of cell populations from single-cell RNA including visualisation, clustering and functional analysis of genes. This will be using the programming language R and packages such as Seurat. Participants are encouraged to bring their own laptop to follow along.

Lesson 1

  • 4.00 - 4.45pm = Setting up
  • 4.45 - 5.00pm = Break, questions
  • 5.00 - 6.00pm = Introduction to scRNA-Seq

Lesson 2

  • 1.00 - 1.45pm = QC, Normalising, Feature Selection
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Scaling, Dimensionality reduction, Determining dimensionality of dataset

Lesson 3

  • 1.00 - 1.45pm = Clustering, UMAP/t-SNE
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Cluster biomarkers, Assigning cell type identity, Differential expression, Enrichment

Lesson 4

  • 1.00 - 1.45pm = Work on dataset from Stanford/literature/own dataset
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Work on dataset from Stanford/literature/own dataset
Tue 3
Chemistry: DD10 Process Chemistry Workshop new (1 of 2) Finished 10:00 - 13:00 Todd-Hamied

In this session, Dr. Mukund S. Chorghade will discuss the pivotal role played by Process Chemistry / Route Selection in the progress of a drug from conception to commercialization. The medicinal chemistry routes for synthesis are usually low yielding and are fraught with capricious reactions, cryogenic temperatures, tedious chromatography and problems in scale-up to multi-kilo and multi-ton levels. Considerable research efforts have to be expended in developing novel, cost efficacious and scalable processes and seamlessly transferring these technologies to manufacturing operations. These principles will be exemplified by process development case studies on a variety of pharmaceutical moieties such as anti-epileptic and an anti-asthma drugs. We were able to also discover a large number of New Chemical Entities by our new “Process Chemistry Driven Medicinal Chemistry”

We will exemplify advances in proprietary in vitro green chemistry-based technology, mimicking in vivo metabolism of several chemical entities used in pharmaceuticals, cosmetics, and agrochemicals. Our catalysts enable prediction of metabolism patterns with soft-spot analysis Metabolites are implicated in adverse drug reactions and are the subject of intense scrutiny in drug R&D. Present-day processes involving animal studies are expensive, labor-intensive and chemically inconclusive. Our catalysts (azamacrocycles) are sterically protected and electronically activated, providing speed, stability and scalability. We predict structures of metabolites, prepare them on a large scale by oxidation, and elucidate chemical structures. Comprehensive safety evaluation enables researchers to conduct more complete in vitro metabolism studies, confirm structure and generate quantitative measures of toxicity.

Chemistry: Contemporary Chemistry to Tackle 21st Century Challenges new (1 of 8) Finished 14:30 - 15:00 Todd-Hamied

Chemistry plays a very crucial role in tackling 21st century global challenges. From climate change mitigation to discovering therapeutic strategies for human health and driving sustainable energy production and usage - we are faced with many challenges for which chemical sciences has been providing and will continue to provide many plausible solutions.

Much of the research involved in developing these initiatives requires a huge drive towards interdisciplinary research networks. As such, this course has been developed with some of our colleagues from across the Chemistry Department who are working on exciting and emerging areas with this multidisciplinary focus.

This course will introduce how chemistry can be used as a tool to solve these challenges. First session will include the introduction. Each lecture following this will focus on a different branch, area or concept of chemistry covering the fundamental chemistry and background of how it works, any advances to date and the applications towards tackling these global challenges.

The first session is compulsory, plus choose optional sessions you wish to attend when you make your booking.

  • Session 1: Introduction
  • Session 2: Organic Electronics
  • Session 3: Electrochemistry (Batteries)
Chemistry: Contemporary Chemistry to Tackle 21st Century Challenges new (2 of 8) Finished 15:00 - 17:00 Todd-Hamied

Chemistry plays a very crucial role in tackling 21st century global challenges. From climate change mitigation to discovering therapeutic strategies for human health and driving sustainable energy production and usage - we are faced with many challenges for which chemical sciences has been providing and will continue to provide many plausible solutions.

Much of the research involved in developing these initiatives requires a huge drive towards interdisciplinary research networks. As such, this course has been developed with some of our colleagues from across the Chemistry Department who are working on exciting and emerging areas with this multidisciplinary focus.

This course will introduce how chemistry can be used as a tool to solve these challenges. First session will include the introduction. Each lecture following this will focus on a different branch, area or concept of chemistry covering the fundamental chemistry and background of how it works, any advances to date and the applications towards tackling these global challenges.

The first session is compulsory, plus choose optional sessions you wish to attend when you make your booking.

  • Session 1: Introduction
  • Session 2: Organic Electronics
  • Session 3: Electrochemistry (Batteries)
Wed 4
Chemistry: DD10 Process Chemistry Workshop new (2 of 2) Finished 10:00 - 13:00 Todd-Hamied

In this session, Dr. Mukund S. Chorghade will discuss the pivotal role played by Process Chemistry / Route Selection in the progress of a drug from conception to commercialization. The medicinal chemistry routes for synthesis are usually low yielding and are fraught with capricious reactions, cryogenic temperatures, tedious chromatography and problems in scale-up to multi-kilo and multi-ton levels. Considerable research efforts have to be expended in developing novel, cost efficacious and scalable processes and seamlessly transferring these technologies to manufacturing operations. These principles will be exemplified by process development case studies on a variety of pharmaceutical moieties such as anti-epileptic and an anti-asthma drugs. We were able to also discover a large number of New Chemical Entities by our new “Process Chemistry Driven Medicinal Chemistry”

We will exemplify advances in proprietary in vitro green chemistry-based technology, mimicking in vivo metabolism of several chemical entities used in pharmaceuticals, cosmetics, and agrochemicals. Our catalysts enable prediction of metabolism patterns with soft-spot analysis Metabolites are implicated in adverse drug reactions and are the subject of intense scrutiny in drug R&D. Present-day processes involving animal studies are expensive, labor-intensive and chemically inconclusive. Our catalysts (azamacrocycles) are sterically protected and electronically activated, providing speed, stability and scalability. We predict structures of metabolites, prepare them on a large scale by oxidation, and elucidate chemical structures. Comprehensive safety evaluation enables researchers to conduct more complete in vitro metabolism studies, confirm structure and generate quantitative measures of toxicity.

Fri 6
Chemistry: IS2 Citation Database Search Skills Finished 10:00 - 12:00 Todd-Hamied

A ‘recommended’ optional course for Chemistry graduates that introduces all the relevant online databases available to you in the university: citation databases such as Web of Science, Scopus, and PubMed, which index all the scientific literature that is published, as well as chemistry and related subject-specific databases. You will be guided on how to search citation databases effectively and the session includes a hands-on element where you can practice - please bring your own laptop.

The session will be most suitable for those who are new to searching citation databases or would like a refresher.

Please note that this session will not cover searching the databases Reaxys and SciFinder. These are covered by IS5.

  • Please bring your own laptop so you can participate in the practical element of the session
Mon 9
Single Cell RNA Sequencing new (2 of 4) Finished 13:00 - 15:00 Todd-Hamied

The course will outlay bioinformatic analysis of cell populations from single-cell RNA including visualisation, clustering and functional analysis of genes. This will be using the programming language R and packages such as Seurat. Participants are encouraged to bring their own laptop to follow along.

Lesson 1

  • 4.00 - 4.45pm = Setting up
  • 4.45 - 5.00pm = Break, questions
  • 5.00 - 6.00pm = Introduction to scRNA-Seq

Lesson 2

  • 1.00 - 1.45pm = QC, Normalising, Feature Selection
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Scaling, Dimensionality reduction, Determining dimensionality of dataset

Lesson 3

  • 1.00 - 1.45pm = Clustering, UMAP/t-SNE
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Cluster biomarkers, Assigning cell type identity, Differential expression, Enrichment

Lesson 4

  • 1.00 - 1.45pm = Work on dataset from Stanford/literature/own dataset
  • 1.45 - 2.00pm = Break, questions
  • 2.00 - 3.00pm = Work on dataset from Stanford/literature/own dataset
Tue 10
Chemistry: Contemporary Chemistry to Tackle 21st Century Challenges new (3 of 8) Finished 15:00 - 17:00 Todd-Hamied

Chemistry plays a very crucial role in tackling 21st century global challenges. From climate change mitigation to discovering therapeutic strategies for human health and driving sustainable energy production and usage - we are faced with many challenges for which chemical sciences has been providing and will continue to provide many plausible solutions.

Much of the research involved in developing these initiatives requires a huge drive towards interdisciplinary research networks. As such, this course has been developed with some of our colleagues from across the Chemistry Department who are working on exciting and emerging areas with this multidisciplinary focus.

This course will introduce how chemistry can be used as a tool to solve these challenges. First session will include the introduction. Each lecture following this will focus on a different branch, area or concept of chemistry covering the fundamental chemistry and background of how it works, any advances to date and the applications towards tackling these global challenges.

The first session is compulsory, plus choose optional sessions you wish to attend when you make your booking.

  • Session 1: Introduction
  • Session 2: Organic Electronics
  • Session 3: Electrochemistry (Batteries)