School Of Chemistry Junior Sophister Handbook 2019/20

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School of ChemistryJunior SophisterHandbook2019/201

Table of ContentsCourse‐specific webpages.2Emergency Procedure .2Contact Details .3Information for all School of Chemistry JS Students .4Junior Sophister 2019/2020 .4Introduction to Chemistry at TCD .4Moderatorships in Chemistry .4Staff, Research and Facilities .5Lectures .5Practicals .6Examinations .6Feedback and Evaluation .7Academic Year Structure .7Key Dates .7Seminars and Special Lectures .7Senior Sophister Year .7Modules to be taken in JS Year of Moderatorship in Chemistry (Chem) .8Modules to be taken in JS Year of Moderatorship in Medicinal Chemistry (MedChem) .10Modules to be taken in JS Year of Moderatorship in Chemistry with Molecular Modelling (CMM) .12Components contributing to module marks.14Visiting students.14Prizes .15Careers .15Library and Reference Databases .15Counselling .15Graduate Attributes .16Useful links to College services and support .17Relevant University Regulations .17Appendix 1: Examination Regulations .18Appendix 2: Description of the European Credit Transfer System (ECTS) .22Appendix 3: College regulation regarding plagiarism .23Appendix 4: Mark scheme and schedule of grades in Sophister years .24Appendix 5: Medical and Self‐Certification .261

Alternative formats of this Handbook can be made available upon request. A large‐print hardcopy is also available to view in the School Office.Course‐specific webpagesEach course offered by the School has a dedicated webpage. For those in N‐PCAM, there is also adedicated nanoscience website at d.ie/Study/current //chemistry.tcd.ie/Study/current dex.phphttp://chemistry.tcd.ie/Study/current tcd.ie/Study/current students/undergraduate/N‐PCAM/index.phpEmergency ProcedureIn the event of an emergency, dial Security Services on extension 1999.Security Services provide a 24‐hour service to the college community, 365 days a year. They arethe liaison to the Fire, Garda and Ambulance services and all staff and students are advised tophone extension 1999 ( 353 1 896 1999) in case of an emergency.Should you require any emergency or rescue services on campus, you must contact SecurityServices. This includes chemical spills, personal injury or first‐aid assistance. It is recommendedthat all students save at least one ICE (in case of emergency) phone number in their mobilephones.2

Contact DetailsPositionPersonE‐mailPhoneHead of SchoolProf. Mike Lyonsheadchem@tcd.ie896 1423Director of TeachingProf. Eoin ScanlanEoin.Scanlan@tcd.ie896 2514Associate DTLUGProf. Yurii Gun’koigounko@tcd.ie896 3543JS Year CoordinatorProf. Mike Southernsoutherj@tcd.ie896 3411MedChem CoordinatorProf. Mathias Sengesengem@tcd.ie896 8537CMM CoordinatorProf. Graeme Watsonwatsong@tcd.ie896 1357N‐PCAM CoordinatorProf. Hongzhou ZhangHongzhou.Zhang@tcd.ie896 4655School ManagerDr. Sinéad Boycesboyce@tcd.ie896 4587School OfficeMs. AnneMarie Farrellfarrea25@tcd.ie896 1726School OfficeMr. Ben Powerpowerbe@tcd.ie896 2040Global OfficerDr. Niamh McGoldricknmcgoldr@tcd.ie896 3463and Learning (DTLUG)Contact details for all staff in the School can be found at http://chemistry.tcd.ie/staff/3

Information for all School of Chemistry JS StudentsJunior Sophister 2019/20Welcome to the School of Chemistry for your JS year. We hope that you have a wonderfulexperience in a year that is quite a transition from the earlier JF and SF years. The JS and SS yearsbring about more in‐depth chemistry education than you have experienced before, with greateremphasis on theoretical as well as practical education and training. We wish you all the best forthis academic year and the staff in the school look forward to working with you. The JS YearCoordinator is Prof. Mike Southern (southerj@tcd.ie).Introduction to Chemistry at TCDChemistry holds a key position among the sciences. It involves the study of matter, i.e., thecomposition, structure and properties of substances and the changes they undergo. Life on earthowes its origin to a series of these chemical changes. Formal chemistry teaching in TCDcommenced in August 1711 as part of the new School of Medicine. The main building includestwo lecture theatres and four research laboratories. The Cocker laboratories were completed in1997 and provide facilities for the teaching of preparative inorganic and organic chemistry. TheSami Nasr Institute for Advanced Materials (SNIAM) building, which was completed in 2000,provides ca. 1500 m2 of accommodation for the School of Chemistry. This includes a PhysicalChemistry teaching laboratory and six research laboratories that house ca. 40 researchers. Thisinstitute also houses the School of Physics. Computational Chemistry research is housed in theLloyd Institute on a multidisciplinary computational‐science floor comprising researchers fromMathematics, Physics, Chemistry and High Performance Computing. In addition, chemists play animportant role in interdisciplinary research taking place in two of TCD’s newest researchinstitutes: (i) The Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN),which was formally opened in January 2008 and (ii) the Trinity Biomedical Sciences Institute(TBSI), which was inaugurated in July 2011.Moderatorships in ChemistryThe School of Chemistry currently offers four QQI‐NFQ Level‐8 moderatorships, namely Science(Chemistry), Medicinal Chemistry (MedChem), Chemistry with Molecular Modelling (CMM), andNanoscience, Physics and Chemistry of Advanced Materials (N‐PCAM), which is a shared coursebetween the Schools of Physics and Chemistry. All of the direct‐entry courses were developed in4

response to changes in the modern subject and identified needs for graduates with special skillsin Ireland.Staff, Research and FacilitiesThe School currently has 25 academic staff and 14 technical staff. The School has an activeresearch programme, with approximately 100 postgraduate students and postdoctoralresearchers. They study a wide range of chemistry subjects in fields such as organic, inorganic,organometallic, physical, theoretical, medicinal, analytical, material, polymer, environmental, andsupramolecular chemistry. Research income is earned from national, international andcommercial sources and the School has held grants in all relevant research programmes fundedby the EU.The College also fosters an interdisciplinary approach to research, with members of the Schoolhaving strong links with colleagues in the physical, technological and biological sciences bothwithin College, nationally and internationally.The School is well equipped for its research activities, having Bruker 600 and 400 MHz NMRs andaccess to an Agilent 400 MHz high‐field multi‐nuclear NMR, FTIR, dispersive IR and UV‐Visspectrometers, high performance liquid chromatography (HPLC) and gas chromatography (GC)equipment, a Bruker SMART Apex Kappa Duo, Bruker D8 Quest ECO single crystal and a Bruker D2Phaser powder diffractometer, a Micromass LCTTM (TOF) mass spectrometer, thermogravimetricanalysis and differential scanning calorimetry, dynamic light scattering, severalspectrofluorimeters for steady‐state and time‐resolved fluorescence measurements, circular andlinear dichroism, and a large range of wave generators and potentiostats for cyclic voltammetry.LecturesLectures should begin on the hour and end 50 minutes later. Timetables will be published throughthe portal https://my.tcd.ie and should be checked regularly for changes to the original schedule.Module descriptors and learning outcomes for your modules are available on Blackboard.Attendance at lectures may be recorded. Lecture notes/quizzes will be provided throughBlackboard (https://tcd.blackboard.com/webapps/login/) and details related to fees, assessment,5

exam timetables etc. can be found on the Academic Registry's website n the JS year, practical classes take place over one‐and‐a‐half days each week. In Semester 1there are 6 weeks of organic chemistry and 4 weeks of inorganic chemistry in the Cocker lab; inSemester 2, there are 2 weeks of inorganic chemistry in the Cocker lab and 6 weeks of physicalchemistry in the Physical Chemistry lab in the SNIAM building. Practical work is assessed in‐course, with the lab marks obtained in each discipline contributing to 50% of the overall mark forthe 10‐ECTS modules CHU33103 (inorganic), CHU33203 (organic) and CHU33304 (physical).Attendance at chemistry practical classes is compulsory for students. You may be deemed non‐satisfactory if you fail to attend and/or submit more than a third of the required coursework forany module.ExaminationsAn overall pass mark of 40% is required to proceed to the Senior Sophister year. Students whosuccessfully complete their JS year may opt to leave with a level‐7 ordinary B.A. (B.A.(Ord.)). Fulldetails of the Junior Sophister Science (TR071) examination regulations may be found in theAppendices. The same regulations apply to the School's direct‐entry courses. Past examinationpapers are available from the Academic Registry's past‐papers/annual/) and can be used to familiarizeyourself with the structure of examination papers. The JS Chemistry mark contributes to 35% ofthe final Moderatorship degree mark. Further information can be found in Appendix 1.6

Feedback and EvaluationThe courses offered by the School benefit from student feedback. Rather than waiting until theend of a module to request online feedback, the School of Chemistry has instituted a SophisterLiaison Committee (SLC). Committee members comprise the DTLUG/Associate DTLUG, the SchoolConvenor, JS and SS class reps, and Heads of Discipline or their representatives and the meetingsare minuted. Class reps should collate feedback from their fellow students to bring to themeeting, which takes place at least once per semester. If you wish to provide feedback on aspecific module, please complete the online form athttps://www.surveymonkey.com/r/module feedback 2019‐20Academic Year StructureAcademic Year Structure 2019/20Key DatesJS Safety WorkshopStudy/Review Weeks Semester 1:Revision Week Semester 1:Study/Review Week Semester 2:Revision Week Semester 2:Trinity week:Formal Assessment weeksSemester 1 examinationsThursday 5 September 2019Monday 21 October to Friday 25 October 2019Monday 2 December to Friday 6 December 2019Monday 2 March to Friday 6 March 2020Monday 13 April to Friday 17 April 2020Monday 20 April to Friday 24 April 2020Semester 2 examinationsMonday 27 April to Saturday 2 May 2020 (othercontingency days may be added at a later date)Saturday 7 December to Friday 13 December 2019Seminars and Special LecturesDuring the year, lectures on various topics will be arranged by the School, the Werner ChemicalSociety, the Royal Society of Chemistry and/or the Institute of Chemistry of Ireland. You will findmany of them interesting and valuable.Senior Sophister YearSemester 1 of the Senior Sophister year is spent working full‐time on a research project in TCD, inindustry or at a university abroad. The School encourages interested students to go abroad if theyso wish. Those achieving a grade of II‐1 or higher in their JS year will have automatic approval togo abroad but for those with lower grades, the request will be reviewed on a case‐by‐case basis.Arrangements for projects abroad are made in the JS year and will be coordinated by Prof. PeterDunne (P.W.Dunne@tcd.ie; ext. 4449).7

Modules to be taken in JS Year of Moderatorship in Chemistry (Chem)This academic year will be based on the following 60 ECTS:Core modules/Practical labs:55 ECTSOptional Module or Trinity Elective:5 ECTSYear Coordinator: Prof. Mike Southern (southerj@tcd.ie; 896 3411)Core Modules:Semester 1 (11 weeks)Semester 2 (11 weeks)Inorganic Chemistry ICHU33103: Organometallics & CoordinationChemistry (10 ECTS)Inorganic Chemistry IICHU33104: Solid State Materials (5 ECTS)Inorganic polymers (11L)Structural inorganic chemistry (8L)Characterisation techniques of solid statematerials (9L)Organometallics (11L)Electronic spectroscopy (11L)Inorganic reaction mechanisms andhomogenous catalysis (11L)Inorganic‐chemistry lab marks (5 ECTS) fromlabs in weeks 11‐14 and 22‐23 will be includedin the mark for this moduleSurface science (6L)Organic Chemistry ICHU33203: Synthetic Organic Chemistry I (10ECTS)Organic Chemistry IICHU33204: Synthetic Organic Chemistry II (5ECTS)Organometallic C‐C couplings (9L)Pericyclic reactions, FMO theory &stereoelectronic effects (15L)Physical organic chemistry (9L)Heterocyclic chemistry (9L)Organoheteroatom chemistry (15L)FGI and retrosynthesis (9L)Organic‐chemistry lab marks (5 ECTS) fromlabs in weeks 4‐8 and week 10 will be includedin the mark for this module8

Semester 1 (11 weeks)Semester 2 (11 weeks)Physical Chemistry ICHU33303: Quantum Mechanical Concepts inPhysical Chemistry (5 ECTS)Physical Chemistry IICHU33304: Molecular Thermodynamics and Kinetics(10 ECTS)Quantum mechanics (15L)Spectroscopy (9L)Group theory (9L)Molecular thermodynamics & statisticalmechanics (15L)Electrochemistry (9L)Kinetics (9L)Physical‐chemistry lab marks (5 ECTS) from labs inweeks 25‐27 and 30‐32 will be included in themark for this moduleInterdisciplinary Module ICHU33403: Analytical Methods (5 ECTS)Interdisciplinary Module IICHU33404: Biomaterials and Macromolecules (5 ECTS)Analytical chemistry (11L)Organic spectroscopy (11L)Structural methods in inorganic chemistry(11L)Bioinorganic chemistry and natural products (11L)Bioinorganic chemistry (11L)Soft matter (11L)Optional Modules:CHU33441 – Introduction to Medicinal Chemistry (5 ECTS)This module covers fundamental medicinal chemistry. It encompasses an introduction to medicinalchemistry, antiviral and anticancer chemistry, and the computational method QSAR.ORTrinity Elective (5 ECTS; https://www.tcd.ie/trinity‐electives/). Applications for Trinity Electiveswere to be made to Academic Registry by 17 April 2019, with electives being allocated by the endof August 2019.Note: The School reserves the right to amend the list of available modules and, in particular towithdraw and add modules.9

Modules to be taken in JS Year of Moderatorship in Medicinal Chemistry(MedChem)Course Director: Prof. Mathias Senge (sengem@tcd.ie; 896 8537)Semester 1 (11 weeks)Inorganic Chemistry ICHU33103: Organometallics & CoordinationChemistry (10 ECTS)Semester 2 (11 weeks)Physical Chemistry IICHU33304: Molecular Thermodynamics andKinetics (10 ECTS)Organometallics (11L)Electronic spectroscopy (11L)Inorganic reaction mechanisms andhomogenous catalysis (11L)Molecular thermodynamics & statisticalmechanics (15L)Electrochemistry (9L)Kinetics (9L)Physical‐chemistry lab marks (5 ECTS) fromlabs in weeks 25‐27 and 30‐32 will be includedin the mark for this moduleInorganic‐chemistry lab marks (5 ECTS) fromlabs in weeks 11‐14 and 22‐23 will be includedin the mark for this moduleOrganic Chemistry ICHU33203: Synthetic Organic Chemistry I (10 ECTS)Organic Chemistry IICHU33204: Synthetic Organic Chemistry II (5 ECTS)Organometallic C‐C couplings (9L)Pericyclic reactions, FMO theory &stereoelectronic effects (15L)Physical organic chemistry (9L)Heterocyclic chemistry (9L)Organoheteroatom chemistry (15L)FGI and retrosynthesis (9L)Organic‐chemistry lab marks (5 ECTS) from labsin weeks 4‐8 and week 10 will be included in themark for this moduleInterdisciplinary Module ICHU33403: Analytical Methods (5 ECTS)Analytical chemistry (11L)Organic spectroscopy (11L)Structural methods in inorganic chemistry (11L)10Interdisciplinary Module IICHU33404: Biomaterials and Macromolecules (5ECTS)Bioinorganic chemistry and natural products(11L)Bioinorganic chemistry (11L)Soft matter (11L)

Semester 1 (11 weeks)CHU33447: Biochemistry and PharmaceuticalChemistry (5 ECTS)Semester 2 (11 weeks)CHU33441: Introduction to Medicinal Chemistry(5 ECTS)Protein structure, function, activity andIntroduction to medicinal chemistry (15L)regulation (15L)QSAR and antiviral (9L 5P)Receptors, drugs and the autonomic nervous Anticancer (9L)system (5‐7L)Anti‐infective agents (11L)Medicinal Chemistry – CHU33446: Microbiologyand Pharmacology (5 ECTS)Antimicrobial agents (12L)Steroids (10L)Antimalarial chemistry (11L)Note: The School reserves the right to amend the list of available modules and, in particular to

Prof. Eoin Scanlan Eoin.Scanlan@tcd.ie 896 2514 Associate DTLUG Prof. Yurii Gun’ko igounko@tcd.ie 896 3543 JS Year Coordinator Prof. Mike Southern southerj@tcd.ie 896 3411 MedChem Coordinator Prof. Mathias Senge sengem@tcd.ie 896 8537 CMM Coordinator Prof. Graeme Watson watsong@tcd.ie 896 1357

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